Items where Subject is "bioinformatics > genomics and proteomics"

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Number of items at this level: 1108.

ENCODE Project Consortium, (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306 (5696). pp. 636-40. ISSN 0036-8075

A

Aberg, K., Adkins, D. E., Bukszár, J., Webb, B. T., Caroff, S. N., Miller, D. D., Sebat, J., Stroup, S., Fanous, A. H., Vladimirov, V. I., McClay, J. L., Lieberman, J. A., Sullivan, P. F., van den Oord, E. J. C. G. (2010) Genomewide Association Study of Movement-Related Adverse Antipsychotic Effects. Biological Psychiatry, 67 (3). pp. 279-282.

Aboukhalil, R., Fendler, B., Atwal, G. S. (2013) Kerfuffle: a web tool for multi-species gene colocalization analysis. BMC Bioinformatics, 14. ISSN 1471-2105

Aboukhalil, Robert (2016) Elucidating Cancer Evolution using Single-Cell Sequencing and Comparative Genomics. PhD thesis, Cold Spring Harbor Laboratory.

Adams, M. D., Kelley, J. M., Gocayne, J. D., Dubnick, M., Polymeropoulos, M. H., Xiao, H., Merril, C. R., Wu, A., Olde, B., Moreno, R. F., Kerlavage, A. R., McCombie, W. R., Venter, J. C. (1991) Complementary DNA sequencing: Expressed sequence tags and human genome project. Science, 252 (5013). pp. 1651-1656. ISSN 00368075 (ISSN)

Adorjan, P., Barna, G., Erdi, P., Grobler, T., Kepecs, A., Lengyel, M., Ventriglia, F. (1996) Multicompartmental modeling of hippocampal pyramidal cells and interneurons with the GENESIS software tool. Neurobiology, 4 (3). pp. 247-249. ISSN 12168068 (ISSN)

Ahn, J., Won, T. W., Zia, A., Reutter, H., Kaplan, D. E., Sparks, R., Gruen, J. R. (2001) Peaks of linkage are localized by a BAC/PAC contig of the 6p reading disability locus. Genomics, 78 (1-2). pp. 19-29. ISSN 0888-7543

Ahola, H., Stenlund, A., Moreno-Lopez, J., Pettersson, U. (1987) Promoters and processing sites within the transforming region of bovine papillomavirus type 1. J Virol, 61 (7). pp. 2240-4. ISSN 0022-538X (Print)0022-538X (Linking)

Ahola, H., Stenlund, A., Moreno-Lopez, J., Pettersson, U. (1983) Sequences of bovine papillomavirus type 1 DNA--functional and evolutionary implications. Nucleic Acids Res, 11 (9). pp. 2639-50. ISSN 0305-1048 (Print)0305-1048 (Linking)

Aksoy, O., Chicas, A., Zeng, T., Zhao, Z., McCurrach, M., Wang, X., Lowe, S. W. (2012) The atypical E2F family member E2F7 couples the p53 and RB pathways during cellular senescence. Genes Dev, 26 (14). pp. 1546-57. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Alestrom, P., Stenlund, A., Li, P., Bellett, A., Pettersson, U. (1982) Sequence homology between avian and human adenoviruses. J Virol, 42 (1). pp. 306-10. ISSN 0022-538X (Print)0022-538X (Linking)

Alestrom, P., Stenlund, A., Li, P., Pettersson, U. (1982) A common sequence in the inverted terminal repetitions of human and avian adenoviruses. Gene, 18 (2). pp. 193-7. ISSN 0378-1119 (Print)0378-1119 (Linking)

Almagro, S., Riveline, D., Hirano, T., Houchmandzadeh, B., Dimitrov, S. (2004) The mitotic chromosome is an assembly of rigid elastic axes organized by structural maintenance of chromosomes (SMC) proteins and surrounded by a soft chromatin envelope. Journal of Biological Chemistry, 279 (7). pp. 5118-5126. ISSN 0021-9258

Andersen, J. N., Jansen, P. G., Echwald, S. M., Mortensen, O. H., Fukada, T., Del Vecchio, R., Tonks, N. K., Moller, N. P. (2004) A genomic perspective on protein tyrosine phosphatases: gene structure, pseudogenes, and genetic disease linkage. FASEB J, 18 (1). pp. 8-30. ISSN 1530-6860 (Electronic)

Andersen, J. N., Tonks, N. K. (2004) Protein tyrosine phosphatase-based therapeutics- lessons from PTP1B. In: Protein phosphatases. Topics in current genetics, 5 . Springer-Verlag, Berlin, pp. 201-230. ISBN 3540205608

Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., Suzuki, T., Ntini, E., Arner, E., Valen, E., Li, K., Schwarzfischer, L., Glatz, D., Raithel, J., Lilje, B., Rapin, N., Bagger, F. O., Jorgensen, M., Andersen, P. R., Bertin, N., Rackham, O., Burroughs, A. M., Baillie, J. K., Ishizu, Y., Shimizu, Y., Furuhata, E., Maeda, S., Negishi, Y., Mungall, C. J., Meehan, T. F., Lassmann, T., Itoh, M., Kawaji, H., Kondo, N., Kawai, J., Lennartsson, A., Daub, C. O., Heutink, P., Hume, D. A., Jensen, T. H., Suzuki, H., Hayashizaki, Y., Muller, F., Forrest, A. R., Carninci, P., Rehli, M., Sandelin, A., FANTOM Consortium, (2014) An atlas of active enhancers across human cell types and tissues. Nature, 507 (7493). pp. 455-61. ISSN 0028-0836

Aras, R. A., Fischer, W., Perez-Perez, G. I., Crosatti, M., Ando, T., Haas, R., Blaser, M. J. (2003) Plasticity of repetitive DNA sequences within a bacterial (type IV) secretion system component. Journal of Experimental Medicine, 198 (9). pp. 1349-1360. ISSN 0022-1007

Aras, R. A., Kang, J., Tschumi, A. I., Harasaki, Y., Blaser, M. J. (2003) Extensive repetitive DNA facilitates prokaryotic genome plasticity. Proceedings of the National Academy of Sciences of the United States of America, 100 (23). pp. 13579-13584. ISSN 0027-8424

Aravin, A. A., Bourc'his, D. (2008) Small RNA guides for de novo DNA methylation in mammalian germ cells. Genes Dev, 22 (8). pp. 970-5.

Aravin, A. A., van der Heijden, G. W., Castaneda, J., Vagin, V. V., Hannon, G. J., Bortvin, A. (2009) Cytoplasmic Compartmentalization of the Fetal piRNA Pathway in Mice. Plos Genetics, 5 (12). e1000764. ISSN 1553-7390

Arbiza, L., Gronau, I., Aksoy, B. A., Hubisz, M. J., Gulko, B., Keinan, A., Siepel, A. (2013) Genome-wide inference of natural selection on human transcription factor binding sites. Nat Genet, 45 (7). pp. 723-9. ISSN 1061-4036

Argout, X., Salse, J., Aury, J. M., Guiltinan, M. J., Droc, G., Gouzy, J., Allegre, M., Chaparro, C., Legavre, T., Maximova, S. N., Abrouk, M., Murat, F., Fouet, O., Poulain, J., Ruiz, M., Roguet, Y., Rodier-Goud, M., Barbosa-Neto, J. F., Sabot, F., Kudrna, D., Ammiraju, J. S. S., Schuster, S. C., Carlson, J. E., Sallet, E., Schiex, T., Dievart, A., Kramer, M. R., Gelley, L., Shi, Z., Bérard, A., Viot, C., Boccara, M., Risterucci, A. M., Guignon, V., Sabau, X., Axtell, M. J., Ma, Z., Zhang, Y, Brown, S., Bourge, M., Golser, W., Song, X., Clement, D., Rivallan, R., Tahi, M., Akaza, J. M., Pitollat, B., Gramacho, K., D'Hont, A., Brunel, D., Infante, D., Kebe, I., Costet, P., Wing, R., McCombie, W. R., Guiderdoni, E., Quetier, F., Panaud, O., Wincker, P., Bocs, S., Lanaud, C. (2011) The genome of Theobroma cacao. Nature Genetics, 43 (2). pp. 101-108. ISSN 10614036

Arun, G., Akhade, V. S., Donakonda, S., Rao, M. R. S. (2012) Mrhl rna, a long noncoding rna, negatively regulates wnt signaling through its protein partner ddx5/p68 in mouse spermatogonial cells. Molecular and Cellular Biology, 32 (15). pp. 3140-3152. ISSN 02707306

Atwal, G. S. (2012) Talk from Mickey Atwal at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Atwal, G. S., Kirchhoff, T., Bond, E. E., Montagna, M., Menin, C., Bertorelle, R., Scaini, M. C., Bartel, F., Böhnke, A., Pempe, C., Gradhand, E., Hauptmann, S., Offit, K., Levine, A. J., Bond, G. L. (2009) Altered tumor formation and evolutionary selection of genetic variants in the human MDM4 oncogene. Proc Natl Acad Sci U S A, 106 (25). pp. 10236-10241. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Autexier, C., Greider, C. W. (1998) Mutational analysis of the Tetrahymena telomerase RNA: identification of residues affecting telomerase activity in vitro. Nucleic Acids Research, 26 (3). pp. 787-95. ISSN 0305-1048

Avraham, S., Tung, C. W., Ilic, K., Jaiswal, P., Kellogg, E. A., McCouch, S., Pujar, A., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L. D., Stevens, P., Vincent, L., Zapata, F., Ware, D. H. (2008) The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res, 36 (Databa). D449-54.

B

Bagchi, A., Mills, A. A. (2008) The quest for the 1p36 tumor suppressor. Cancer Res, 68 (8). pp. 2551-6.

Bakin, A. V., Safina, A., Rinehart, C., Daroqui, C., Darbary, H., Helfman, D. M. (2004) A critical role of tropomyosins in TGF-beta regulation of the actin cytoskeleton and cell motility in epithelial cells. Molecular Biology of the Cell, 15 (10). pp. 4682-4694. ISSN 1059-1524

Ballouz, S., Liu, J. Y., George, R. A., Bains, N., Liu, A., Oti, M., Gaeta, B., Fatkin, D., Wouters, M. A. (2013) Gentrepid V2.0: a web server for candidate disease gene prediction. BMC Bioinformatics, 14. ISSN 1471-2105

Ballouz, S., Verleyen, W., Gillis, J. (2015) Guidance for RNA-seq co-expression network construction and analysis: safety in numbers. Bioinformatics. ISSN 1367-4803

Banerjee, N., Zhang, M. Q. (2002) Functional genomics as applied to mapping transcription regulatory networks. Current Opinion in Microbiology, 5 (3). pp. 313-317. ISSN 1369-5274

Banerjee, N., Zhang, M. Q. (2003) Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Research, 31 (23). pp. 7024-7031. ISSN 0305-1048

Banks, R. E., Dunn, M. J., Forbes, M. A., Stanley, A., Pappin, D., Naven, T., Gough, M., Harnden, P., Selby, P. J. (1999) The potential use of laser capture microdissection to selectively obtain distinct populations of cells for proteomic analysis--preliminary findings. Electrophoresis, 20 (4-5). pp. 689-700. ISSN 0173-0835 (Print)0173-0835 (Linking)

Banks, R. E., Dunn, M. J., Hochstrasser, D. F., Sanchez, J. C., Blackstock, W., Pappin, D. J., Selby, P. J. (2000) Proteomics: new perspectives, new biomedical opportunities. Lancet, 356 (9243). pp. 1749-56. ISSN 0140-6736 (Print)0140-6736 (Linking)

Bar-Sagi, D., Lees, J., Sherr, C., Weiss, W. (2010) MECHANISMS & MODELS OF CANCER. In: 2010 meeting of MECHANISMS & MODELS OF CANCER, August 17–August 21, 2010, Cold Spring Harbor Laboratory.

Barberis, D., Casazza, A., Sordella, R., Corso, S., Artigiani, S., Settleman, J., Comoglio, P. M., Tamagnone, L. (2005) p190 Rho-GTPase activating protein associates with plexins and it is required for semaphorin signalling. Journal of Cell Science, 118 (Pt 20). pp. 4689-700. ISSN 0021-9533

Barretina, J., Taylor, B. S., Banerji, S., Ramos, A. H., Lagos-Quintana, M., Decarolis, P. L., Shah, K., Socci, N. D., Weir, B. A., Ho, A., Chiang, D. Y., Reva, B., Mermel, C. H., Getz, G., Antipin, Y., Beroukhim, R., Major, J. E., Hatton, C., Nicoletti, R., Hanna, M., Sharpe, T., Fennell, T. J., Cibulskis, K., Onofrio, R. C., Saito, T., Shukla, N., Lau, C., Nelander, S., Silver, S. J., Sougnez, C., Viale, A., Winckler, W., Maki, R. G., Garraway, L. A., Lash, A., Greulich, H., Root, D. E., Sellers, W. R., Schwartz, G. K., Antonescu, C. R., Lander, E. S., Varmus, H. E., Ladanyi, M., Sander, C., Meyerson, M., Singer, S. (2010) Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nat Genet, 42 (8). pp. 715-21. ISSN 1546-1718 (Electronic)1061-4036 (Linking)

Baslan, T., Kendall, J. T., Rodgers, L., Cox, H., Riggs, M., Stepansky, A., Troge, J. E., Ravi, K., Esposito, D., Lakshmi, B., Wigler, M., Navin, N. E., Hicks, J. B. (2012) Genome-wide copy number analysis of single cells. Nat Protoc, 7 (6). pp. 1024-41. ISSN 1750-2799 (Electronic)1750-2799 (Linking)

Bastow, R., Mylne, J. S., Lister, C., Lippman, Z., Martienssen, R. A., Dean, C. (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature, 427 (6970). pp. 164-7. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Batut, P. J., Dobin, A., Plessy, C., Carninci, P., Gingeras, T. R. (2013) High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res, 23 (1). pp. 169-180. ISSN 1549-5469 (Electronic)1088-9051 (Linking)

Baumann, U., Targosz, B. S., Lemeer, S., Nikolova, V., Kratzat, S., Fernandez-Saiz, V., Reiter, C., Rudelius, M., Miething, C., Kuster, B., Peschel, C., Keller, U., Bassermann, F. (2011) SCF(Fbxo25) suppresses B cell lymphomagenesis by targeting Hax-1 for ubiquitin mediated proteasomal degradation. Onkologie, 34. p. 190. ISSN 0378-584X

Baumbusch, L. O., Aaroe, J., Johansen, F. E., Hicks, J. B., Sun, H., Bruhn, L., Gunderson, K., Naume, B., Kristensen, V. N., Liestol, K., Borresen-Dale, A. L., Lingjaerde, O. C. (2008) Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors. BMC Genomics, 9. p. 379.

Bayer, M., Nawy, T., Giglione, C., Galli, M., Meinnel, T., Lukowitz, W. (2009) Paternal Control of Embryonic Patterning in Arabidopsis thaliana. Science, 323 (5920). pp. 1485-1488. ISSN 0036-8075

Bejerano, G., Siepel, A. C., Kent, W. J., Haussler, D. (2005) Computational screening of conserved genomic DNA in search of functional noncoding elements. Nat Methods, 2 (7). pp. 535-45. ISSN 1548-7091 (Print)1548-7091

Bekritsky, M. (2014) Detecting de novo microsatellite mutations in a population of families with sporadic autism. PhD thesis, Cold Spring Harbor Laboratory.

Bell, S. P., Marahrens, Y., Rao, H., Stillman, B. (1993) The replicon model and eukaryotic chromosomes. Cold Spring Harbor Symposia on Quantitative Biology, 58. pp. 435-442. ISSN 00917451 (ISSN)

Belvin, M. P., Zhou, H., Yin, J. C. (1999) The Drosophila dCREB2 gene affects the circadian clock. Neuron, 22 (4). pp. 777-87. ISSN 0896-6273 (Print)

Bemer, M., Wolters-Arts, M., Grossniklaus, U., Angenent, G. C. (2008) The MADS Domain Protein DIANA Acts Together with AGAMOUS-LIKE80 to Specify the Central Cell in Arabidopsis Ovules. Plant Cell, 20 (8). pp. 2088-2101.

Ben-Hur, V., Denichenko, P., Siegfried, Z., Maimon, A., Krainer, A., Davidson, B., Karni, R. (2013) S6K1 Alternative Splicing Modulates Its Oncogenic Activity and Regulates mTORC1. Cell Reports, 3 (1). pp. 103-115. ISSN 22111247

Benetti, R., Gonzalo, S., Jaco, I., Munoz, P., Gonzalez, S., Schoeftner, S., Murchison, E. P., Andl, T., Chen, T. P., Klatt, P., Li, E., Serrano, M., Millar, S., Hannon, G. J., Blasco, M. A. (2008) A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases. Nature Structural & Molecular Biology, 15 (3). pp. 268-279. ISSN 1545-998515459993 (ISSN)

Benita, Y., Kikuchi, H., Smith, A. D., Zhang, M. Q., Chung, D. C., Xavier, R. J. (2009) An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic Acids Res, 37 (14). 4587–4602.

Berg, L., Lusky, M., Stenlund, A., Botchan, M. R. (1986) Repression of bovine papilloma virus replication is mediated by a virally encoded trans-acting factor. Cell, 46 (5). pp. 753-62. ISSN 0092-8674 (Print)0092-8674 (Linking)

Bergmann, J. H., Martins, N. M. C., Larionov, V., Masumoto, H., Earnshaw, W. C. (2012) HACking the centromere chromatin code: Insights from human artificial chromosomes. Chromosome Research, 20 (5). pp. 505-519.

Bergmann, Jan H., Spector, David L. (2014) Long non-coding RNAs: modulators of nuclear structure and function. Current Opinion in Cell Biology, 26. pp. 10-18. ISSN 0955-0674

Berriman, M., Parkhill, J., Carlton, J., Weinstock, G. (2010) INFECTIOUS DISEASE GENOMICS & GLOBAL HEALTH. In: Joint Cold Spring Harbor Laboratory/Wellcome Trust Conference on INFECTIOUS DISEASE GENOMICS & GLOBAL HEALTH, September 12–September 15, 2010, Wellcome Conference Center.

Bestman, J. E., Cline, H. T. (2008) The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A, 105 (51). 20494-20499 .

Bevan, M., Bancroft, I., Mewes, H. W., Martienssen, R., McCombie, R. (1999) Clearing a path through the jungle: Progress in Arabidopsis genomics. Bioessays, 21 (2). pp. 110-120. ISSN 02659247 (ISSN)

Bevan, M., Bennetzen, J. L., Martienssen, R. (1998) Genome studies and molecular evolution commonalities, contrasts, continuity and change in plant genomes. Current Opinion in Plant Biology, 1 (2). pp. 101-102. ISSN 1369-5266

Bina, M., Wyss, P., Ren, W. H., Szpankowski, W., Thomas, E., Randhawa, R., Reddy, S., John, P. M., Pares-Matos, E. I., Stein, A., Xu, H., Lazarus, S. A. (2004) Exploring the characteristics of sequence elements in proximal promoters of human genes. Genomics, 84 (6). pp. 929-940. ISSN 0888-7543

Birbrair, A., Zhang, T., Wang, Z. M., Messi, M. L., Enikolopov, G. N., Mintz, A., Delbono, O. (2013) Skeletal muscle pericyte subtypes differ in their differentiation potential. Stem Cell Research, 10 (1). pp. 67-84. ISSN 1873-5061

Birol, I., Champ, M., Cant, J. (2010) GENOME INFORMATICS. In: Joint Cold Spring Harbor Laboratory/Wellcome Trust Conference on GENOME INFORMATICS, September 15–September 19, 2010, Wellcome Conference Center.

Bish, R. A., Fregoso, O. I., Piccini, A., Myers, M. P. (2008) Conjugation of Complex Polyubiquitin Chains to WRNIP1. J Proteome Res, 7 (8). 3481-3489 .

Blakeslee, Albert Francis, Belling, John, Farnham, M. E. (1920) Chromosomal duplication and Mendelian phenomena in datura mutants. Science, 52 (1347). pp. 388-390.

Boersema, P. J., Taouatas, N., Altelaar, A. F. M., Gouw, J. W., Ross, P. L., Pappin, D. J., Heck, A. J. R., Mohammed, S. (2009) Straightforward and de Novo Peptide Sequencing by MALDI-MS/MS Using a Lys-N Metalloendopeptidase. Molecular & Cellular Proteomics, 8 (4). pp. 650-660. ISSN 1535-9476

Boettner, B., Van Aelst, L. (2009) Control of cell adhesion dynamics by Rap1 signaling. Curr Opin Cell Biol, 21 (5). 684-693 .

Boettner, B., Van Aelst, L. (2013) Introduction to the ECR special issue on the roles of small GTPases. Experimental Cell Research, 319 (15). p. 2309. ISSN 00144827

Bogdanove, A. J., Koebnik, R., Lu, H., Furutani, A., Angiuoli, S. V., Patil, P. B., Van Sluys, M. A., Ryan, R. P., Meyer, D. F., Han, S. W., Aparna, G., Rajaram, M., Delcher, A. L., Phillippy, A. M., Puiu, D., Schatz, M. C., Shumway, M., Sommer, D. D., Trapnell, C., Benahmed, F., Dimitrov, G., Madupu, R., Radune, D., Sullivan, S., Jha, G., Ishihara, H., Lee, S. W., Pandey, A., Sharma, V., Sriariyanun, M., Szurek, B., Vera-Cruz, C. M., Dorman, K. S., Ronald, P. C., Verdier, V., Dow, J. M., Sonti, R. V., Tsuge, S., Brendel, V. P., Rabinowicz, P. D., Leach, J. E., White, F. F., Salzberg, S. L. (2011) Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. Journal of Bacteriology, 193 (19). pp. 5450-5464. ISSN 00219193 (ISSN)

Bohland, J. W., Bokil, H., Pathak, S. D., Lee, C. K., Ng, L., Lau, C., Kuan, C., Hawrylycz, M., Mitra, P. P. (2010) Clustering of spatial gene expression patterns in the mouse brain and comparison with classical neuroanatomy. Methods, 50 (2). pp. 105-112.

Boivin, B., Vaniotis, G., Allen, B. G., Hebert, T. E. (2008) G protein-coupled receptors in and on the cell nucleus: a new signaling paradigm? J Recept Signal Transduct Res, 28 (1-2). pp. 15-28.

Boivin, B., Zhang, S. H., Arbiser, J. L., Zhang, Z.-Y., Tonks, N. K. (2008) A modified cysteinyl-labeling assay reveals reversible oxidation of classical and dual specificity phosphatases in angiomyolipoma cells. Proc Natl Acad Sci U S A, 105 (29). pp. 9959-9964.

Boles, M. K., Wilkinson, B. M., Maxwell, A., Lai, L., Mills, A. A., Nishijima, I., Salinger, A. P., Moskowitz, I., Hirschi, K. K., Liu, B., Bradley, A., Justice, M. J. (2009) A mouse chromosome 4 balancer ENU-mutagenesis screen isolates eleven lethal lines. BMC Genet, 10 (1). p. 12.

Bommert, P., Nagasawa, N. S., Jackson, D. (2013) Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus. Nature Genetics, 45 (3). pp. 334-337. ISSN 1061-4036

Bommert, P., Satoh-Nagasawa, N., Jackson, D. P., Hirano, H.Y. (2005) Genetics and evolution of inflorescence and flower development in grasses. Plant Cell Physiol, 46 (1). pp. 69-78. ISSN 0032-0781 (Print)

Bordeleau, M. E., Robert, F., Gerard, B., Lindqvist, L., Chen, S. M., Wendel, H. G., Brem, B., Greger, H., Lowe, S. W., Porco, J. A., Pelletier, J. (2008) Therapeutic suppression of translation initiation modulates chemosensitivity in a mouse lymphoma model. J Clin Invest, 118 (7). 2651- 2660.

Borges, F., Martienssen, R. A. (2013) Establishing epigenetic variation during genome reprogramming. RNA Biology, 10 (4). pp. 490-4. ISSN 1555-8584 (Electronic)1547-6286 (Linking)

Bortiri, E., Jackson, D. P., Hake, S. (2006) Advances in maize genomics: The emergence of positional cloning. Current Opinion in Plant Biology, 9 (2). pp. 164-171. ISSN 13695266

Botcheva, K., McCorkle, S. R., McCombie, W. R., Dunn, J. J., Anderson, C. W. (2011) Distinct p53 genomic binding patterns in normal and cancer-derived human cells. Cell Cycle, 10 (24). pp. 4237-4249. ISSN 1538-4101

Boyle, B., Hopkins, N., Lu, Z. Y., Garay, J. A. R., Mozzherin, D., Rees, T., Matasci, N., Narro, M. L., Piel, W. H., McKay, S. J., Lowry, S., Freeland, C., Peet, R. K., Enquist, B. J. (2013) The taxonomic name resolution service: an online tool for automated standardization of plant names. BMC Bioinformatics, 14. ISSN 1471-2105

Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., Boisvert, S., Chapman, J. A., Chapuis, G., Chikhi, R., Chitsaz, H., Chou, W. C., Corbeil, J., Del Fabbro, C., Docking, T. R., Durbin, R., Earl, D., Emrich, S., Fedotov, P., Fonseca, N. A., Ganapathy, G., Gibbs, R. A., Gnerre, S., Godzaridis, E., Goldstein, S., Haimel, M., Hall, G., Haussler, D., Hiatt, J. B., Ho, I. Y., Howard, J., Hunt, M., Jackman, S. D., Jaffe, D. B., Jarvis, E. D., Jiang, H., Kazakov, S., Kersey, P. J., Kitzman, J. O., Knight, J. R., Koren, S., Lam, T. W., Lavenier, D., Laviolette, F., Li, Y., Li, Z., Liu, B., Liu, Y., Luo, R., Maccallum, I., Macmanes, M. D., Maillet, N., Melnikov, S., Naquin, D., Ning, Z., Otto, T. D., Paten, B., Paulo, O. S., Phillippy, A. M., Pina-Martins, F., Place, M., Przybylski, D., Qin, X., Qu, C., Ribeiro, F. J., Richards, S., Rokhsar, D. S., Ruby, J. G., Scalabrin, S., Schatz, M. C., Schwartz, D. C., Sergushichev, A., Sharpe, T., Shaw, T. I., Shendure, J., Shi, Y., Simpson, J. T., Song, H., Tsarev, F., Vezzi, F., Vicedomini, R., Vieira, B. M., Wang, J., Worley, K. C., Yin, S., Yiu, S. M., Yuan, J., Zhang, G., Zhang, H., Zhou, S., Korf, I. F. (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience, 2 (1). p. 10. ISSN 2047-217x

Brenchley, R., Spannagl, M., Pfeifer, M., Barker, G. L. A., D'Amore, R., Allen, A. M., McKenzie, N., Kramer, M., Kerhornou, A., Bolser, D., Kay, S., Waite, D., Trick, M., Bancroft, I., Gu, Y., Huo, N., Luo, M. C., Sehgal, S., Gill, B., Kianian, S., Anderson, O., Kersey, P., Dvorak, J., McCombie, W. R., Hall, A., Mayer, K. F. X., Edwards, K. J., Bevan, M. W., Hall, N. (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature, 491 (7426). pp. 705-710. ISSN 00280836

Brenner, E. D., Stevenson, D. W., McCombie, R. W., Katari, M. S., Rudd, S. A., Mayer, K. F., Palenchar, P. M., Runko, S. J., Twigg, R. W., Dai, G., Martienssen, R. A., Benfey, P. N., Coruzzi, G. M. (2003) Expressed sequence tag analysis in Cycas, the most primitive living seed plant. Genome Biology, 4 (12). R78. ISSN 1474-7596

Broach, J. R., Li, Y. Y., Feldman, J., Jayaram, M., Abraham, J., Nasmyth, K. A., Hicks, J. B. (1982) Localization and sequence analysis of yeast origins of DNA replication. Cold Spring Harbor Symposia on Quantitative Biology, 47 (2). pp. 1165-1173. ISSN 00917451 (ISSN)

Brooks, L., Strable, J., Zhang, X., Ohtsu, K., Zhou, R., Sarkar, A., Hargreaves, S., Elshire, R. J., Eudy, D., Pawlowska, T., Ware, D. H., Janick-Buckner, D., Buckner, B., Timmermans, M. C. P., Schnable, P. S., Nettleton, D., Scanlon, M. J. (2009) Microdissection of shoot meristem functional domains. PLoS Genet, 5 (5). e1000476.

Brown, P., Cervenáková, L., Goldfarb, L. G., McCombie, W. R., Rubenstein, R., Will, R. G., Pocchiari, M., Martinez-Lage, J. F., Scalici, C., Masullo, C., Graupera, G., Ligan, J., Gajdusek, D. C. (1994) Iatrogenic Creutzfeldt-Jakob disease: An example of the interplay between ancient genes and modern medicine. Neurology, 44 (2). pp. 291-293. ISSN 00283878 (ISSN)

Brown, P., Goldfarb, L. G., McCombie, W. R., Nieto, A., Squillacote, D., Sheremata, W., Little, B. W., Godec, M. S., Gibbs Jr, C. J., Gajdusek, D. C. (1992) Atypical Creutzfeldt-Jakob disease in an American family with an insert mutation in the PRNP amyloid precursor gene. Neurology, 42 (2). pp. 422-427. ISSN 00283878 (ISSN)

Bruskiewich, R., Coe, E. H., Jaiswal, P., McCouch, S., Polacco, M., Stein, L., Vincent, L., Ware, D. (2002) The Plant Ontology (TM) Consortium and plant ontologies. Comparative and Functional Genomics, 3 (2). pp. 137-142. ISSN 1531-6912

Buckler, E. S., Holland, J. B., Bradbury, P. J., Acharya, C. B., Brown, P. J., Browne, C., Ersoz, E., Flint-Garcia, S., Garcia, A., Glaubitz, J. C., Goodman, M. M., Harjes, C., Guill, K., Kroon, D. E., Larsson, S., Lepak, N. K., Li, H., Mitchell, S. E., Pressoir, G., Peiffer, J. A., Rosas, M. O., Rocheford, T. R., Romay, M. C., Romero, S., Salvo, S., Sanchez Villeda, H., da Silva, H. S., Sun, Q., Tian, F., Upadyayula, N., Ware, D. H., Yates, H., Yu, J., Zhang, Z., Kresovich, S., McMullen, M. D. (2009) The genetic architecture of maize flowering time. Science, 325 (5941). pp. 714-8. ISSN 1095-9203 (Electronic)

Buell, C. R., McCombie, W. R., Wing, R. A., Yuan, Q., Ouyang, S., Liu, J., Zhu, W., Wang, A., Maiti, R., Haas, B., Wortman, J., Pertea, M., Jones, K. M., Kim, M., Overton, L., Tsitrin, T., Fadrosh, D., Bera, J., Weaver, J., Jin, S., Johri, S., Reardon, M., Webb, K., Hill, J., Moffat, K., Tallon, L., Van Aken, S., Lewis, M., Utterback, T., Feldblyum, T., Zismann, V., Iobst, S., Hsiao, J., De Vazeille, A. R., Salzberg, S. L., White, O., Fraser, C., Yu, Y., Kim, H., Rambo, T., Currie, J., Collura, K., Kernodle-Thompson, S., Wei, F., Kudrna, D., Ammiraju, J. S. S., Luo, M., Goicoechea, J. L., Henry, D., Oates, R., Palmer, M., Pries, G., Saski, C., Simmons, J., Soderlund, C., Nelson, W., De La Bastide, M., Spiegel, L., Nascimento, L., Huang, E., Preston, R., Zutavern, T., Palmer, L., O'Haughnessy, A., Dike, S., Minx, P., Cordum, H., Wilson, R., Jin, W., Lee, H. R., Jiang, J., Jackson, S. (2005) Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. The Rice Chromosome 3 Sequencing Consortium. Genome Research, 15 (9). pp. 1284-1291. ISSN 10889051 (ISSN)

Burger, P. B., Yuan, H. J., Karakas, E., Geballe, M., Furukawa, H., Liotta, D. C., Snyder, J. P., Traynelis, S. F. (2012) Mapping the Binding of GluN2B-Selective N-Methyl-D-aspartate Receptor Negative Allosteric Modulators. Molecular Pharmacology, 82 (2). pp. 344-359. ISSN 0026-895X

Byrne, M., Kidney, C., Martienssen, R. (2004) Homeobox genes in Arabidopsis and their epigenetic regulation. Developmental Biology, 271 (2). p. 553. ISSN 0012-1606

Byrne, M. E., Kidner, C. A., Martienssen, R. A. (2003) Plant stem cells: divergent pathways and common themes in shoots and roots. Current Opinion in Genetics & Development, 13 (5). pp. 551-7. ISSN 0959-437X

Bywater, M. J., Poortinga, G., Sanij, E., Hein, N., Peck, A., Cullinane, C., Wall, M., Cluse, L., Drygin, D., Anderes, K., Huser, N., Proffitt, C., Bliesath, J., Haddach, M., Schwaebe, M. K., Ryckman, D. M., Rice, W. G, Schmitt, C., Lowe, Scott W, Johnstone, R. W., Pearson, R. B., McArthur, G. A., Hannan, R. D. (2012) Inhibition of RNA Polymerase I as a Therapeutic Strategy to Promote Cancer-Specific Activation of p53. Cancer Cell, 22 (1). pp. 51-65. ISSN 1535-6108

C

Cabal, R., Khanin, R., Viali, A., Socci, N., Lucito, R., Olshen, A., Zhang, J., Gerald, W., Powers, S., Ladanyi, M. (2011) Testing and Validating High Throughput Genomic Analysis of FFPE Samples: Systematic Gene Expression Differences between Matched Frozen and FFPE Samples Due to Rapid mRNA Degradation Signals. Modern Pathology, 24. p. 1875. ISSN 0893-3952

Cai, C. L., Rajaram, M., Zhou, X., Liu, Q., Marchica, J., Li, J. Y., Powers, R. S. (2012) Activation of multiple cancer pathways and tumor maintenance function of the 3q amplified oncogene FNDC3B. Cell Cycle, 11 (9). pp. 1773-1781. ISSN 1538-4101

Calarco, J. P., Borges, F., Donoghue, M, Van Ex, F., Jullien, P. E., Lopes, T., Gardner, R., Berger, F., Feijó, J. A, Becker, J. D., Martienssen, R. A. (2012) Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA. Cell, 151 (1). pp. 194-205. ISSN 0092-8674

Calarco, Joseph P. (2013) Chromatin Dynamics during Germline Development. PhD thesis, Cold Spring Harbor Laboratory.

Campagna, L., Gronau, I., Silveira, L. F., Siepel, A., Lovette, I. J. (2015) Distinguishing Noise from Signal in Patterns of Genomic Divergence in a Highly Polymorphic Avian Radiation. Mol Ecol, 24 (16). pp. 4238-4251. ISSN 1365-294X (Electronic)0962-1083 (Linking)

Cannon, S. B., McCombie, W. R., Sato, S., Tabata, S., Denny, R., Palmer, L., Katari, M., Young, N. D., Stacey, G. (2003) Evolution and microsynteny of the apyrase gene family in three legume genomes. Molecular Genetics and Genomics, 270 (4). pp. 347-361. ISSN 1617-4615

Carlton, J. M., Hirt, R. P., Silva, J. C., Delcher, A. L., Schatz, M., Zhao, Q., Wortman, J. R., Bidwell, S. L., Alsmark, U. C. M., Besteiro, S., Sicheritz-Ponten, T., Noel, C. J., Dacks, J. B., Foster, P. G., Simillion, C., Van De Peer, Y., Miranda-Saavedra, D., Barton, G. J., Westrop, G. D., Müller, S., Dessi, D., Fiori, P. L., Ren, Q., Paulsen, I., Zhang, H., Bastida-Corcuera, F. D., Simoes-Barbosa, A., Brown, M. T., Hayes, R. D., Mukherjee, M., Okumura, C. Y., Schneider, R., Smith, A. J., Vanacova, S., Villalvazo, M., Haas, B. J., Pertea, M., Feldblyum, T. V., Utterback, T. R., Shu, C. L., Osoegawa, K., De Jong, P. J., Hrdy, I., Horvathova, L., Zubacova, Z., Dolezal, P., Malik, S. B., Logsdon Jr, J. M., Henze, K., Gupta, A., Wang, C. C., Dunne, R. L., Upcroft, J. A., Upcroft, P., White, O., Salzberg, S. L., Tang, P., Chiu, C. H., Lee, Y. S., Embley, T. M., Coombs, G. H., Mottram, J. C., Tachezy, J., Fraser-Liggett, C. M., Johnson, P. J. (2007) Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science, 315 (5809). pp. 207-212. ISSN 00368075 (ISSN)

Casey, Will, Mishra, Bud (2003) A Nearly Linear-Time General Algorithm for Genome-Wide Bi-allele Haplotype Phasing. In: High Performance Computing - HiPC 2003. Lecture Notes in Computer Science, 2913 . Springer Berlin Heidelberg, pp. 204-215. ISBN 978-3-540-20626-2

Castel, S. E., Martienssen, R. A. (2013) RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet, 14 (2). pp. 100-12. ISSN 1471-0064 (Electronic)1471-0056 (Linking)

Castle, J. C., Zhang, C., Shah, J. K., Kulkarni, A.t V., Kalsotra, A., Cooper, T. A., Johnson, J. M. (2008) Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat Genet, 40 (12). pp. 1416-1425.

Celniker, S. E., Dillon, L. A., Gerstein, M. B., Gunsalus, K. C., Henikoff, S., Karpen, G. H., Kellis, M., Lai, E. C., Lieb, J. D., MacAlpine, D. M., Micklem, G., Piano, F., Snyder, M., Stein, L. D., White, K. P., Waterston, R. H. (2009) Unlocking the secrets of the genome. Nature, 459 (7249). pp. 927-30. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Celniker, S., Clark, A., Ponting, C., Weinstock, G. (2010) THE BIOLOGY OF GENOMES. In: 2010 meeting of THE BIOLOGY OF GENOMES, May 11–May 15, 2010, Cold Spring Harbor Laboratory.

Chakraborty, A. A., Tansey, W. P. (2009) Adenoviral E1A Function through Myc. Cancer Res, 69 (1). pp. 6-9.

Chakraborty, A. A. , Tansey, W. P. (2009) Inference of cell cycle-dependent proteolysis by laser scanning cytometry. Experimental Cell Research, 315 (10). pp. 1772-1778.

Chen, C. D., Helfman, D. M. (1999) Donor site competition is involved in the regulation of alternative splicing of the rat beta-tropomyosin pre-mRNA. Rna, 5 (2). pp. 290-301. ISSN 1355-8382 (Print)

Chen, C. M., Chiu, S. L., Shen, W., Cline, H. T. (2009) Co-expression of Argonaute2 Enhances Short Hairpin RNA-induced RNA Interference in Xenopus CNS Neurons In Vivo. Frontiers in Neuroscience, 3. p. 63.

Chen, G., Hata, N., Zhang, M. Q. (2004) Transcription factor binding element detection using functional clustering of mutant expression data. Nucleic Acids Res, 32 (8). pp. 2362-71. ISSN 1362-4962 (Electronic)

Chen, H. H., Luche, R., Wei, B., Tonks, N. K. (2004) Characterization of two distinct dual specificity phosphatases encoded in alternative open reading frames of a single gene located on human chromosome 10q22.2. J Biol Chem, 279 (40). pp. 41404-13. ISSN 0021-9258 (Print)

Chen, N. (2004) Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics, Chapte. Unit 4.10.

Chen, N., Lawson, D., Bradnam, K., Harris, T. W., Stein, L. D. (2004) WormBase as an integrated platform for the C. elegans ORFeome. Genome Res, 14 (10B). pp. 2155-61. ISSN 1088-9051 (Print)

Chen, Y. C., Carter, H., Parla, J., Kramer, M., Goes, F. S., Pirooznia, M., Zandi, P. P., McCombie, W. R., Potash, J. B., Karchin, R. (2013) A Hybrid Likelihood Model for Sequence-Based Disease Association Studies. PLoS Genetics, 9 (1). ISSN 15537390 (ISSN)

Chen, Z., Trotman, L. C., Shaffer, D., Lin, H. K., Dotan, Z. A., Niki, M., Koutcher, J. A., Scher, H. I., Ludwig, T., Gerald, W., Cordon-Cardo, C., Pandolfi, P. P. (2005) Crucial role of p53-dependent cellular senescence in suppression of Pten-deficient tumorigenesis. Nature, 436 (7051). pp. 725-30. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Chen, Z., Jaafar, L., Agyekum, D. G., Xiao, H., Wade, M. F., Kumaran, R. I., Spector, D. L., Bao, G., Porteus, M. H., Dynan, W. S., Meiler, S. E. (2013) Receptor-mediated delivery of engineered nucleases for genome modification. Nucleic Acids Research, 41 (19). ISSN 03051048 (ISSN)

Cheng, C., Alexander, R., Min, R. Q., Leng, J., Yip, K. Y., Rozowsky, J., Yan, K. K., Dong, X. J., Djebali, S., Ruan, Y. J., Davis, C. A., Carninci, P., Lassman, T., Gingeras, T. R., Guigo, R., Birney, E., Weng, Z. P., Snyder, M., Gerstein, M. (2012) Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Research, 22 (9). pp. 1658-1667. ISSN 1088-9051

Cherepinsky, V., Feng, J. W., Rejali, M., Mishra, B. (2003) Shrinkage-based similarity metric for cluster analysis of microarray data. Proceedings of the National Academy of Sciences of the United States of America, 100 (17). pp. 9668-9673. ISSN 0027-8424

Chi, S. W., Hannon, G. J., Darnell, R. B. (2012) An alternative mode of microRNA target recognition. Nature Structural and Molecular Biology, 19 (3). pp. 321-327. ISSN 15459993 (ISSN)

Chia, J. M., Song, C., Bradbury, P. J., Costich, D., de Leon, N., Doebley, J., Elshire, R. J., Gaut, B., Geller, L., Glaubitz, J. C., Gore, M., Guill, K. E., Holland, J., Hufford, M. B., Lai, J., Li, M., Liu, X., Lu, Y., McCombie, R., Nelson, R., Poland, J., Prasanna, B. M., Pyhajarvi, T., Rong, T., Sekhon, R. S., Sun, Q., Tenaillon, M. I., Tian, F., Wang, J., Xu, X., Zhang, Z., Kaeppler, S. M., Ross-Ibarra, J., McMullen, M. D., Buckler, E. S., Zhang, G., Xu, Y., Ware, D. (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet, 44 (7). 803-U238. ISSN 1546-1718 (Electronic)1061-4036 (Linking)

Chicas, A., Kapoor, A., Wang, X. W., Aksoy, O., Evertts, A. G., Zhang, M. Q., Garcia, B. A., Bernstein, E., Lowe, S. W. (2012) H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence. Proceedings of the National Academy of Sciences of the United States of America, 109 (23). pp. 8971-8976. ISSN 0027-8424

Chien, Y., Scuoppo, C., Wang, X., Fang, X., Balgley, B., Bolden, J. E., Premsrirut, P., Luo, W., Chicas, A., Lee, C. S., Kogan, S. C., Lowe, S. W. (2011) Control of the senescence-associated secretory phenotype by NF-kappaB promotes senescence and enhances chemosensitivity. Genes Dev, 25 (20). pp. 2125-36. ISSN 1549-5477 (Electronic) 0890-9369 (Linking)

Chitwood, D. H., Nogueira, F. T. S., Howell, M. D., Montgomery, T. A., Carrington, J. C., Timmermans, M. C. P. (2009) Pattern formation via small RNA mobility. Genes Dev, 23 (5). pp. 549-554. ISSN 0890-9369

Choe, L., D'Ascenzo, M., Relkin, N. R., Pappin, D., Ross, P., Williamson, B., Guertin, S., Pribil, P., Lee, K. H. (2007) 8-plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease. Proteomics, 7 (20). pp. 3651-60. ISSN 1615-9853 (Print)1615-9853 (Linking)

Choi, K., Reinhard, C., Serra, H., Ziolkowski, P. A., Underwood, C. J., Zhao, X., Hardcastle, T. J., Yelina, N. E., Griffin, C., Jackson, M., Mezard, C., McVean, G., Copenhaver, G. P., Henderson, I. R. (2016) Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes. PLoS Genet, 12 (7). e1006179. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Choi, S. C., Rasmussen, M. D., Hubisz, M. J., Gronau, I., Stanhope, M. J., Siepel, A. (2012) Replacing and additive horizontal gene transfer in Streptococcus. Mol Biol Evol, 29 (11). pp. 3309-20. ISSN 0737-4038

Choisne, N., Demange, N., Orjeda, G., Samain, S., D'Hont, A., Cattolico, L., Pelletier, E., Couloux, A., Segurens, B., Wincker, P., Scarpelli, C., Weissenbach, J., Salanoubat, M., Quetier, F., Singh, N. K., Mohapatra, T., Sharma, T. R., Gaikwad, K., Singh, A., Dalal, V., Srivastava, S. K., Dixit, A., Pal, A. K., Ghazi, I. A., Yadav, M., Pandit, A., Bhargava, A., Sureshbabu, K., Dixit, R., Singh, H., Swain, S. C., Pal, S., Ragiba, M., Singh, P. K., Singhal, V., Mendiratta, S. D., Batra, K., Raghuvanshi, S., Mohanty, A., Bharti, A. K., Gaur, A., Gupta, V., Kumar, D., Vydianathan, R., Vij, S., Kapur, A., Khurana, P., Sharma, S., Khurana, J. P., Tyagi, A. K., Yuan, Q. P., Ouyang, S., Liu, J., Zhu, W., Wang, A. H., Lin, H. N., Hamilton, J., Haas, B., Wortman, J., Jones, K. M., Kim, M., Overton, L., Tsitrin, T., Fadrosh, D., Bera, J., Weaver, B., Jin, S. H., Johri, S., Reardon, M., Vuong, H., Tallon, L., Van Aken, S., Lewis, M., Utterback, T., Feldblyum, T., Zismann, V., Iobst, S., Hsiao, J., de Vazeille, A. R., Salzberg, S. L., White, O., Fraser, C., Buell, C. R., Yu, Y., Rambo, T., Currie, J., Collura, K., Kim, H. R., Stum, D., Wang, W. M., Kudrna, D., Mueller, C., Wing, R. A., Kramer, M., Spiegel, L., Nascimento, L., Preston, R., Zutavern, T., Palmer, L., O'Shaughnessy, A., McCombie, W. R. (2005) The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biology, 3. ISSN 1741-7007

Chou, S. T., Bailey, C. L., Hardison, R. C., Blobel, G. A., Vakoc, C. R., Weiss, M. J. (2007) GATA-1 represses PU.1/Sfpi-1 gene transcription in erythroMegakaryocytic progenitors. Blood, 110 (11). 371A-371A. ISSN 0006-4971

Chou, S. T., Khandros, E., Bailey, L. C., Nichols, K. E., Vakoc, C. R., Yao, Y., Huang, Z., Crispino, J. D., Hardison, R. C., Blobel, G. A., Weiss, M. J. (2009) Graded repression of PU.1/Sfpi1 gene transcription by GATA factors regulates hematopoietic cell fate. Blood, 114 (5). pp. 983-994.

Christensen, S. A., Nemchenko, A., Borrego, E., Murray, I., Sobhy, I. S., Bosak, L., Deblasio, S., Erb, M., Robert, C. A., Vaughn, K. A., Herrfurth, C., Tumlinson, J., Feussner, I., Jackson, D., Turlings, T. C., Engelberth, J., Nansen, C., Meeley, R., Kolomiets, M. V. (2013) The maize lipoxygenase, ZmLOX10, mediates green leaf volatile, jasmonate and herbivore-induced plant volatile production for defense against insect attack. Plant Journal, 74 (1). pp. 59-73. ISSN 09607412 (ISSN)

Church, Deanna M., Goodstadt, Leo, Hillier, LaDeana W., Zody, Michael C., Goldstein, Steve, She, Xinwe, Bult, Carol J., Agarwala, Richa, Cherry, Joshua L., DiCuccio, Michael, Hlavina, Wratko, Kapustin, Yuri, Meric, Peter, Maglott, Donna, Birtle, Zoë, Marques, Ana C., Graves, Tina, Zhou, Shiguo, Teague, Brian, Potamousis, Konstantinos, Churas, Christopher, Place, Michael, Herschleb, Jill, Runnheim, Ron, Forrest, Daniel, Amos-Landgraf, James, Schwartz, David C., Cheng, Ze, Lindblad-Toh, Kerstin, Eichler, Evan E., Ponting, Chris P., The Mouse Genome Sequencing, Consortium (2009) Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse. PLoS Biol, 7 (5). e1000112.

Church, G., Flicek, P., Ribbs, R., Mardis, E. (2010) PERSONAL GENOMES. In: 2010 meeting on PERSONAL GENOMES, September 10–September 12, 2010.

Clark, A. G., Eisen, M. B., Smith, D. R., Bergman, C. M., Oliver, B., Markow, T. A., Kaufman, T. C., Kellis, M., Gelbart, W., Iyer, V. N., Pollard, D. A., Sackton, T. B., Larracuente, A. M., Singh, N. D., Abad, J. P., Abt, D. N., Adryan, B., Aguade, M., Akashi, H., Anderson, W. W., Aquadro, C. F., Ardell, D. H., Arguello, R., Artieri, C. G., Barbash, D. A., Barker, D., Barsanti, P., Batterham, P., Batzoglou, S., Begun, D., Bhutkar, A., Blanco, E., Bosak, S. A., Bradley, R. K., Brand, A. D., Brent, M. R., Brooks, A. N., Brown, R. H., Butlin, R. K., Caggese, C., Calvi, B. R., Bernardo De Carvalho, A., Caspi, A., Castrezana, S., Celniker, S. E., Chang, J. L., Chapple, C., Chatterji, S., Chinwalla, A., Civetta, A., Clifton, S. W., Comeron, J. M., Costello, J. C., Coyne, J. A., Daub, J., David, R. G., Delcher, A. L., Delehaunty, K., Do, C. B., Ebling, H., Edwards, K., Eickbush, T., Evans, J. D., Filipski, A., Findeiß, S., Freyhult, E., Fulton, L., Fulton, R., Garcia, A. C. L., Gardiner, A., Garfield, D. A., Garvin, B. E., Gibson, G., Gilbert, D., Gnerre, S., Godfrey, J., Good, R., Gotea, V., Gravely, B., Greenberg, A. J., Griffiths-Jones, S., Gross, S., Guigo, R., Gustafson, E. A., Haerty, W., Hahn, M. W., Halligan, D. L., Halpern, A. L., Halter, G. M., Han, M. V., Heger, A., Hillier, L., Hinrichs, A. S., Holmes, I., Hoskins, R. A., Hubisz, M. J., Hultmark, D., Huntley, M. A., Jaffe, D. B., Jagadeeshan, S. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450 (7167). pp. 203-218. ISSN 00280836 (ISSN)

Cole, C. N., Hammell, C. M. (1998) Nucleocytoplasmic transport: Driving and directing transport. Current Biology, 8 (11). R368-R372. ISSN 09609822 (ISSN)

Cole, Charles N., Heath, Catherine V., Hodge, Christine A., Hammell, Christopher M., Amberg, David C. (2002) Analysis of RNA export. In: Methods in Enzymology. Academic Press, pp. 568-587. ISBN 0076-6879

Collins, F. S., Watson, J. D. (2003) Genetic discrimination: Time to act. Science, 302 (5646). p. 745. ISSN 0036-8075

Collins, G. A., Lipford, J. R., Deshaies, R. J., Tansey, W. P. (2009) Gal4 turnover and transcription activation. Nature, 461 (7265). E7-E7.

Conklin, D. S. (2003) RNA-interference-based silencing of mammalian gene expression. Chembiochem, 4 (10). pp. 1033-1039. ISSN 1439-4227

Consortium, 1000 Genomes Project (2015) A global reference for human genetic variation. Nature, 526 (7571). pp. 68-74. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Consortium, Arabidopsis Interactome Mapping (2011) Evidence for Network Evolution in an Arabidopsis Interactome Map. Science, 333 (6042). pp. 601-607.

Copenhaver, G. P., Nickel, K., Kuromori, T., Benito, M. I., Kaul, S., Lin, X., Bevan, M., Murphy, G., Harris, B., Parnell, L. D., McCombie, W. R., Martienssen, R. A., Marra, M., Preuss, D. (1999) Genetic definition and sequence analysis of Arabidopsis centromeres. Science, 286 (5449). pp. 2468-2474. ISSN 00368075 (ISSN)

Cranston, K. A., Hurwitz, B. L., Ware, D. H., Stein, L. D., Wing, R. A. (2009) Species Trees from Highly Incongruent Gene Trees in Rice. Systematic Biology, 58 (5). pp. 489-500. ISSN 1063-5157

Creasey, K. M., Martienssen, R. A. (2011) Germline Reprogramming of Heterochromatin in Plants. Cold Spring Harbor Symposia on Quantitative Biology, 75. pp. 269-274. ISSN 00917451 (ISSN)

Croft, D., Mundo, A. F., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M. R., Jassal, B., Jupe, S., Matthews, L., May, B., Palatnik, S., Rothfels, K., Shamovsky, V., Song, H., Williams, M., Birney, E., Hermjakob, H., Stein, L., D'Eustachio, P. (2014) The Reactome pathway knowledgebase. Nucleic Acids Research, 42 (Databa). D472-7. ISSN 0305-1048

Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B., Jupe, S., Kalatskaya, I., MayMahajan, S., May, B., Ndegwa, N., Schmidt, E., Shamovsky, V., Yung, C., Birney, E., Hermjakob, H., D'Eustachio, P., Stein, L. D. (2011) Reactome: A database of reactions, pathways and biological processes. Nucleic Acids Research, 39 (SUPPL.).

D

Daulny, A., Tansey, W. P. (2009) Damage control: DNA repair, transcription, and the ubiquitin-proteasome system. DNA Repair, 8 (4). pp. 444-448.

Davuluri, R. V., Grosse, I., Zhang, M. Q. (2001) Computational identification of promoters and first exons in the human genome. Nature Genetics, 29 (4). pp. 412-417. ISSN 1061-4036

Davuluri, R. V., Suzuki, Y., Sugano, S., Zhang, M. Q. (2000) CART classification of human 5 ' UTR sequences. Genome Research, 10 (11). pp. 1807-1816. ISSN 1088-9051

De Araújo, M. M., Bonnal, S., Hastings, M. L., Krainer, A. R., Valcárcel, J. (2009) Differential 3′ splice site recognition of SMN1 and SMN2 transcripts by U2AF and U2 snRNP. RNA, 15 (4). pp. 515-523.

Deck, Courtney A., McKay, Sheldon J., Fiedler, Tristan J., LeMoine, Christophe M. R., Kajimura, Makiko, Nawata, C. Michele, Wood, Chris M., Walsh, Patrick J. (2013) Transcriptome responses in the rectal gland of fed and fasted spiny dogfish shark (Squalus acanthias) determined by suppression subtractive hybridization. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics. ISSN 1744-117X

Dedhia, N. N., McCombie, W. R. (1998) Kaleidaseq: A Web-based tool to monitor data flow in a high throughput sequencing facility. Genome Research, 8 (3). pp. 313-318. ISSN 10889051 (ISSN)

Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D. G., Lagarde, J., Veeravalli, L., Ruan, X. A., Ruan, Y. J., Lassmann, T., Carninci, P., Brown, J. B., Lipovich, L., Gonzalez, J. M., Thomas, M., Davis, C. A., Shiekhattar, R., Gingeras, T. R., Hubbard, T. J., Notredame, C., Harrow, J., Guigo, R. (2012) The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Research, 22 (9 Spe). pp. 1775-1789. ISSN 1088-9051

Desai, A., Connelly, J. J., March, M., Hou, C., Chiavacci, R. , Kim, C., Lyon, G., Hadley, D., Hakonarson, H. (2016) Systematic data-querying of large pediatric biorepository identifies novel Ehlers-Danlos Syndrome variant. BMC Musculoskelet Disord, 17 (1). p. 80.

Desjardins, C. A., Gundersen-Rindal, D. E., Hostetler, J. B., Tallon, L. J., Fadrosh, D. W., Fuester, R. W., Pedroni, M. J., Haas, B. J., Schatz, M. C., Jones, K. M., Crabtree, J., Forberger, H., Nene, V. (2008) Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps. Genome Biology, 9 (12). ISSN 14656914 (ISSN)

Desjardins, C. A., Gundersen-Rindal, D. E., Hostetler, J. B., Tallon, L. J., Fuester, R. W., Schatz, M. C., Pedroni, M. J., Fadrosh, D. W., Haas, B. J., Toms, B. S., Chen, D., Nene, V. (2007) Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus. BMC Microbiology, 7. ISSN 14712180 (ISSN)

Desnoyers, S., Hengartner, M. O. (1997) Genetics of apoptosis. Advances in Pharmacology, 41. pp. 35-56. ISSN 1054-3589 (Print)

Deutsch, C. K., Malhotra, D., Krause, V., McCarthy, S. E., Krastoshevsky, O., Coleman, M., Francis, R. W., Bodkin, J. A., Boling, L., Cole, J., Gibbs, A., Johnson, F., Lerbinger, J., Mendell, N. R., Sebat, J., Levy, D. L. (2009) Rare Gene Copy Number Variations Are Associated with Specific Endophenotypes in Schizophrenia. Schizophrenia Bulletin, 35 (Suppl.). p. 117. ISSN 0586-7614

Dharmawardhana, P., Ren, L. Y., Amarasinghe, V., Monaco, M., Thomason, J., Ravenscroft, D., McCouch, S., Ware, D., Jaiswal, P. (2013) A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. Rice, 6 (1). pp. 1-15. ISSN 1939-8425

Dimitrova, N., Chen, Y. C. M., Spector, D. L., de Lange, T. (2008) 53BP1 promotes non-homologous end joining of telomeres by increasing chromatin mobility. Nature, 456 (7221). pp. 524-528.

Ding, D., Zhang, L., Wang, H., Liu, Z., Zhang, Z., Zheng, Y. (2009) Differential expression of miRNAs in response to salt stress in maize roots. Ann Bot, 103 (1). pp. 29-38.

Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., Xue, C., Marinov, G. K., Khatun, J., Williams, B. A., Zaleski, C., Rozowsky, J., Röder, M., Kokocinski, F., Abdelhamid, R. F., Alioto, T., Antoshechkin, I., Baer, M. T., Bar, N. S., Batut, P., Bell, K., Bell, I., Chakrabortty, S., Chen, X., Chrast, J., Curado, J., Derrien, T., Drenkow, J., Dumais, E., Dumais, J., Duttagupta, R., Falconnet, E., Fastuca, M., Fejes-Toth, K., Ferreira, P., Foissac, S., Fullwood, M. J., Gao, H., Gonzalez, D., Gordon, A., Gunawardena, H., Howald, C., Jha, S., Johnson, R., Kapranov, P., King, B., Kingswood, C., Luo, O. J., Park, E., Persaud, K., Preall, J. B., Ribeca, P., Risk, B., Robyr, D., Sammeth, M., Schaffer, L., See, L. H., Shahab, A., Skancke, J., Suzuki, A. M., Takahashi, H., Tilgner, H., Trout, D., Walters, N., Wang, H., Wrobel, J., Yu, Y., Ruan, X., Hayashizaki, Y., Harrow, J., Gerstein, M., Hubbard, T., Reymond, A., Antonarakis, S. E., Hannon, G., Giddings, M. C., Ruan, Y., Wold, B., Carninci, P., Guig, R., Gingeras, T. R. (2012) Landscape of transcription in human cells. Nature, 489 (7414). pp. 101-108. ISSN 0028-0836

Djebali, S., Kapranov, P., Foissac, S., Lagarde, J., Reymond, A., Ucla, C., Wyss, C., Drenkow, J., Dumais, E., Murray, R. R., Lin, C., Szeto, D., Denoeud, F., Calvo, M., Frankish, A., Harrow, J., Makrythanasis, P., Vidal, M., Salehi-Ashtiani, K., Antonarakis, S. E., Gingeras, T. R., Guigo, R. (2008) Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nature Methods, 5 (7). pp. 629-35. ISSN 15487091 (ISSN)

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., Gingeras, T. R. (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29 (1). pp. 15-21. ISSN 1367-4803

Dobin, A., Gingeras, T. R. (2016) Optimizing RNA-Seq Mapping with STAR. Methods Mol Biol, 1415. pp. 245-262. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Doerfel, Max, Lyon, Gholson J. (2015) The biological functions of Naa10 – from amino-terminal acetylation to human disease. Gene, 567 (2). pp. 103-131. ISSN 0378-1119

Doerfel, Max, Lyon, Gholson J. (2014) Molecular and cellular effects of the Ogden syndrome S37P mutation on the function of the N-terminal acetyltransferase Naa10. In: 64th Annual Meeting of the American Society of Human Genetics (ASHG), October 2014, San Diego, California. (Unpublished)

Domsic, J. K., Wang, Y. B., Mayeda, A., Krainer, A. R., Stoltzfus, C. M. (2003) Human immunodeficiency virus type 1 hnRNP A/B-Dep endent exonic splicing silencer ESSV antagonizes binding of U2AF65 to viral polypyrimidine tracts. Molecular and Cellular Biology, 23 (23). pp. 8762-8772. ISSN 0270-7306

Dong, X., Greven, M. C., Kundaje, A., Djebali, S., Brown, J. B., Cheng, C., Gingeras, T. R., Gerstein, M., Guigó, R., Birney, E., Weng, Z. (2012) Modeling gene expression using chromatin features in various cellular contexts. Genome Biology, 13 (9).

Doolittle, W. F., Fraser, P., Gerstein, M. B., Graveley, B. R., Henikoff, S., Huttenhower, C., Oshlack, A., Ponting, C. P., Rinn, J. L., Schatz, M. C., Ule, J., Weigel, D., Weinstock, G. M. (2013) Sixty years of genome biology. Genome Biology, 14 (4). ISSN 1474-7596

Dore, L. C., Vakoc, C. R., Blobel, G. A., Hardison, R. C., Bodine, D. M., Gallagher, P. G., Weiss, M. J. (2005) Genomic organization, chromatin structure, and transcriptional regulation of the murine Alpha Hemoglobin Stabilizing Protein (AHSP) gene. Blood, 106 (11). 1012A-1012A. ISSN 0006-4971

Dorfel, M. J., Fang, H., Crain, J., Klingener, M., Weiser, J., Lyon, G. J. (2017) Proteomic and genomic characterization of a yeast model for Ogden syndrome. Yeast, 34 (1). pp. 19-37. ISSN 1097-0061 (Electronic)0749-503X (Linking)

Dowell, R. D., Jokerst, R. M., Day, A., Eddy, S. R., Stein, L. (2001) The distributed annotation system. BMC Bioinformatics, 2. p. 7.

Dowen, Jill M., Bilodeau, Steve, Orlando, David A., Hübner, Michael R., Abraham, Brian J., Spector, David L., Young, Richard A. (2013) Multiple Structural Maintenance of Chromosome Complexes at Transcriptional Regulatory Elements. Stem Cell Reports, 1 (5). pp. 371-378. ISSN 2213-6711

Dunham, I., Kundaje, A., Aldred, S. F., Collins, P. J., Davis, C., Doyle, F., Epstein, C. B., Frietze, S., Harrow, J., Kaul, R., Khatun, J., Lajoie, B. R., Landt, S. G., Lee, B. K., Pauli, F., Rosenbloom, K. R., Sabo, P., Safi, A., Sanyal, A., Shoresh, N., Simon, J. M., Song, L., Trinklein, N. D., Altshuler, R. C., Birney, E., Brown, J. B., Cheng, C., Djebali, S., Dong, X. J., Ernst, J., Furey, T. S., Gerstein, M., Giardine, B., Greven, M., Hardison, R. C., Harris, R. S., Herrero, J., Hoffman, M. M., Iyer, S., Kellis, M., Kheradpour, P., Lassmann, T., Li, Q. H., Lin, X., Marinov, G. K., Merkel, A., Mortazavi, A., Parker, S. C. J., Reddy, T. E., Rozowsky, J., Schlesinger, F., Thurman, R. E., Wang, J., Ward, L. D., Whitfield, T. W., Wilder, S. P., Wu, W., Xi, H. L. S., Yip, K. Y., Zhuang, J. L., Bernstein, B. E., Green, E. D., Gunter, C., Snyder, M., Pazin, M. J., Lowdon, R. F., Dillon, L. A. L., Adams, L. B., Kelly, C. J., Zhang, J., Wexler, J. R., Good, P. J., Feingold, E. A., Crawford, G. E., Dekker, J., Elnitski, L., Farnham, P. J., Giddings, M. C., Gingeras, T. R., Guigo, R., Hubbard, T. J., Kent, W. J., Lieb, J. D., Margulies, E. H., Myers, R. M., Stamatoyannopoulos, J. A., Tenenbaum, S. A., Weng, Z. P., White, K. P., Wold, B., Yu, Y., Wrobel, J., Risk, B. A., Gunawardena, H. P., Kuiper, H. C., Maier, C. W., Xie, L., Chen, X., Mikkelsen, T. S., Gillespie, S. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489 (7414). pp. 57-74. ISSN 0028-0836

Dunn, E. F., Hammell, C. M., Hodge, C. A., Cole, C. N. (2005) Yeast poly(A)-binding protein, Pab1, and PAN, a poly(A) nuclease complex recruited by Pab1, connect mRNA biogenesis to export. Genes and Development, 19 (1). pp. 90-103. ISSN 08909369 (ISSN)

E

Eakin, A. E., Mills, A. A., Harth, G., McKerrow, J. H., Craik, C. S. (1992) The sequence, organization, and expression of the major cysteine protease (cruzain) from Trypanosoma cruzi. Journal of Biological Chemistry, 267 (11). pp. 7411-7420. ISSN 00219258 (ISSN)

Eckersley-Maslin, M. A., Bergmann, J. H., Lazar, Z., Spector, D. L. (2013) Lamin A/C is Expressed in Pluripotent Mouse Embryonic Stem Cells. Nucleus, 4 (1). pp. 53-60. ISSN 1949-1042 (Electronic)1949-1042 (Linking)

Egeblad, M., Werb, Z. (2002) New functions for the matrix metalloproteinases in cancer progression. Nature Reviews Cancer, 2 (3). pp. 161-174. ISSN 1474175X (ISSN)

Eifert, C., Powers, R. S. (2012) From cancer genomes to oncogenic drivers, tumour dependencies and therapeutic targets. Nat Rev Cancer, 12 (8). pp. 572-578. ISSN 1474-1768 (Electronic)1474-175X (Linking)

Elia, J., Glessner, J. T., Wang, K., Takahashi, N., Shtir, C. J., Hadley, D., Sleiman, P. M. A., Zhang, H., Kim, C. E., Robison, R., Lyon, G. J., Flory, J. H., Bradfield, J. P., Imielinski, M., Hou, C., Frackelton, E. C., Chiavacci, R. M., Sakurai, T., Rabin, C., Middleton, F. A., Thomas, K. A., Garris, M., Mentch, F., Freitag, C. M., Steinhausen, H. C., Todorov, A. A., Reif, A., Rothenberger, A., Franke, B., Mick, E. O., Roeyers, H., Buitelaar, J., Lesch, K. P., Banaschewski, T., Ebstein, R. P., Mulas, F., Oades, R. D., Sergeant, J., Sonuga-Barke, E., Renner, T. J., Romanos, M., Romanos, J., Warnke, A., Walitza, S., Meyer, J., Pálmason, H., Seitz, C., Loo, S. K., Smalley, S. L., Biederman, J., Kent, L., Asherson, P., Anney, R. J. L., Gaynor, J. W., Shaw, P., Devoto, M., White, P. S., Grant, S. F. A., Buxbaum, J. D., Rapoport, J. L., Williams, N. M., Nelson, S. F., Faraone, S. V., Hakonarson, H. (2012) Genome-wide copy number variation study associates metabotropic glutamate receptor gene networks with attention deficit hyperactivity disorder. Nature Genetics, 44 (1). pp. 78-84. ISSN 1061-4036

Ellis, L., Bots, M., Lindemann, R. K., Bolden, J. E., Newbold, A., Cluse, L. A., Scott, C. L., Strasser, A., Atadja, P., Lowe, S. W., Johnstone, R. W. (2009) The histone deacetylase inhibitors LAQ824 and LBH589 do not require death receptor signaling or a functional apoptosome to mediate tumor cell death or therapeutic efficacy. Blood, 114 (2). pp. 380-393.

Erlich, Y., Chang, K., Gordon, A., Ronen, R., Navon, O., Rooks, M., Hannon, G. J. (2009) DNA Sudoku - Harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Research, 19 (7). pp. 1243-1253. ISSN 10889051 (ISSN)

Erlich, Y., Mitra, P. P., Delabastide, M., McCombie, W. R., Hannon, G. J. (2008) Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nature Methods, 5 (8). 679 - 682.

Erlich, Y., Williams, J. B., Glazer, D., Yocum, K., Farahany, N., Olson, M., Narayanan, A., Stein, L. D., Witkowski, J. A., Kain, R. C. (2014) Redefining genomic privacy: trust and empowerment. Plos Biology, 12 (11). e1001983. ISSN 1544-9173

Ernst, P., Vakoc, C. R. (2012) WRAD: enabler of the SET1-family of H3K4 methyltransferases. Briefings in Functional Genomics, 11 (3). pp. 217-226. ISSN 2041-2649

Ezhkova, E., Pasolli, H. A., Parker, J. S., Stokes, N., Su, I. H., Hannon, G. J., Tarakhovsky, A., Fuchs, E. (2009) Ezh2 Orchestrates Gene Expression for the Stepwise Differentiation of Tissue-Specific Stem Cells. Cell, 136 (6). pp. 1122-1135. ISSN 0092-8674

F

Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., Matthews, L., May, B., Milacic, M., Rothfels, K., Shamovsky, V., Webber, M., Weiser, J., Williams, M., Wu, G., Stein, L., Hermjakob, H., D'Eustachio, P. (2016) The Reactome pathway Knowledgebase. Nucleic Acids Res, 44 (D1). D481-487. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Fagegaltier, D., Bougé, A.-L., Berry, B., Poisot, É., Sismeiro, O., Coppée, J.-Y., Théodore, L., Voinnet, O., Antoniewski, C. (2009) The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila. Proceedings of the National Academy of Sciences of the United States of America, 106 (50). pp. 21258-21263.

Fan, G., Wrzeszczynski, K. O., Fu, C., Su, G., Pappin, D. J., Lucito, R., Tonks, N. K. (2015) A quantitative proteomics-based signature of platinum sensitivity in ovarian cancer cell lines. Biochem J, 465 (3). pp. 433-42. ISSN 0264-6021

Fan, S., Zhang, M. Q., Zhang, X. (2008) Histone methylation marks play important roles in predicting the methylation status of CpG islands. Biochemical and Biophysical Research Communications, 374 (3). pp. 559-564. ISSN 0006291X

Fang, F., Hodges, E., Molaro, A., Dean, M., Hannon, G. J., Smith, A. D. (2012) Genomic landscape of human allele-specific DNA methylation. Proceedings of the National Academy of Sciences of the United States of America, 109 (19). pp. 7332-7337. ISSN 00278424 (ISSN)

Fang, Han (2014) "Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions". Journal Club. (Unpublished)

Fang, Han (2013) Finding the sources of missing heritability in a yeast cross. Journal Club. (Unpublished)

Fang, Han (2014) "Towards Better Understanding of Artifacts in Variant Calling from High-Coverage Samples". Journal Club. (Unpublished)

Fang, Han, Lyon, Gholson J. (2015) Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation. Journal Club . (Unpublished)

Fang, Han, Lyon, Gholson J. (2014) Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Journal Club. (Unpublished)

Fang, Han, Lyon, Gholson J. (2014) Reducing INDEL calling errors in whole genome and exome sequencing data. In: Cold Spring Harbor Laboratory Personal Genomes Meeting, November 2014, Cold Spring Harbor, NY . (Unpublished)

Fang, Han, Lyon, Gholson J. (2014) Reducing INDEL calling errors in whole genome and exome sequencing data. In: Cold Spring Harbor Laboratory Biological Data Science Meeting, November 8, 2014, Cold Spring Harbor, NY. (Unpublished)

Fang, Han, Lyon, Gholson J. (2014) Reducing INDEL calling errors in whole-genome and exome sequencing. In: 64th Annual Meeting of the American Society of Human Genetics (ASHG), October 2014, San Diego, California. (Unpublished)

Fang, Han, Lyon, Gholson J. (2014) Whole genome analysis of an extended pedigree with Prader-Willi Syndrome, Hereditary Hemochromatosis, Familial Dysautonomia, Tourette Syndrome and other illnesses. In: Cold Spring Harbor Laboratory Personal Genomes Meeting, November 2014, Cold Spring Harbor, NY. (Unpublished)

Fang, Han, Lyon, Gholson J. (2014) Genetic influences on translation in yeast. [Teaching Resource] (Unpublished)

Fang, Han, Wu, Yiyang, Narzisi, G., O'Rawe, Jason, Jimenez Barron, Laura, Rosenbaum, J., Ronemus, M., Iossifov, I., Schatz, M. C., Lyon, Gholson J. (2014) Reducing INDEL calling errors in whole genome and exome sequencing data. Genome Med, 6 (10). p. 89.

Fang, Han, Wu, Yiyang, O'Rawe, Jason, Mittelman, David, Lyon, Gholson J. (2013) Whole genome sequencing analysis of a family with familial dysautonomia and neuropsychiatric symptoms. In: Cold Spring Harbor Laboratory Precision Medicine Meeting, November 2013, Cold Spring Harbor, New York. (Unpublished)

Farmer, A. A., Loftus, T. M., Mills, A. A., Sato, K. Y., Neill, J. D., Tron, T., Yang, M., Trumpower, B. L., Stanbridge, E. J. (1994) Extreme evolutionary conservation of QM, a novel c-Jun associated transcription factor. Human Molecular Genetics, 3 (5). pp. 723-728. ISSN 09646906 (ISSN)

Fendler, B., Atwal, G. (2012) Systematic deciphering of cancer genome networks. Yale Journal of Biology and Medicine, 85 (3). pp. 339-45. ISSN 1551-4056 (Electronic)0044-0086 (Linking)

Finigan, P., Martienssen, R. A. (2008) Nucleolar dominance and DNA methylation directed by small interfering RNA. Molecular Cell, 32 (6). pp. 753-4. ISSN 1097-2765

Fouts, D. E., Mongodin, E. F., Mandrell, R. E., Miller, W. G., Rasko, D. A., Ravel, J., Brinkac, L. M., Deboy, R. T., Parker, C. T., Daugherty, S. C., Dodson, R. J., Scott Durkin, A., Madupu, R., Sullivan, S. A., Shetty, J. U., Ayodeji, M. A., Shvartsbeyn, A., Schatz, M. C., Badger, J. H., Fraser, C. M., Nelson, K. E. (2005) Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biology, 3 (1). ISSN 15449173 (ISSN)

Fraser, C. M., Arakawa, S., McCombie, W. R., Venter, J. C. (1989) Cloning, sequence analysis, and permanent expression of a human α2-adrenergic receptor in Chinese hamster ovary cells. Evidence for independent pathways of receptor coupling to adenylate cyclase attenuation and activation. Journal of Biological Chemistry, 264 (20). pp. 11754-11761. ISSN 00219258 (ISSN)

Freedman, A. H., Schweizer, R. M., Ortega-Del Vecchyo, D., Han, E., Davis, B. W., Gronau, I., Silva, P. M., Galaverni, M., Fan, Z., Marx, P., Lorente-Galdos, B., Ramirez, O., Hormozdiari, F., Alkan, C., Vila, C., Squire, K., Geffen, E., Kusak, J., Boyko, A. R., Parker, H. G., Lee, C., Tadigotla, V., Siepel, A., Bustamante, C. D., Harkins, T. T., Nelson, S. F., Marques-Bonet, T., Ostrander, E. A., Wayne, R. K., Novembre, J. (2016) Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs. PLoS Genet, 12 (3). e1005851. ISSN 1553-7390

Fregoso, O. I. (2010) Elucidating the Functions of Splicing Regulatory Proteins Through the Use of High-Throughput Proteomics. PhD thesis, Cold Spring Harbor Laboratory.

Fregoso, O. I., Das, S., Akerman, M., Krainer, A. R. (2013) Splicing-Factor Oncoprotein SRSF1 Stabilizes p53 via RPL5 and Induces Cellular Senescence. Molecular Cell, 50 (1). pp. 56-66. ISSN 1097-2765

Fridman, J. S., Hernando, E., Hemann, M. T., de Stanchina, E., Cordon-Cardo, C., Lowe, S. W. (2003) Tumor promotion by Mdm2 splice variants unable to bind p53. Cancer Research, 63 (18). pp. 5703-5706. ISSN 0008-5472

Fridman, J. S., Lowe, S. W. (2003) Control of apoptosis by p53. Oncogene, 22 (56). pp. 9030-9040. ISSN 0950-9232

G

Gajer, P., Schatz, M., Salzberg, S. L. (2004) Automated correction of genome sequence errors. Nucleic Acids Research, 32 (2). pp. 562-569. ISSN 03051048 (ISSN)

Garcia, E. L., Mills, A. A. (2002) Getting around lethality with inducible Cre-mediated excision. Seminars in Cell & Developmental Biology, 13 (2). pp. 151-158. ISSN 1084-9521

Gerhard, D. S., Clemons, P. A., Shamji, A. F., Hon, C., Wagner, B. K., Schreiber, S. L., Krasnitz, A., Sordella, R., Sander, C., Lowe, S. W., Powers, S., Smith, K., Aburi, M., Iavarone, A., Lasorella, A., Silva, J., Stockwell, B. R., Califano, A., Boehm, J. S., Vazquez, F., Weir, B. A., Hahn, W. C., Khuri, F. R., Moreno, C. S., Johns, M., Fu, H., Nikolova, O., Mendez, E., Gadi, V. K., Margolin, A. A., Grandori, C., Kemp, C. J., Warren, E. H., Riddell, S. R., McIntosh, M. W., Gevaert, O., Kuo, C. J., Ji, H. P., Dhruv, H., Finlay, D., Kiefer, J., Kim, S., Vuori, K., Berens, M. E., Hangauer, M., Boettcher, M., Weissman, J. S., Bivona, T. G., Bandyopadhyay, S., McManus, M. T., McCormick, F., Aksoy, O., Simonds, E. F., Zheng, T., Chen, J., An, Z., Balmain, A., Weiss, W. A., Chen, K., Liang, H., Scott, K. L., Mills, G. B., Posner, B. A., MacMillan, J., Minna, J., White, M., Roth, M. G., Jagu, S., Mazerik, J. (2016) Transforming Big Data into cancer-relevant insight: An initial, multi-tier approach to assess reproducibility and relevance. Mol Cancer Res. ISSN 1557-3125 (Electronic)1541-7786 (Linking)

Ghafoori, A., Lee, C., Perez, B., Johnston, S., Rodrigues, R., Badea, C., Kim, Y., Lowe, S. W., Kirsch, D. G. (2009) In Vivo shRNA to Study the Molecular Mechanisms of Radiation Response of Primary Cancers in Mice. International Journal of Radiation Oncology Biology Physics, 75 (3). S171-S172. ISSN 0360-3016

Ghedin, E., Wang, S., Spiro, D., Caler, E., Zhao, Q., Crabtree, J., Allen, J. E., Delcher, A. L., Guiliano, D. B., Miranda-Saavedra, D., Angiuoli, S. V., Creasy, T., Amedeo, P., Haas, B., El-Sayed, N. M., Wortman, J. R., Feldblyum, T., Tallon, L., Schatz, M., Shumway, M., Koo, H., Salzberg, S. L., Schobel, S., Pertea, M., Pop, M., White, O., Barton, G. J., Carlow, C. K. S., Crawford, M. J., Daub, J., Dimmic, M. W., Estes, C. F., Foster, J. M., Ganatra, M., Gregory, W. F., Johnson, N. M., Jin, M., Komuniecki, R., Korf, I., Kumar, S., Laney, S., Li, B. W., Li, W., Lindblom, T. H., Lustigman, S., Ma, D., Maina, C. V., Martin, D. M. A., McCarter, J. P., McReynolds, L., Mitreva, M., Nutman, T. B., Parkinson, J., Peregrín-Alvarez, J. M., Poole, C., Ren, Q., Saunders, L., Sluder, A. E., Smith, K., Stanke, M., Unnasch, T. R., Ware, J., Wei, A. D., Weil, G., Williams, D. J., Zhang, Y., Williams, S. A., Fraser-Liggett, C., Slatko, B., Blaxter, M. L., Scott, A. L. (2007) Draft genome of the filarial nematode parasite Brugia malayi. Science, 317 (5845). pp. 1756-1760. ISSN 00368075 (ISSN)

Gholson, Lyon (2014) "Clinical genetics of neurodevelopmental disorders". In: Mount Sinai Medical Center - Invited Speaker, June 20th 2014, Department of Genetics and Genomic Sciences and the Institute for Genomics and Multiscale Biology at the Mount Sinai Medical Center. (Unpublished)

Gibbs, R. A., Belmont, J. W., Hardenbol, P., Willis, T. D., Yu, F. L., Yang, H. M., Ch'ang, L. Y., Huang, W., Liu, B., Shen, Y., Tam, P. K. H., Tsui, L. C., Waye, M. M. Y., Wong, J. T. F., Zeng, C. Q., Zhang, Q. R., Chee, M. S., Galver, L. M., Kruglyak, S., Murray, S. S., Oliphant, A. R., Montpetit, A., Hudson, T. J., Chagnon, F., Ferretti, V., Leboeuf, M., Phillips, M. S., Verner, A., Kwok, P. Y., Duan, S. H., Lind, D. L., Miller, R. D., Rice, J. P., Saccone, N. L., Taillon-Miller, P., Xiao, M., Nakamura, Y., Sekine, A., Sorimachi, K., Tanaka, T., Tanaka, Y., Tsunoda, T., Yoshino, E., Bentley, D. R., Deloukas, P., Hunt, S., Powell, D., Altshuler, D., Gabriel, S. B., Qiu, R. Z., Ken, A., Dunston, G. M., Kato, K., Niikawa, N., Knoppers, B. M., Foster, M. W., Clayton, E. W., Wang, V. O., Watkin, J., Gibbs, R. A., Belmont, J. W., Sodergren, E., Weinstock, G. M., Wilson, R. K., Fulton, L. L., Rogers, J., Birren, B. W., Han, H., Wang, H. G., Godbout, M., Wallenburg, J. C., L'Archeveque, P., Bellemare, G., Todani, K., Fujita, T., Tanaka, S., Holden, A. L., Lai, E. H., Collins, F. S., Brooks, L. D., McEwen, J. E., Guyer, M. S., Jordan, E., Peterson, J. L., Spiegel, J., Sung, L. M., Zacharia, L. F., Kennedy, K., Dunn, M. G., Seabrook, R., Shillito, M., Skene, B., Stewart, J. G., Valle, D. L., Clayton, E. W., Jorde, L. B., Belmont, J. W., Chakravarti, A., Cho, M. K., Duster, T. (2003) The International HapMap Project. Nature, 426 (6968). pp. 789-796. ISSN 0028-0836

Gibbs, R. A., Rogers, J., Katze, M. G., Bumgarner, R., Weinstock, G. M., Mardis, E. R., Remington, K. A., Strausberg, R. L., Venter, J. C., Wilson, R. K., Batzer, M. A., Bustamante, C. D., Eichler, E. E., Hahn, M. W., Hardison, R. C., Makova, K. D., Miller, W., Milosavljevic, A., Palermo, R. E., Siepel, A., Sikela, J. M., Attaway, T., Bell, S., Bernard, K. E., Buhay, C. J., Chandrabose, M. N., Dao, M., Davis, C., Delehaunty, K. D., Ding, Y., Dinh, H. H., Dugan-Rocha, S., Fulton, L. A., Gabisi, R. A., Garner, T. T., Godfrey, J., Hawes, A. C., Hernandez, J., Hines, S., Holder, M., Hume, J., Jhangiani, S. N., Joshi, V., Khan, Z. M., Kirkness, E. F., Cree, A., Fowler, R. G., Lee, S., Lewis, L. R., Li, Z., Liu, Y. S., Moore, S. M., Muzny, D., Nazareth, L. V., Ngo, D. N., Okwuonu, G. O., Pai, G., Parker, D., Paul, H. A., Pfannkoch, C., Pohl, C. S., Rogers, Y. H., Ruiz, S. J., Sabo, A., Santibanez, J., Schneider, B. W., Smith, S. M., Sodergren, E., Svatek, A. F., Utterback, T. R., Vattathil, S., Warren, W., White, C. S., Chinwalla, A. T., Feng, Y., Halpern, A. L., Hillier, L. W., Huang, X., Minx, P., Nelson, J. O., Pepin, K. H., Qin, X., Sutton, G. G., Venter, E., Walenz, B. P., Wallis, J. W., Worley, K. C., Yang, S. P., Jones, S. M., Marra, M. A., Rocchi, M., Schein, J. E., Baertsch, R., Clarke, L., Csuros, M., Glasscock, J., Harris, R. A., Havlak, P., Jackson, A. R., Jiang, H. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science, 316 (5822). pp. 222-34. ISSN 0036-8075

Gill, B. S., Appels, R., Botha-Oberholster, A. M., Buell, C. R., Bennetzen, J. L., Chalhoub, B., Chumley, F., Dvořák, J., Iwanaga, M., Keller, B., Li, W., McCombie, W. R., Ogihara, Y., Quetier, F., Sasaki, T. (2004) A workshop report on wheat genome sequencing: International genome research on wheat consortium. Genetics, 168 (2). pp. 1087-1096. ISSN 00166731 (ISSN)

Gillis, J. (2012) Talk from Jessie Gillis at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Gillis, J., Mistry, M., Pavlidis, P. (2010) Gene function analysis in complex data sets using ErmineJ. Nature Protocols, 5 (6). pp. 1148-1159. ISSN 17502799 (ISSN)

Gillis, J., Pavlidis, P. (2013) Assessing identity, redundancy and confounds in Gene Ontology annotations over time. Bioinformatics, 29 (4). pp. 476-82. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

Gillis, J., Pavlidis, P. (2013) Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA). BMC Bioinformatics, 14 (Suppl). S15. ISSN 1471-2105 (Electronic)1471-2105 (Linking)

Gillis, J., Pavlidis, P. (2013) Cross-validation calculation from "Guilt by Association" Is the Exception Rather Than the Rule in Gene Networks Gillis, J. and Pavlidis, P. (2012) PLoS Computational Biology, 8 (3). [Dataset]

Gillis, J., Pavlidis, P. (2013) Data from "Assessing identity, redundancy and confounds in Gene Ontology annotations over time". [Dataset]

Gillis, J., Pavlidis, P. (2012) Exceptional Edges matrices from "Guilt by Association" Is the Exception Rather Than the Rule in Gene Networks Gillis, J. and Pavlidis, P. (2012) PLoS Computational Biology, 8 (3). [Dataset]

Gillis, J., Pavlidis, P. (2011) Figure data from "The role of indirect connections in gene networks in predicting function" Gillis, J. and Pavlidis, P. (2011) Bioinformatics, 27 (13). pp. 1860-1866. [Dataset]

Gillis, J., Pavlidis, P. (2012) Gene Ontology matrices (with descriptions, IDs, etc) from "Guilt by Association" Is the Exception Rather Than the Rule in Gene Networks. Gillis, J. and Pavlidis, P. (2012) PLoS Computational Biology, 8 (3). [Dataset]

Gillis, J., Pavlidis, P. (2011) Gene Ontology matrices from The role of indirect connections in gene networks in predicting function Gillis, J. and Pavlidis, P. (2011) Bioinformatics, 27 (13). pp. 1860-1866. [Dataset]

Gillis, J., Pavlidis, P. (2012) Gene lists from Gillis, J. and Pavlidis, P. (2012) PLoS Computational Biology, 8 (3). [Dataset]

Gillis, J., Pavlidis, P. (2011) Gene lists from The role of indirect connections in gene networks in predicting function Gillis, J. and Pavlidis, P. (2011) Bioinformatics, 27 (13). pp. 1860-1866. [Dataset]

Gillis, J., Pavlidis, P. (2011) Network data from The role of indirect connections in gene networks in predicting function Gillis, J. and Pavlidis, P. (2011)Bioinformatics, 27 (13). pp. 1860-1866. [Dataset]

Gillis, J., Pavlidis, P. (2013) Use case: The postsynaptic proteome, from "Assessing identity, redundancy and confounds in Gene Ontology annotations over time". [Dataset]

Gillis, J., Pavlidis, P. (2011) The impact of multifunctional genes on guilt "by association "analysis. PLoS One, 6 (2). ISSN 19326203 (ISSN)

Gillis, J., Pavlidis, P. (2009) A methodology for the analysis of differential coexpression across the human lifespan. BMC Bioinformatics, 10. p. 306. ISSN 14712105 (ISSN)

Gillis, J., Pavlidis, P. (2011) The role of indirect connections in gene networks in predicting function. Bioinformatics, 27 (13). pp. 1860-1866. ISSN 13674803 (ISSN)

Gingeras, T. R. (2008) Mapping the strand-specific transcriptome of fission yeast. Nature Genetics, 40 (8). pp. 935-936. ISSN 1061-4036

Gingeras, T. R. (2012) Patience is a virtue. Nature, 482 (7385). pp. 310-311. ISSN 0028-0836

Gingeras, T. R. (2004) RNA reference materials for gene expression studies. Difficult first steps. Clinical Chemistry, 50 (8). pp. 1289-1290. ISSN 00099147 (ISSN)

Gingeras, T. R. (1980) Restriction endonucleases and their role in genomic analysis. In: Gene structure and expression. Ohio State University Biosciences Colloquia. Ohio State University Press, pp. 3-20.

Gingeras, T. R. (1991) Restriction-modification systems. Genetic sentries and useful systems in the study of molecular genetics. In: Modern Microbial Genetics. Wiley-Liss, New York, pp. 301-322. ISBN 9780471568452

Gingeras, T. R., Roberts, R. J. (1981) Computer assisted methods for nucleic acid sequencing. In: Genetic Engineering: Principles and Methods. Plenum Press, pp. 319-338. ISBN 9780306439193

Girard, A., Hannon, G. J. (2008) Conserved themes in small-RNA-mediated transposon control. Trends Cell Biol, 18 (3). pp. 136-148.

Goff, S. A, Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E, Gessler, D. , Matasci, N., Wang, L., Hanlon, M., Lenards, A., Muir, A., Merchant, N., Lowry, S., Mock, S., Helmke, M., Kubach, A., Narro, M., Hopkins, N., Micklos, D., Hilgert, U., Gonzales, M, Jordan, C., Skidmore, E., Dooley, R., Cazes, J., McLay, R., Lu, Z., Pasternak, S., Koesterke, L., Piel, W. H., Grene, R., Noutsos, C., Gendler, K., Feng, X., Tang, C., Lent, M., Kim, S. J., Kvilekval, K., Manjunath, B.S., Tannen, V., Stamatakis, A., Sanderson, M. J., Welch, S. M., Cranston, K. , Soltis, P. , Soltis, D., O'Meara, B., Ane, C., Brutnell, T., Kleibenstein, D. J., White, J. W., Leebens-Mack, J., Donoghue, M. J., Spalding, E. P., Vision, T. J., Myers, C. R., Lowenthal, D., Enquist, B. J., Boyle, B., Akoglu, A., Andrews, G., Ram, S., Ware, D., Stein, L., Stanzione, D. (2011) The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers in Plant Science, 2. ISSN 1664-462X

Goldfarb, L. G., Brown, P., Haltia, M., Cathala, F., McCombie, W. R., Kovanen, J., Červeňáková, L., Goldin, L., Nieto, A., Godec, M. S., Asher, D. M., Gajdusek, D. C. (1992) Creutzfeldt-Jakob disease cosegregates with the codon 178Asn PRNP mutation in families of European origin. Annals of neurology, 31 (3). pp. 274-281. ISSN 03645134 (ISSN)

Goldfarb, L. G., Brown, P., McCombie, W. R., Goldgaber, D., Swergold, G. D., Wills, P. R., Cervenakova, L., Baron, H., Gibbs Jr, C. J., Gajdusek, D. C. (1991) Transmissible familial Creutzfeldt-Jakob disease associated with five, seven, and eight extra octapeptide coding repeats in the PRNP gene. Proceedings of the National Academy of Sciences of the United States of America, 88 (23). pp. 10926-10930. ISSN 00278424 (ISSN)

Goldfarb, L. G., Brown, P., Nuez, A. N., McCombie, W. R., Goldgaber, D., Asher, D. M., Gaidusek, D. C. (1991) FAMILIAL CREUTZFELDT-JAKOB DISEASE IS ASSOCIATED WITH 3 SEPARATE MUTATIONS. American Journal of Human Genetics, 49 (4). p. 188. ISSN 0002-9297

Goldfarb, L. G., Brown, P., Rubenstein, R., McCombie, W. R., Cervenakova, L., Graupera, G., Ligan, J., Sulima, M., Gibbs, C. J., Gajdusek, D. C. (1992) Genetic-characteristics of infectious forms of the transmissible spongiform encephalopathies. Annals of neurology, 32 (2). p. 233. ISSN 0364-5134

Goldfarb, L. G., Brown, P., Vrbovska, A., Baron, H., McCombie, W. R., Cathala, F., Gibbs Jr, C. J., Gajdusek, D. C. (1992) An insert mutation in the chromosome 20 amyloid precursor gene in a Gerstmann-Straussler-Scheinker family. Journal of the Neurological Sciences, 111 (2). pp. 189-194. ISSN 0022510X (ISSN)

Goldfarb, L. G., Haltia, M., Brown, P., Nieto, A., Kovanen, J., McCombie, W. R., Trapp, S., Carleton Gajdusek, D. (1991) New mutation in scrapie amyloid precursor gene (at codon 178) in finnish Creutzfield-Jakob kindred. Lancet, 337 (8738). p. 425. ISSN 01406736 (ISSN)

Gordon, D., Finch, S. J., Jacobs, A. L., Mendell, N. R., Single, R. M., Marr, T. G. (1997) Association of posterior p-values of S.A.G.E. SIBPAL proportion-IBD and Haseman-Elston statistics for ACTHR112. Genetic Epidemiology, 14 (6). pp. 629-34. ISSN 0741-0395 (Print)

Gore, M. A., Chia, J. M., Elshire, R. J., Sun, Q., Ersoz, E. S., Hurwitz, B. L., Peiffer, J. A., McMullen, M. D., Grills, G. S., Ross-Ibarra, J., Ware, D. H., Buckler, E. S. (2009) A first-generation haplotype map of maize. Science, 326 (5956). pp. 1115-1117. ISSN 0036-8075

Gracheva, E., Dus, M., Elgin, S. C. (2009) Drosophila RISC Component VIG and Its Homolog Vig2 Impact Heterochromatin Formation. PLoS ONE, 4 (7). e6182.

Gramza, Joyce, Lyon, Gholson J. (2012) Humane Treatment for Patients: How to Handle Genetic Information. [Audio]

Graveley, B. R., Brooks, A. N., Carlson, J., Duff, M. O., Landolin, J. M., Yang, L., Artieri, C. G., van Baren, M. J., Boley, N., Booth, B. W., Brown, J. B., Cherbas, L., Davis, C. A., Dobin, A., Li, R. H., Lin, W., Malone, J. H., Mattiuzzo, N. R., Miller, D., Sturgill, D., Tuch, B. B., Zaleski, C., Zhang, D. Y., Blanchette, M., Dudoit, S., Eads, B., Green, R. E., Hammonds, A., Jiang, L. C., Kapranov, P., Langton, L., Perrimon, N., Sandler, J. E., Wan, K. H., Willingham, A., Zhang, Y., Zou, Y., Andrews, J., Bickel, P. J., Brenner, S. E., Brent, M. R., Cherbas, P., Gingeras, T. R., Hoskins, R. A., Kaufman, T. C., Oliver, B., Celniker, S. E. (2011) The developmental transcriptome of Drosophila melanogaster. Nature, 471 (7339). pp. 473-479. ISSN 0028-0836

Gregory, G. D., Vakoc, C. R., Rozovskaia, T., Zheng, X., Patel, S., Nakamura, T., Canaani, E., Blobel, G. A. (2007) Mammalian ASH1L is a histone methyltransferase that occupies the transcribed region of active genes. Molecular and Cellular Biology, 27 (24). pp. 8466-8479. ISSN 02707306 (ISSN)

Grinevich, V., Kolleker, A., Eliava, M., Takada, N., Takuma, H., Fukazawa, Y., Shigemoto, R., Kuhl, D., Waters, J., Seeburg, P.H., Osten, P. (2009) Fluorescent Arc/Arg3.1 indicator mice: A versatile tool to study brain activity changes in vitro and in vivo. Journal of Neuroscience Methods, 184 (1). pp. 25-36.

Gronau, I., Arbiza, L., Mohammed, J., Siepel, A. (2013) Inference of natural selection from interspersed genomic elements based on polymorphism and divergence. Mol Biol Evol, 30 (5). pp. 1159-71. ISSN 0737-4038

Groover, A. T., Fontana, J. R., Arroyo, J. M., Yordan, C., McCombie, W. R., Martienssen, R. A. (2003) Secretion trap tagging of secreted and membrane-spanning proteins using Arabidopsis gene traps. Plant Physiology, 132 (2). pp. 698-708. ISSN 00320889 (ISSN)

Gruntman, E., Qi, Y., Slotkin, R. K., Roeder, T., Martienssen, R. A., Sachidanandam, R. (2008) Kismeth: analyzer of plant methylation states through bisulfite sequencing. BMC bioinformatics, 9. p. 371. ISSN 1471-2105 (Electronic)1471-2105 (Linking)

Guberman, J. M., Ai, J., Arnaiz, O., Baran, J., Blake, A., Baldock, R., Chelala, C., Croft, D., Cros, A., Cutts, R. J., Di Génova, A., Forbes, S., Fujisawa, T., Gadaleta, E., Goodstein, D. M., Gundem, G., Haggarty, B., Haider, S., Hall, M., Harris, T., Haw, R., Hu, S., Hubbard, S., Hsu, J., Iyer, V., Jones, P., Katayama, T., Kinsella, R., Kong, L., Lawson, D., Liang, Y., Lopez-Bigas, N., Luo, J., Lush, M., Mason, J., Moreews, F., Ndegwa, N., Oakley, D., Perez-Llamas, C., Primig, M., Rivkin, E., Rosanoff, S., Shepherd, R., Simon, R., Skarnes, B., Smedley, D., Sperling, L., Spooner, W., Stevenson, P., Stone, K., Teague, J., Wang, J., Whitty, B., Wong, D. T., Wong-Erasmus, M., Yao, L., Youens-Clark, K., Yung, C., Zhang, J., Kasprzyk, A. (2011) BioMart Central Portal: an open database network for the biological community. Database : the journal of biological databases and curation, 2011. ISSN 17580463 (ISSN)

Guha, S., Rees, E., Darvasi, A., Ivanov, D., Ikeda, M., Bergen, S. E., Magnusson, P. K., Cormican, P., Morris, D., Gill, M., Cichon, S., Rosenfeld, J. A., Lee, A., Gregersen, P. K., Kane, J. M., Malhotra, A. K., Rietschel, M., Nothen, M. M., Degenhardt, F., Priebe, L., Breuer, R., Strohmaier, J., Ruderfer, D. M., Moran, J. L., Chambert, K. D., Sanders, A. R., Shi, J. X., Kendler, K., Riley, B., O'Neill, T., Walsh, D., Malhotra, D., Corvin, A., Purcell, S., Sklar, P., Iwata, N., Hultman, C. M., Sullivan, P. F., Sebat, J., McCarthy, S., Gejman, P. V., Levinson, D. F., Owen, M. J., O'Donovan, M. C., Lencz, T., Kirov, G. (2013) Implication of a Rare Deletion at Distal 16p11.2 in Schizophrenia. Jama Psychiatry, 70 (3). pp. 253-260. ISSN 2168-622X

Gunnery, S., Ma, Y., Mathews, M. B. (1999) Termination sequence requirements vary among genes transcribed by RNA polymerase III. Journal of Molecular Biology, 286 (3). pp. 745-57. ISSN 0022-2836 (Print)

Guo, M., Thomas, J., Collins, G. A., Timmermans, M. C. P. (2008) Direct Repression of KNOX Loci by the ASYMMETRIC LEAVES1 Complex of Arabidopsis. Plant Cell, 20 (1). pp. 48-58.

Guo, X., Keyes, W. M., Papazoglu, C., Zuber, J., Li, W., Lowe, S. W., Vogel, H., Mills, A. A. (2009) TAp63 induces senescence and suppresses tumorigenesis in vivo. Nat Cell Biol, 11 (12). 1451–1457.

Gupta, Parul, Naithani, Sushma, Tello-Ruiz, Marcela Karey, Chougule, Kapeel, D’Eustachio, Peter, Fabregat, Antonio, Jiao, Yinping, Keays, Maria, Lee, Young Koung, Kumari, Sunita, Mulvaney, Joseph, Olson, Andrew, Preece, Justin, Stein, Joshua, Wei, Sharon, Weiser, Joel, Huerta, Laura, Petryszak, Robert, Kersey, Paul, Stein, Lincoln D., Ware, Doreen, Jaiswal, Pankaj (2016) Gramene Database: Navigating Plant Comparative Genomics Resources. Current Plant Biology, 7-8. pp. 10-15. ISSN 2214-6628

Gurtowski, J., Schatz, M. C., Langmead, B. (2012) Genotyping in the cloud with crossbow. Current Protocols in Bioinformatics. 15.3. ISSN 1934-340X (Electronic)1934-3396 (Linking)

Gutiérrez, R. A., Stokes, T. L., Thum, K., Xu, X., Obertello, M., Katari, M. S., Tanurdzic, M., Dean, A., Nero, D. C., McClung, C. R., Coruzzi, G. M. (2008) Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc Natl Acad Sci U S A, 105 (12). pp. 4939-4944. ISSN 0027-8424

Gutschner, T., Hammerle, M., Eißmann, M., Hsu, J., Kim, Y., Hung, G., Revenko, A., Arun, G., Stentrup, M., Groß, M., Zörnig, M., MacLeod, A. R., Spector, D. L., Diederichs, S. (2013) The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. Cancer Research, 73 (3). pp. 1180-1189. ISSN 00085472 (ISSN)

Guzzardo, P. M., Muerdter, F., Hannon, G. J. (2013) The piRNA pathway in flies: highlights and future directions. Curr Opin Genet Dev, 23 (1). pp. 44-52. ISSN 1879-0380 (Electronic)0959-437X (Linking)

Guzzardo, Paloma M. (2013) Identification and characterization of novel components of the Drosophila piRNA pathway. PhD thesis, Cold Spring Harbor Laboratory.

Gyrd-Hansen, M., Darding, M., Miasari, M., Santoro, M. M., Zender, L., Xue, W., Tenev, T., da Fonseca, P. C., Zvelebil, M., Bujnicki, J. M., Lowe, S. W., Silke, J., Meier, P. (2008) IAPs contain an evolutionarily conserved ubiquitin-binding domain that regulates NF-kappaB as well as cell survival and oncogenesis. Nat Cell Biol, 10 (11). pp. 1309-17.

H

Hacisalihoglu, G., Hilgert, U., Nash, E. B., Micklos, D. A. (2008) An innovative plant genomics and gene annotation program for high school, community college, and university faculty. CBE Life Sci Educ, 7 (3). pp. 310-6.

Hall, I. M., Grewal, S. I. S. (2003) Structure and function of heterochromatin: implications for epigenetic gene silencing and genome organization. In: RNAi : a guide to gene silencing. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. , pp. 205-232. ISBN 978-087969641-2

Hammell, C. M. (2008) The microRNA-argonaute complex: a platform for mRNA modulation. RNA Biology, 5 (3). pp. 123-7. ISSN 1555-8584 (Electronic)1547-6286 (Linking)

Hammell, C. M., Gross, S., Zenklusen, D., Heath, C. V., Stutz, F., Moore, C., Cole, C. N. (2002) Coupling of termination, 3′ processing, and mRNA export. Molecular and Cellular Biology, 22 (18). pp. 6441-6457. ISSN 02707306 (ISSN)

Hammell, C. M., Hannon, G. J. (2012) Inducing RNAi in C. elegans by Feeding with dsRNA-expressing E. coli. Cold Spring Harb Protoc, 2012 (12). ISSN 1559-6095 (Electronic)1559-6095 (Linking)

Hammell, C. M., Karp, X., Ambros, V. (2009) A feedback circuit involving let-7-family miRNAs and DAF-12 integrates environmental signals and developmental timing in Caenorhabditis elegans. Proc Natl Acad Sci U S A, 106 (44). pp. 18668-73. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Hammell, C. M., Lubin, I., Boag, P. R., Blackwell, T. K., Ambros, V. (2009) nhl-2 Modulates microRNA activity in Caenorhabditis elegans. Cell, 136 (5). pp. 926-38. ISSN 1097-4172 (Electronic)0092-8674 (Linking)

Hammell, M. (2011) Talk from Molly Hammell at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Han, H., Pappin, D. J., Ross, P. L., McLuckey, S. A. (2008) Electron transfer dissociation of iTRAQ labeled peptide ions. J Proteome Res, 7 (9). pp. 3643-8. ISSN 1535-3893 (Print)1535-3893 (Linking)

Hannon, G. J. (2012) Talk from Greg Hannon at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Hannon, Gregory J., Zamore, Phillip D. (2003) Small RNAs, big biology: biochemical studies of RNA interference. In: RNAi: a guide to gene silencing. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y., pp. 87-108. ISBN 978-087969641-2

Harger, C., Skupski, M., Allen, E., Clark, C., Crowley, D., Dickinson, E., Easley, D., Espinosa-Lujan, A., Farmer, A., Fields, C., Flores, L., Harris, L., Keen, G., Manning, M., McLeod, M., O'Neill, J., Pumilia, M., Reinert, R., Rider, D., Rohrlich, J., Romero, Y., Schwertfeger, J., Seluja, G., Siepel, A., Schad, P. A. (1997) The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes. Nucleic Acids Res, 25 (1). pp. 18-23. ISSN 0305-1048 (Print)0305-1048

Harger, C., Skupski, M., Bingham, J., Farmer, A., Hoisie, S., Hraber, P., Kiphart, D., Krakowski, L., McLeod, M., Schwertfeger, J., Seluja, G., Siepel, A., Singh, G., Stamper, D., Steadman, P., Thayer, N., Thompson, R., Wargo, P., Waugh, M., Zhuang, J. J., Schad, P. A. (1998) The Genome Sequence DataBase (GSDB): improving data quality and data access. Nucleic Acids Res, 26 (1). pp. 21-6. ISSN 0305-1048 (Print)0305-1048

Harrington, L. A., Greider, C. W. (1990) Sequence Requirements for Telomerase Primer Elongation. Yeast, 6 (SPEC. ). S43.

Harris, T. W., Lee, R., Schwarz, E., Bradnam, K., Lawson, D., Chen, W., Blasier, D., Kenny, E., Cunningham, F., Kishore, R., Chan, J., Muller, H. M., Petcherski, A., Thorisson, G., Day, A., Bieri, T., Rogers, A., Chen, C. K., Spieth, J., Sternberg, P., Durbin, R., Stein, L. D. (2003) WormBase: a cross-species database for comparative genomics. Nucleic Acids Research, 31 (1). pp. 133-137. ISSN 0305-1048

Harter, M. L., Lewis, J. B. (1978) Adenovirus type 2 early proteins synthesized in vitro and in vivo: identification in infected cells of the 38,000- to 50,000- molecular-weight protein encoded by the left end of the adenovirus type 2 genome. J Virol, 26 (3). pp. 736-49. ISSN 0022-538X (Print)0022-538X (Linking)

Harvey, C. D., Yasuda, R., Zhong, H., Svoboda, K. (2008) The spread of ras activity triggered by activation of a single dendritic spine. Science, 321 (5885). pp. 136-40.

Hatchwell, E., Tegay, D. H., Wang, C., O'Brien, J. E., Allen, W., Tan, T., Prucka, S., Pettenati, M. J., Montagna, C., Nowak, N. J., Toriello, H. V. (2007) Genetic dissection using a novel whole genome tiling path BAC array reveals dramatic heterogeneity in Toriello-Carey syndrome, including a novel microdeletion syndrome at 22q12. Cellular Oncology, 29 (2). p. 143. ISSN 1570-5870

Hatchwell, E., Tommerup, N., Kristoffersson, U., Stanyon, R., Kantarci, S. (2003) Joubert syndrome: a patient with a de novo t(2;22)(q13;q11.1). American Journal of Human Genetics, 73 (5). p. 566. ISSN 0002-9297

Hauser, F., Chen, W. X., Deinlein, U., Chang, K., Ossowski, S., Fitz, J., Hannon, G. J., Schroeder, J. I. (2013) A Genomic-Scale Artificial MicroRNA Library as a Tool to Investigate the Functionally Redundant Gene Space in Arabidopsis. Plant Cell, 25 (8). pp. 2848-2863. ISSN 1040-4651

Haw, R. A., Croft, D., Yung, C. K., Ndegwa, N., D'Eustachio, P., Hermjakob, H., Stein, L. D. (2011) The Reactome BioMart. Database : the journal of biological databases and curation, 2011. ISSN 17580463 (ISSN)

He, F., Yoo, S., Wang, D., Kumari, S., Gerstein, M., Ware, D., Maslov, S. (2016) Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis. Plant J, 86 (6). pp. 472-80. ISSN 1365-313X (Electronic)0960-7412 (Linking)

He, H., Roschke, A., Yonescu, R., Hatchwell, E., Ried, T., Kirsch, I. (2003) Genome-wide analysis of genetic alterations in tumor cell lines by Ccap BAC microarray. American Journal of Human Genetics, 73 (5). p. 254. ISSN 0002-9297

Hein, N., Bywater, M. J., Stanley, K., Verbrugge, I., Cullinane, C., Baker, A., Zuber, H., Rappaport, A., Drygin, D., Huser, N., Bliesath, J., Ryckman, D. M., Rice, W. G., Lowe, S. W., Johnstone, R. W., Pearson, R. B., McArthur, G. A., Hannan, R. D. (2011) Inhibition of RNA Polymerase I Transcription by CX-5461 As a Therapeutic Strategy for the Cancer-Specific Activation of p53 in MLL-Rearranged Acute Myeloid Leukemias. Blood, 118 (21). p. 673. ISSN 0006-4971

Hemmings, B. A., Restuccia, D., Tonks, N. K. (2009) Targeting the Kinome II. Curr Opin Cell Biol, 21 (2). pp. 135-139.

Herrera, V. L., Steffen, M., Moran, A. M., Tan, G. A., Pasion, K. A., Rivera, K., Pappin, D. J., Ruiz-Opazo, N. (2016) Confirmation of translatability and functionality certifies the dual endothelin1/VEGFsp receptor (DEspR) protein. BMC Mol Biol, 17 (1). p. 15. ISSN 1471-2199 (Electronic)1471-2199 (Linking)

Herrero, J., Muffato, M., Beal, K., Fitzgerald, S., Gordon, L., Pignatelli, M., Vilella, A. J., Searle, S. M., Amode, R., Brent, S., Spooner, W., Kulesha, E., Yates, A., Flicek, P. (2016) Ensembl comparative genomics resources. Database : the journal of biological databases and curation, 2016. ISSN 17580463 (ISSN)

Herrmann, H., Blatt, K., Shi, J. W., Rappaport, A. R., Gleixner, K. V., Cerny-Reiterer, S., Peter, B., Wang, E., Sperr, W. R., Bradner, J. E., Lowe, S. W., Vakoc, C. R., Zuber, J., Valent, P. (2011) Small-Molecule Inhibition of BRD4 Is a Novel Promising Approach to Therapeutically Target Leukemia Stem Cells in AML. Blood, 118 (21). p. 1487. ISSN 0006-4971

Heyer, J., Kwong, L. N., Lowe, S. W., Chin, L. (2010) Non-germline genetically engineered mouse models for translational cancer research. Nature Reviews Cancer, 10 (7). pp. 470-480. ISSN 1474-175X

Hicks, J. B. (2012) Talk from Jim Hicks at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Hicks, J. B., Navin, N. E., Kendall, J. T., Levy, D., Wigler, M. H. (2010) Tracing Tumor Lineage and Progression through Genomic Copy Number Profiling at the Single Cell Level. Annals of Oncology, 21 (S4). iv49. ISSN 0923-7534

Hinrichs, A. S., Karolchik, D., Baertsch, R., Barber, G. P., Bejerano, G., Clawson, H., Diekhans, M., Furey, T. S., Harte, R. A., Hsu, F., Hillman-Jackson, J., Kuhn, R. M., Pedersen, J. S., Pohl, A., Raney, B. J., Rosenbloom, K. R., Siepel, A., Smith, K. E., Sugnet, C. W., Sultan-Qurraie, A., Thomas, D. J., Trumbower, H., Weber, R. J., Weirauch, M., Zweig, A. S., Haussler, D., Kent, W. J. (2006) The UCSC Genome Browser Database: update 2006. Nucleic Acids Res, 34 (Databa). D590-8. ISSN 0305-1048

Hinton, S. D., Yang, D. Z., Eckberg, W. R. (2003) Protein tyrosine phosphatases in Chaetopterus egg activation. Development Growth & Differentiation, 45 (5-6). pp. 405-415. ISSN 0012-1592

Hirschtritt, Matthew, Darrow, Sabrina M., Illmann, Cornelia, Osiecki, Lisa, Grados, Marco, Sandor, Paul, Dion, Yves, King, Robert A., Pauls, David, Budman, Cathy L., Cath, Danielle C., Greenberg, Erica, Lyon, Gholson J., Yu, Dongmei, McGrath, Lauren M., McMahon, William M., Lee, Paul C., Delucchi, Kevin L., Scharf, Jeremiah M., Mathews, Carol A. (2017) Genetic and Phenotypic Overlap of Specific Obsessive-Compulsive Subtypes with Tourette Syndrome. Biological Psychiatry, 81 (10, Su). S361-S362. ISSN 0006-3223

Hirschtritt, ME, Lee, PC, Pauls, DL, Dion, Yves, Grados, MA, Illmann, C, King, RA, Sandor, P., McMahon, W. M., Lyon, Gholson J., Cath, Danielle C., Kurlan, Roger, Robertson, M. M., Osiecki, L., Scharf, Jeremiah M., Matthews, Carol A. (2015) Lifetime Prevalence, Age of Risk, and Etiology of Comorbid Psychiatric Disorders in Tourette Syndrome. Tourette Syndrome Association International Consortium for Genetics.

Ho, J. M., Reynolds, N. M., Rivera, K., Connolly, M., Guo, L. T., Ling, J. Q., Pappin, D. J., Church, G. M., Soll, D. (2016) Efficient Reassignment of a Frequent Serine Codon in Wild-Type Escherichia coli. ACS Synthetic Biology, 5 (2). pp. 163-171. ISSN 2161-5063

Holste, D., Grosse, I., Beirer, S., Schieg, P., Herzel, H. (2003) Repeats and correlations in human DNA sequences. Physical Review E, 67 (6). ISSN 1063-651X

Holste, D., Grosse, I., Herzel, H. (2001) Statistical analysis of the DNA sequence of human chromosome 22. Physical Review E, 6404 (4). ISSN 1063-651X

Hong, W., Nakazawa, M., Chen, Y. Y., Kori, R., Vakoc, C. R., Rakowski, C., Blobel, G. A. (2005) FOG-1 recruits the NuRD repressor complex to mediate transcriptional repression by GATA-1. Embo Journal, 24 (13). pp. 2367-2378. ISSN 0261-4189

Hossain, M., Stillman, B. (2012) Meier-Gorlin syndrome mutations disrupt an Orc1 CDK inhibitory domain and cause centrosome reduplication. Genes and Development, 26 (16). pp. 1797-810. ISSN 08909369 (ISSN)

Hou, V. C., Lersch, R., Gee, S. L., Ponthier, J. L., Lo, A. J., Wu, M., Turck, C. W., Koury, M., Krainer, A. R., Mayeda, A., Conboy, J. G. (2002) Decrease in hnRNP A/B expression during erythropoiesis mediates a pre-mRNA splicing switch. Embo Journal, 21 (22). pp. 6195-6204. ISSN 0261-4189

Hsieh, M. C., Das, D., Sambandam, N., Zhang, M. Q., Nahle, Z. (2008) Regulation of the PDK4 isozyme by the Rb-E2F1 complex. J Biol Chem, 283 (41). pp. 27410-7.

Hsu, D. S., Acharya, C. R., Balakumaran, B. S., Riedel, R. F., Kim, M. K., Stevenson, M., Tuchman, S., Mukherjee, S., Barry, W., Dressman, H. K., Nevins, J. R., Powers, S., Mu, D., Potti, A. (2009) Characterizing the developmental pathways TTF-1, NKX2-8, and PAX9 in lung cancer. Proc Natl Acad Sci U S A, 106 (13). pp. 5312-5317. ISSN 0027-8424 (Print)1091-6490 (Electronic)

Hsu, H. C., Wang, C. L., Wang, M., Yang, N., Chen, Z., Sternglanz, R., Xu, R. M. (2013) Structural basis for allosteric stimulation of Sir2 activity by sir4 binding. Genes and Development, 27 (1). pp. 64-73. ISSN 08909369

Hsu, H. C., Stillman, B., Xu, R. M. (2005) Structural basis for origin recognition complex 1 protein-silence information regulator 1 protein interaction in epigenetic silencing. Proc Natl Acad Sci U S A, 102 (24). pp. 8519-24. ISSN 0027-8424 (Print)

Hu, H. L., Qin, Y., Bochorishvili, G., Zhu, Y. H., Van Aelst, L., Zhu, J. J. (2008) Ras signaling mechanisms underlying impaired GluR1-dependent plasticity associated with fragile X syndrome. Journal of Neuroscience, 28 (31). pp. 7847-7862. ISSN 0270-6474

Hu, M., Retz, W., Baader, M., Pesold, B., Adler, G., Henn, F. A., Rosler, M., Thome, J. (2000) Promoter polymorphism of the 5-HT transporter and Alzheimer's disease. Neuroscience Letters, 294 (1). pp. 63-5. ISSN 03043940 (ISSN)

Hu, P., Wu, S., Hernandez, N. (2003) A minimal RNA polymerase III transcription system from human cells reveals positive and negative regulatory roles for CK2. Molecular Cell, 12 (3). pp. 699-709. ISSN 1097-2765

Hu, P., Wu, S., Sun, Y. L., Yuan, C. C., Kobayashi, R., Myers, M. P., Hernandez, N. (2003) A minimal RNA polymerase III transcription system from higher eucaryotic cells. Faseb Journal, 17 (5). A1185-A1185. ISSN 0892-6638

Hu, W., Feng, Z., Atwal, G. S., Levine, A. J. (2008) p53: a new player in reproduction. Cell Cycle, 7 (7). pp. 848-52. ISSN 1551-4005 (Electronic)1551-4005 (Linking)

Hua, Y., Krainer, A. R. (2012) Antisense-mediated exon inclusion. Methods Mol Biol, 867. pp. 307-323. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Hua, Y., Vickers, T. A., Okunola, H. L., Bennett, C. F., Krainer, A. R. (2008) Antisense Masking of an hnRNP A1/A2 Intronic Splicing Silencer Corrects SMN2 Splicing in Transgenic Mice. Am J Hum Genet, 82 (4). pp. 834-48.

Huanca-Mamani, W., Garcia-Aguilar, M., Leon-Martinez, G., Grossniklaus, U., Vielle-Calzada, J. P. (2005) CHR11, a chromatin-remodeling factor essential for nuclear proliferation during female gametogenesis in Arabidopsis thaliana. Proc Natl Acad Sci U S A, 102 (47). pp. 17231-17236. ISSN 0027-8424

Huang, M., Rech, J. E., Northington, S. J., Flicker, P. F., Mayeda, A., Krainer, A. R., Lestourgeon, W. M. (1994) The C-protein tetramer binds 230 to 240 nucleotides of pre-mRNA and nucleates the assembly of 40S heterogeneous nuclear ribonucleoprotein particles. Molecular and Cellular Biology, 14 (1). pp. 518-533. ISSN 0270-7306

Huang, S., Deerinck, T. J., Ellisman, M. H. , Spector, D. L. (1998) The perinucleolar compartment and transcription. Journal of Cell Biology, 143 (1). pp. 35-47. ISSN 0021-9525

Huang, S., Spector, D. L. (1996) Dynamic organization of pre-mRNA splicing factors. Journal of Cellular Biochemistry, 62 (2). pp. 191-197. ISSN 0730-2312

Huang, S., Spector, D. L. (1996) Intron-dependent recruitment of pre-mRNA splicing factors to sites of transcription. Journal of Cell Biology, 133 (4). pp. 719-732. ISSN 0021-9525

Huang, S., Spector, D. L. (1992) U1 and U2 small nuclear RNAs are present in nuclear speckles. Proceedings of the National Academy of Sciences of the United States of America, 89 (1). pp. 305-308. ISSN 0027-8424

Huang, S., Spector, D. L. (1992) Will the real splicing sites please light up? Current Biology, 2 (4). pp. 188-190. ISSN 0960-9822

Hubner, M. R., Eckersley-Maslin, M. A., Spector, D. L. (2013) Chromatin organization and transcriptional regulation. Current Opinion in Genetics & Development, 23 (2). pp. 89-95. ISSN 0959-437X

Hufford, M. B., Xu, X., van Heerwaarden, J., Pyhajarvi, T., Chia, J. M., Cartwright, R. A., Elshire, R. J., Glaubitz, J. C., Guill, K. E., Kaeppler, S. M., Lai, J. S., Morrell, P. L., Shannon, L. M., Song, C., Springer, N. M., Swanson-Wagner, R. A., Tiffin, P., Wang, J., Zhang, G. Y., Doebley, J., McMullen, M. D., Ware, D., Buckler, E. S., Yang, S., Ross-Ibarra, J. (2012) Comparative population genomics of maize domestication and improvement. Nature Genetics, 44 (7). pp. 808-811. ISSN 1061-4036

Humbey, O., Pimkina, J., Zilfou, J. T., Jarnik, M., Dominguez-Brauer, C., Burgess, D. J., Eischen, C. M., Murphy, M. E. (2008) The ARF Tumor Suppressor Can Promote the Progression of Some Tumors. Cancer Res, 68 (23). pp. 9608-9613.

Husbands, A. Y., Aggarwal, V., Ha, T., Timmermans, M. C. (2016) In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes. Plant Cell, 28 (8). pp. 1783-94. ISSN 1532-298X (Electronic)1040-4651 (Linking)

I

Igartua, C., Turner, E. H., Ng, S. B., Hodges, E., Hannon, G. J., Bhattacharjee, A., Rieder, M. J., Nickerson, D. A., Shendure, J. (2010) Targeted enrichment of specific regions in the human genome by array hybridization. Current Protocols in Human Genetics (SUPPL.). 18.3.1-18.3.14. ISSN 19348266 (ISSN)

Inanobe, A., Furukawa, H., Gouaux, E. (2005) Mechanism of partial agonist action at the NR1 subunit of NMDA receptors. Neuron, 47 (1). pp. 71-84. ISSN 0896-6273 (Print)0896-6273 (Linking)

International Chicken Genome SequencingConsortium, (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432 (7018). pp. 695-716. ISSN 0028-0836

Iossifov, I., Rodriguez-Esteban, R., Mayzus, I., Millen, K. J., Rzhetsky, A. (2009) Looking at Cerebellar Malformations through Text-Mined Interactomes of Mice and Humans. PLoS Comput Biol, 5 (11). e1000559.

Iossifov, I., Ronemus, M., Levy, D., Wang, Z. H., Hakker, I., Rosenbaum, J., Yamrom, B., Lee, Y. H., Narzisi, G., Leotta, A., Kendall, J., Grabowska, E., Ma, B. C., Marks, S., Rodgers, L., Stepansky, A., Troge, J., Andrews, P., Bekritsky, M., Pradhan, K., Ghiban, E., Kramer, M., Parla, J., Demeter, R., Fulton, L. L., Fulton, R. S., Magrini, V. J., Ye, K., Darnell, J. C., Darnell, R. B., Mardis, E. R., Wilson, R. K., Schatz, M. C., McCombie, W. R., Wigler, M. (2012) De Novo Gene Disruptions in Children on the Autistic Spectrum. Neuron, 74 (2). pp. 285-299. ISSN 0896-6273

Iossifov, I., Zheng, T., Baron, M., Gilliam, T. C., Rzhetsky, A. (2008) Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network. Genome Res, 18 (7). pp. 1150-62. ISSN 1088-9051 (Print)1088-9051 (Linking)

Ipsaro, J. J., Haase, A. D., Knott, S. R., Joshua-Tor, L., Hannon, G. J. (2012) The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis. Nature, 491 (7423). pp. 279-282. ISSN 00280836 (ISSN)

Irvine, D. V., Goto, D. B., Vaughn, M. W., Nakaseko, Y., McCombie, W. R., Yanagida, M., Martienssen, R. (2009) Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing. Genome research, 19 (6). pp. 1077-83. ISSN 1088-9051 (Print)1088-9051 (Linking)

Issa, G. C., Delmore, J. E., McKeown, M. R., Lemieux, M. E., Rahl, P. B., Jacobs, H. M., Kastritis, E., Gilpatrick, T., Paranal, R. M., Qi, J., Shi, J. W., Chesi, M., Schinzel, A. C., Vakoc, C. R., Bergsagel, P. L., Richardson, P. G., Young, R., Hahn, W. C., Ghobrial, I. M., Anderson, K. C., Kung, A. L., Mitsiades, C. S., Bradner, J. E. (2011) Inhibition of c-Myc Expression and Function in Hematologic Malignancies. Blood, 118 (21). pp. 613-614. ISSN 0006-4971

Italiano, A., Chen, C. L., Thomas, R., Breen, M., Bonnet, F., Sevenet, N., Longy, M., Maki, R. G., Coindre, J. M., Antonescu, C. R. (2012) Alterations of the p53 and PIK3CA/AKT/mTOR pathways in angiosarcomas: a pattern distinct from other sarcomas with complex genomics. Cancer, 118 (23). pp. 5878-87. ISSN 1097-0142 (Electronic)0008-543X (Linking)

Itoh, T., Tanaka, T., Barrero, R. A., Yamasaki, C., Fujii, Y., Hilton, P. B., Antonio, B. A., Aono, H., Apweiler, R., Bruskiewich, R., Bureau, T., Burr, F., De Oliveira, A. C., Fuks, G., Habara, T., Haberer, G., Han, B., Harada, E., Hiraki, A. T., Hirochika, H., Hoen, D., Hokari, H., Hosokawa, S., Hsing, Y. I., Ikawa, H., Ikeo, K., Imanishi, T., Ito, Y., Jaiswal, P., Kanno, M., Kawahara, Y., Kawamura, T., Kawashima, H., Khurana, J. P., Kikuchi, S., Komatsu, S., Koyanagi, K. O., Kubooka, H., Lieberherr, D., Lin, Y. C., Lonsdale, D., Matsumoto, T., Matsuya, A., McCombie, W. R., Messing, J., Miyao, A., Mulder, N., Nagamura, Y., Nam, J., Namiki, N., Numa, H., Nurimoto, S., O'Donovan, C., Ohyanagi, H., Okido, T., Oota, S., Osato, N., Palmer, L. E., Quetier, F., Raghuvanshi, S., Saichi, N., Sakai, H., Sakai, Y., Sakata, K., Sakurai, T., Sato, F., Sato, Y., Schoof, H., Seki, M., Shibata, M., Shimizu, Y., Shinozaki, K., Shinso, Y., Singh, N. K., Smith-White, B., Takeda, J. I., Tanino, M., Tatusova, T., Thongjuea, S., Todokoro, F., Tsugane, M., Tyagi, A. K., Vanavichit, A., Wang, A., Wing, R. A., Yamaguchi, K., Yamamoto, M., Yamamoto, N., Yu, Y., Zhang, H., Zhao, Q., Higo, K., Burr, B., Gojobori, T., Sasaki, T. (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana: The Rice Annotation Project. Genome Research, 17 (2). pp. 175-183. ISSN 10889051 (ISSN)

J

Jacob, Y., Martienssen, R. A. (2011) Chromatin reprogramming: gender equality during Arabidopsis germline differentiation. Current biology, 21 (1). R20-2. ISSN 1879-0445 (Electronic)0960-9822 (Linking)

Jaiswal, P., Ware, D., Ni, J. J., Chang, K., Zhao, W., Schmidt, S., Pan, X. K., Clark, K., Teytelman, L., Cartinhour, S., Stein, L., McCouch, S. (2002) Gramene: development and integration of trait and gene ontologies for rice. Comparative and Functional Genomics, 3 (2). pp. 132-136. ISSN 1531-6912

Janas, J. A., Van Aelst, L. (2011) Oncogenic tyrosine kinases target Dok-1 for ubiquitin-mediated proteasomal degradation to promote cell transformation. Molecular and Cellular Biology, 31 (13). pp. 2552-2565. ISSN 0270-7306

Javelle, M., Klein-Cosson, C., Vernoud, V., Boltz, V., Maher, C., Timmermans, M. C. P., Depege-Fargeix, N., Rogowsky, P. M. (2011) Genome-Wide Characterization of the HD-ZIP IV Transcription Factor Family in Maize: Preferential Expression in the Epidermis. Plant Physiology, 157 (2). pp. 790-803. ISSN 0032-0889

Javelle, M., Timmermans, M. C. (2012) In situ localization of small RNAs in plants by using LNA probes. Nat Protoc, 7 (3). pp. 533-41. ISSN 1750-2799 (Electronic)1750-2799 (Linking)

Jeffrey Chen, Z., Wang, J., Tian, L., Lee, H. S., Wang, J. J., Chen, M., Lee, J. J., Josefsson, C., Madlung, A., Watson, B., Lippman, Z., Vaughn, M., Chris Pires, J., Colot, V., Doerge, R. W., Martienssen, R. A., Comai, L., Osborn, T. C. (2004) The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biological journal of the Linnean Society. Linnean Society of London, 82 (4). pp. 689-700. ISSN 0024-4066 (Print)0024-4066 (Linking)

Jiang, H., Zhang, J., Han, Z., Yang, J., Ge, C., Wu, Q. (2017) Revealing new insights into different phosphorus-starving responses between two maize (Zea mays) inbred lines by transcriptomic and proteomic studies. Scientific Reports, 7. p. 44294. ISSN 20452322

Jiao, Y., Burke, J. J., Chopra, R., Burow, G., Chen, J., Wang, B., Hayes, C., Emendack, Y., Ware, D., Xin, Z. (2016) A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses. Plant Cell, 28 (7). pp. 1551-1562. ISSN 1532-298X (Electronic)1040-4651 (Linking)

Jiao, Y. N., Leebens-Mack, J., Ayyampalayam, S., Bowers, J. E., McKain, M. R., McNeal, J., Rolf, M., Ruzicka, D. R., Wafula, E., Wickett, N. J., Wu, X. L., Zhang, Y., Wang, J., Zhang, Y. T., Carpenter, E. J., Deyholos, M. K., Kutchan, T. M., Chanderbali, A. S., Soltis, P. S., Stevenson, D. W., McCombie, R., Pires, J. C., Wong, G. K. S., Soltis, D. E., dePamphilis, C. W. (2012) A genome triplication associated with early diversification of the core eudicots. Genome Biology, 13 (1). R3. ISSN 1474-7596

Jimenez Barron, Laura, Lyon, Gholson J. (2014) Genome Wide Variant Analysis of families with Autism Spectrum Disorder (ASD) using an Integrative Bioinformatics Pipeline. In: Cold Spring Harbor Laboratory Personal Genomes Meeting , November 2014, Cold Spring Harbor, NY . (Unpublished)

Jimenez Barron, Laura, Lyon, Gholson J. (2014) "Variant Analysis of Simplex Autism Families". In: CSHL Woodbury Genomic In-House Seminar, June 16th 2014, CSHL Woodbury Genome Center. (Unpublished)

Jimenez-Barron, Laura (2014) "Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources". Journal Club. (Unpublished)

Jimenez-Garcia, L. F., Segura-Valdez, M. L., Ochs, R. L., Rothblum, L. I., Hannan, R., Spector, D. L. (1994) Nucleologenesis: U3 snRNA-containing prenucleolar bodies move to sites of active pre-rRNA transcription after mitosis. Molecular Biology of the Cell, 5 (9). pp. 955-966. ISSN 1059-1524

Jimenez-Garcia, L. F., Spector, D. L. (1993) In vivo evidence that transcription and splicing are coordinated by a recruiting mechanism. Cell, 73 (1). pp. 47-59. ISSN 0092-8674

Jing, H., Vakoc, C. R., Wang, H., Mandat, S., Miller, J., Gregory, P. D., Reik, A., Blobel, G. A. (2007) Regulation of higher order chromatin organization by GATA-1. Blood Cells Molecules and Diseases, 38 (2). p. 126. ISSN 1079-9796

Jing, H., Vakoc, C. R., Ying, L., Mandat, S., Wang, H., Zheng, X., Blobel, G. A. (2008) Exchange of GATA Factors Mediates Transitions in Looped Chromatin Organization at a Developmentally Regulated Gene Locus. Molecular Cell, 29 (2). pp. 232-242. ISSN 10972765 (ISSN)

Johnson, A. F., Lodhi, M. A., McCombie, W. R. (1996) Fluorescence-based sequencing of double-stranded DNA by hexamer string priming. Analytical Biochemistry, 241 (2). pp. 228-237. ISSN 00032697 (ISSN)

Jones, L., Sevcikova, S., Phan, V., Jain, S., Shieh, A., Dubansky, J., Li, M., Maunakea, M. L., Zhu, G., Tennant, T. R., Lowe, S. W., Le Beau, M. M., Kogan, S. C. (2008) Myc Drives Chromosomal Gain in Acute Myeloid Leukemia. Blood, 112 (11). p. 294. ISSN 0006-4971

Joshi-Tope, G., Gillespie, M., Vastrik, I., D'Eustachio, P., Schmidt, E., de Bono, B., Jassal, B., Gopinath, G. R., Wu, G. R., Matthews, L., Lewis, S., Birney, E., Stein, L. D. (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res, 33 (Databa). D428-32. ISSN 1362-4962 (Electronic)

Joshi-Tope, G., Vastrik, I., Gopinath, G. R., Matthews, L., Schmidt, E., Gillespie, M., D'Eustachio, P., Jassal, B., Lewis, S., Wu, G., Birney, E., Stein, L. (2003) The genome knowledgebase: A resource for biologists and bioinformaticists. Cold Spring Harbor Symposia on Quantitative Biology, 68. pp. 237-243. ISSN 0091-7451

Joshua-Tor, L., Johnston, S. A. (2004) The Bleomycin Hydrolases. In: Handbook of Proteolytic Enzymes. Elsevier Academic Press, pp. 1197-1201. ISBN 9780120796120

K

Kaaij, L. T. J., van de Wetering, M., Fang, F., Decato, B., Molaro, A., van de Werken, H. J. G., van Es, J. H., Schuijers, J., de Wit, E., de Laat, W., Hannon, G. J., Clevers, H. C., Smith, A. D., Ketting, R. F. (2013) DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus. Genome Biology, 14 (5). ISSN 1465-6906

Kamalakaran, Sitharthan, Varadan, Vinay, Janevski, Angel, Banerjee, Nilanjana, Tuck, David, McCombie, Richard, Dimitrova, Nevenka, Harris, Lyndsay N. (2013) Translating Next Generation Sequencing to practice: opportunities and necessary steps. Molecular Oncology, 7 (4). pp. 743-755. ISSN 1574-7891

Kang, H., Davis-Dusenbery, B. N., Nguyen, P. H., Lal, A., Lieberman, J., Van Aelst, L., Lagna, G., Hata, A. (2012) Bone morphogenetic protein 4 promotes vascular smooth muscle contractility by activating microRNA-21 (miR-21), which down-regulates expression of family of dedicator of cytokinesis (DOCK) proteins. Journal of Biological Chemistry, 287 (6). pp. 3976-3986. ISSN 00219258 (ISSN)

Kang, H. J., Feng, Z., Sun, Y., Atwal, G., Murphy, M. E., Rebbeck, T. R., Rosenwaks, Z., Levine, A. J., Hu, W. (2009) Single-nucleotide polymorphisms in the p53 pathway regulate fertility in humans. Proc Natl Acad Sci U S A, 106 (24). pp. 9761-6. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Kang, B., Pu, M., Hu, G., Wen, W., Dong, Z., Zhao, K., Stillman, B., Zhang, Z. (2011) Phosphorylation of H4 Ser 47 promotes HIRA-mediated nucleosome assembly. Genes and Development, 25 (13). pp. 1359-1364. ISSN 08909369 (ISSN)

Kani, K., Sordella, R., Mallick, P. (2012) Investigation of acquired resistance to EGFR-targeted therapies in lung cancer using cDNA microarrays. Methods in Molecular Biology, 795. pp. 233-53. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Kantarci, S., Apak, M. Y., Eraslan, S., Nayir, A., Kayserili, H., Kirdar, B. (2003) Haplotype analysis in autosomal recessive polycystic kidney disease (ARPKD) families and the determination of allele frequencies of used markers in the Turkish population. American Journal of Human Genetics, 73 (5). p. 477. ISSN 0002-9297

Karni, R., Hippo, Y., Lowe, S. W., Krainer, A. R. (2008) The splicing-factor oncoprotein SF2/ASF activates mTORC1. Proc Natl Acad Sci U S A, 105 (40). pp. 15323-7.

Karni-Schmidt, O., Castillo-Martin, M., HuaiShen, T., Gladoun, N., Domingo-Domenech, J., Sanchez-Carbayo, M., Li, Y., Lowe, S. W., Prives, C., Cordon-Cardo, C. (2011) Distinct Expression Profiles of p63 Variants during Urothelial Development and Bladder Cancer Progression. The American Journal of Pathology, 178 (3). pp. 1350-1360. ISSN 0002-9440

Karp, X., Hammell, M., Ow, M. C., Ambros, V. (2011) Effect of life history on microRNA expression during C. elegans development. RNA, 17 (4). pp. 639-651. ISSN 13558382 (ISSN)

Kato, H., Goto, D. B., Martienssen, R. A., Urano, T., Furukawa, K., Murakami, Y. (2005) RNA polymerase II is required for RNAi-dependent heterochromatin assembly. Science, 309 (5733). pp. 467-469. ISSN 00368075 (ISSN)

Kato, M., Kawaguchi, T., Ishikawa, S., Umeda, T., Nakamichi, R., Shapero, M. H., Jones, K. W., Nakamura, Y., Aburatani, H., Tsunoda, T. (2010) Population-genetic nature of copy number variations in the human genome. Human Molecular Genetics, 19 (5). pp. 761-773.

Kaul, S., Koo, H. L., Jenkins, J., Rizzo, M., Rooney, T., Tallon, L. J., Feldblyum, T., Nierman, W., Benito, M. I., Lin, X., Town, C. D., Venter, J. C., Fraser, C. M., Tabata, S., Nakamura, Y., Kaneko, T., Sato, S., Asamizu, E., Kato, T., Kotani, H., Sasamoto, S., Ecker, J. R., Theologis, A., Federspiel, N. A., Palm, C. J., Osborne, B. I., Shinn, P., Dewar, K., Kim, C. J., Buehler, E., Dunn, P., Chao, Q., Chen, H., Vysotskaia, V. S., Lenz, C. A., Hansen, N. F., Liu, S. X., Alta, H., Sakano, H., Lam, B., Pham, P. K., Nguyen, M., Yu, G., Southwick, A., Lee, J. M., Miranda, M., Toriumi, M. J., Davis, R. W., Conway, A. B., Conn, L., Hootan, A., Wambutt, R., Murphy, G., Düsterhöft, A., Stiekema, W., Pohl, T., Entian, K. D., Terryn, N., Volckaert, G., Salanoubat, M., Choisne, N., Artiguenave, F., Weissenbach, J., Quetier, F., Rieger, M., Ansorge, W., Unseld, M., Fartmann, B., Valle, G., Wilson, R. K., Sekhon, M., Pepin, K., Murray, J., Johnson, D., Hillier, L., de la Bastide, M., Huang, E., Spiegel, L., Gnoj, L., Habermann, K., Dedhia, N., Parnell, L., Preston, R., Marra, M., McCombie, W. R., Chen, E., Martienssen, R., Mayer, K., Lemcke, K., Haas, B., Haase, D., Rudd, S., Schoof, H., Frishman, D., Morgenstern, B., Zaccaria, P., Mewes, H. W., White, O., Creasy, T. H., Bielke, C. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408 (6814). pp. 796-815. ISSN 00280836 (ISSN)

Kawahara, Y., de la Bastide, M., Hamilton, J. P., Kanamori, H., McCombie, W. R., Ouyang, S., Schwartz, D. C., Tanaka, T., Wu, J., Zhou, S., Childs, K. L., Davidson, R. M., Lin, H., Quesada-Ocampo, L., Vaillancourt, B., Sakai, H., Lee, S. S., Kim, J., Numa, H., Itoh, T., Buell, C. R., Matsumoto, T. (2013) Improvement of the oryza sativa nipponbare reference genome using next generation sequence and optical map data. Rice, 6 (1). pp. 3-10. ISSN 19398425 (ISSN)

Kendall, J. T., Lakshmi, B. (2008) Quality Assessment for Short Oligonucleotide Microarray Data Comment. Technometrics, 50 (3). pp. 274-276.

Keng, V. W., Villanueva, A., Chiang, D. Y., Dupuy, A. J., Ryan, B. J., Matise, I., Silverstein, K. A. T., Sarver, A., Starr, T. K., Akagi, K., Tessarollo, L., Collier, L. S., Powers, S., Lowe, S. W., Jenkins, N. A., Copeland, N. G., Llovet, J. M., Largaespada, D. A. (2009) A conditional transposon-based insertional mutagenesis screen for genes associated with mouse hepatocellular carcinoma. Nature Biotechnology, 27 (3). pp. 264-274. ISSN 1087-0156

Kerschensteiner, D., Liu, H., Cheng, C. W., Demas, J., Cheng, S. H., Hui, C. c., Chow, R. L., Wong, R. O. L. (2008) Genetic Control of Circuit Function: Vsx1 and Irx5 Transcription Factors Regulate Contrast Adaptation in the Mouse Retina. J. Neurosci., 28 (10). pp. 2342-2352.

Kersey, P. J., Allen, J. E., Armean, I., Boddu, S., Bolt, B. J., Carvalho-Silva, D., Christensen, M., Davis, P., Falin, L. J., Grabmueller, C., Humphrey, J., Kerhornou, A., Khobova, J., Aranganathan, N. K., Langridge, N., Lowy, E., McDowall, M. D., Maheswari, U., Nuhn, M., Ong, C. K., Overduin, B., Paulini, M., Pedro, H., Perry, E., Spudich, G., Tapanari, E., Walts, B., Williams, G., Tello-Ruiz, M., Stein, J., Wei, S., Ware, D., Bolser, D. M., Howe, K. L., Kulesha, E., Lawson, D., Maslen, G., Staines, D. M. (2016) Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Res, 44 (D1). D574-80. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Kessels, H. W., Kopec, C. D., Klein, M. E., Malinow, R. (2009) Roles of stargazin and phosphorylation in the control of AMPA receptor subcellular distribution. Nat Neurosci, 12 (7). pp. 888-896.

Keyes, W. M., Mills, A. A. (2003) Inducible systems see the light. Trends in Biotechnology, 21 (2). pp. 53-55. ISSN 0167-7799

Keyes, W. M., Mills, A. A. (2006) p63: a new link between senescence and aging. Cell Cycle, 5 (3). pp. 260-265. ISSN 15384101

Keyes, W. M., Vogel, H., Koster, M. I., Guo, X., Qi, Y., Petherbridge, K. M., Roop, D. R., Bradley, A., Mills, A. A. (2006) p63 heterozygous mutant mice are not prone to spontaneous or chemically induced tumors. Proc Natl Acad Sci U S A, 103 (22). pp. 8435-40. ISSN 0027-8424 (Print)

Keyes, W. M. , Pecoraro, M., Aranda, V., Vernersson-Lindahl, E., Li, W., Vogel, H., Guo, X., Garcia, E. L., Michurina, T. V., Enikolopov, G. N., Muthuswamy, S. K., Mills, A. A. (2011) DeltaNp63alpha Is an Oncogene that Targets Chromatin Remodeler Lsh to Drive Skin Stem Cell Proliferation and Tumorigenesis. Cell Stem Cell, 8 (2). pp. 164-76. ISSN 1875-9777 (Electronic)

Khan, Z., Amini, S., Bloom, J. S., Ruse, C., Caudy, A. A., Kruglyak, L., Singh, M., Perlman, D. H., Tavazoie, S. (2011) Accurate proteome-wide protein quantification from high-resolution N-15 mass spectra. Genome Biology, 12 (12). ISSN 1474-7596

Khoo, B., Krainer, A. R. (2009) Splicing therapeutics in SMN2 and APOB. Current Opinion in Molecular Therapeutics, 11 (2). pp. 108-115. ISSN 1464-8431

Kidner, C. A., Martienssen, R. A. (2003) Macro effects of microRNAs in plants. Trends in Genetics, 19 (1). pp. 13-16. ISSN 0168-9525

Kim, W., Gordon, D., Sebat, J., Ye, K. Q., Finch, S. J. (2008) Computing power and sample size for case-control association studies with copy number polymorphism: application of mixture-based likelihood ratio test. PLoS ONE, 3 (10). e3475.

Kim, Y. C., Wu, Q., Chen, J., Xuan, Z., Jung, Y.-C., Zhang, M. Q., Rowley, J. D., Wang, S. M. (2009) The transcriptome of human CD34+ hematopoietic stem-progenitor cells. Proc Natl Acad Sci U S A, 106 (20). pp. 8278-8283.

Kinney, J. B. (2011) Talk from Justin Kinney at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Klar, A. J., Strathern, J. N., Hicks, J. B. (1984) Developmental Pathways in Yeast. 1984 . CSHL Press.

Klar, A. J. S., Strathern, J. N., Hicks, J. B., Prudente, D. (1983) Efficient production of a ring derivative of chromosome III by the mating-type switching mechanism in Saccharomyces cerevisiae. Molecular and Cellular Biology, 3 (5). pp. 803-810. ISSN 02707306 (ISSN)

Kloc, A., Martienssen, R. (2008) RNAi, heterochromatin and the cell cycle. Trends in genetics, 24 (10). pp. 511-7. ISSN 0168-9525 (Print)0168-9525 (Linking)

Kloc, A., Zaratiegui, M., Nora, E., Martienssen, R. (2008) RNA interference guides histone modification during the S phase of chromosomal replication. Current biology, 18 (7). pp. 490-5. ISSN 0960-9822 (Print)0960-9822 (Linking)

Knauer, S., Holt, A.L., Rubio-Somoza, I., Tucker, E. J., Hinze, A., Pisch, M., Javelle, M., Timmermans, M. C. P., Tucker, M. R., Laux, T. (2013) A Protodermal miR394 Signal Defines a Region of Stem Cell Competence in the Arabidopsis Shoot Meristem. Developmental Cell. ISSN 15345807

Kole, R., Krainer, A. R., Altman, S. (2012) RNA therapeutics: Beyond RNA interference and antisense oligonucleotides. Nature Reviews Drug Discovery, 11 (2). pp. 125-140. ISSN 14741776 (ISSN)

Korshunova, Y., Maloney, R. K., Lakey, N., Citek, R. W., Bacher, B., Budiman, A., Ordway, J. M., McCombie, W. R., Leon, J., Jeddeloh, J. A., McPherson, J. D. (2008) Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA. Genome Research, 18 (1). pp. 19-29.

Kota, Prashant, Lyon, Gholson J. (2014) "The N-Terminal Methionine of Cellular Proteins as a Degradation Signal". Journal Club. (Unpublished)

Kouros-Mehr, H., Bechis, S. K., Slorach, E. M., Littlepage, L. E., Egeblad, M., Ewald, A. J., Pai, S. Y., Ho, I. C., Werb, Z. (2008) GATA-3 Links Tumor Differentiation and Dissemination in a Luminal Breast Cancer Model. Cancer Cell, 13 (2). pp. 141-152. ISSN 15356108 (ISSN)

Krainer, A. R. (2011) Oligonucleotide therapeutics for correcting defective RNA splicing. FEBS Journal, 278 (Issue ). p. 11. ISSN 1742-464X

Krainer, A. R. (1988) Pre-mRNA splicing by complementation with purified human U1, U2, U4/U6 and U5 snRNPs. Nucleic Acids Research, 16 (20). pp. 9415-9429. ISSN 0305-1048

Krainer, A. R. (2011) Talk from Adrian Krainer at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Krainer, A. R., Conway, G. C., Kozak, D. (1990) Purification and characterization of pre-mRNA splicing factor SF2 from HeLa cells. Genes & Development, 4 (7). pp. 1158-1171. ISSN 0890-9369

Krainer, A. R., Conway, G. C., Kozak, D. (1990) The essential pre-mRNA splicing factor SF2 influences 5' splice site selection by activating proximal sites. Cell, 62 (1). pp. 35-42. ISSN 0092-8674

Krasnitz, A. (2012) Talk from Alex Krasnitz at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Krasnitz, A., Sun, G., Andrews, P., Wigler, M. (2013) Target inference from collections of genomic intervals. Proceedings of the National Academy of Sciences of the United States of America, 110 (25). E2271-E2278. ISSN 0027-8424

Krasnov, P., Michurina, T. V., Packer, M. A., Stasiv, Y., Nakaya, N., Moore, K. A., Drazan, K. E., Enikolopov, G. N. (2008) Neuronal nitric oxide synthase contributes to the regulation of hematopoiesis. Molecular Medicine, 14 (3-4). pp. 141-149. ISSN 1076-1551

Kresovich, S., Barbazuk, B., Bedell, J. A., Borrell, A., Buell, C. R., Burke, J., Clifton, S., Cordonnier-Pratt, M. M., Cox, S., Dahlberg, J., Erpelding, J., Fulton, T. M., Fulton, B., Fulton, L., Gingle, A. R., Hash, C. T., Huang, Y., Jordan, D., Klein, P. E., Klein, R. R., Magalhaes, J., McCombie, R., Moore, P., Mullet, J. E., Ozias-Akins, P., Paterson, A. H., Porter, K., Pratt, L., Roe, B., Rooney, W., Schnable, P. S., Stelly, D. M., Tuinstra, M., Ware, D., Warek, U. (2005) Toward sequencing the sorghum genome. A U.S. National Science Foundation-sponsored workshop report. Plant Physiology, 138 (4). pp. 1898-1902. ISSN 00320889 (ISSN)

Krishnan, K., Salomonis, N., Guo, S. (2008) Identification of Spt5 Target Genes in Zebrafish Development Reveals Its Dual Activity In Vivo. PLoS ONE, 3 (11). e3621.

Krishnan, N., Fu, C., Pappin, D. J., Tonks, N. K. (2011) H2S-induced sulfhydration of the phosphatase PTP1B and its role in the endoplasmic reticulum stress response. Science Signaling, 4 (203). ISSN 19450877 (ISSN)

Krishnan, N., Jeong, D. G., Jung, S.-k., Ryu, S. E., Xiao, A., Allis, C. D., Kim, S. J., Tonks, N. K. (2009) Dephosphorylation of the C-terminal tyrosyl residue of the DNA damage-related histone H2A.X is mediated by the protein phosphatase eyes absent. Journal of Biological Chemistry, 284 (24). pp. 16066-16070.

Krizhanovsky, V., Lowe, S. W. (2009) Stem cells: The promises and perils of p53. Nature, 460 (7259). pp. 1085-1086.

Kubota, T., Roca, X., Kimura, T., Kokunai, Y., Nishino, I., Sakoda, S., Krainer, A. R., Takahashi, M. P. (2011) A mutation in a rare type of intron in a sodium-channel gene results in aberrant splicing and causes myotonia. Human Mutation, 32 (7). pp. 773-782. ISSN 10597794 (ISSN)

Kuhn, C. D., Joshua-Tor, L. (2013) Eukaryotic Argonautes come into focus. Trends in Biochemical Sciences, 38 (5). pp. 263-271. ISSN 09680004 (ISSN)

Kumar, A., Bhandari, A., Sinha, R., Goyal, P., Grapputo, A. (2011) Spliceosomal Intron Insertions in Genome Compacted Ray-Finned Fishes as Evident from Phylogeny of MC Receptors, Also Supported by a Few Other GPCRs. PLoS ONE, 6 (8). ISSN 1932-6203

Kumar, Rajeev, Conklin, Douglas S., Mittal, Vivek (2003) High-throughput selection of effective RNAi probes for gene silencing. Genome Research, 13 (10). pp. 2333-2340. ISSN 1088-9051

Kumar, S., Sun, X., Sharma, S., Aggarwal, S., R., Kandasamy, Fineman, J. R., Black, S. M. (2009) GTP cyclohydrolase I expression is regulated by nitric oxide: role of cyclic AMP. Am J Physiol Lung Cell Mol Physiol, 297 (2). L309-317.

Kumari, S., Ware, D. (2013) Genome-Wide Computational Prediction and Analysis of Core Promoter Elements across Plant Monocots and Dicots. PLoS ONE, 8 (10). Art no. e79011. ISSN 1932-6203

Kurland, J. F., Tansey, W. P. (2008) Myc-mediated transcriptional repression by recruitment of histone deacetylase. Cancer Res, 68 (10). pp. 3624-9.

Kurtz, S., Narechania, A., Stein, J. C., Ware, D. H. (2008) A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics, 9. p. 517.

Kwofie, M. A., Skowronski, J. (2008) Specific recognition of Rac2 and Cdc42 by DOCK2 and DOCK9 guanine nucleotide exchange factors. Journal of Biological Chemistry, 283 (6). pp. 3088-3096. ISSN 0021-9258

L

Lalanne, E., Michaelidis, C., Moore, J. M., Gagliano, W., Johnson, A., Patel, R., Howden, R., Vielle-Calzada, J. P., Grossniklaus, U., Twell, D. (2004) Analysis of transposon insertion mutants highlights the diversity of mechanisms underlying male progamic development in arabidopsis. Genetics, 167 (4). pp. 1975-1986. ISSN 0016-6731

Lamonica, J. M., Vakoc, C. R., Blobel, G. A. (2006) Acetylation of GATA-1 is required for chromatin occupancy. Blood, 108 (11). 348A-348A. ISSN 0006-4971

Lamonica, J. M., Vakoc, C. R., Blobel, G. A. (2006) Acetylation of GATA-1 is required for chromatin occupancy. Blood, 108 (12). pp. 3736-3738. ISSN 00064971 (ISSN)

Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., Fitzhugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., Levine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J. P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J. C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, R. H., Wilson, R. K., Hillier, L. W., McPherson, J. D., Marra, M. A., Mardis, E. R., Fulton, L. A., Chinwalla, A. T., Pepin, K. H., Gish, W. R., Chissoe, S. L., Wendl, M. C., Delehaunty, K. D., Miner, T. L., Delehaunty, A., Kramer, J. B., Cook, L. L., Fulton, R. S., Johnson, D. L., Minx, P. J., Clifton, S. W., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J. F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E., Frazier, M. (2001) Initial sequencing and analysis of the human genome. Nature, 409 (6822). pp. 860-921. ISSN 00280836 (ISSN)

Laska, M. J., Lowe, S. W., Zender, L., Hearn, S. A., Vogel, U., Jensen, U. B., Bric, A., Nexo, B. A. (2009) Enforced expression of PPP1R13L increases tumorigenesis and invasion through p53-dependent and p53-independent mechanisms. Mol Carcinog, 48 (9). pp. 832-42.

Lassus, P., Rodriguez, J., Lazebnik, Y. (2002) Confirming specificity of RNAi in mammalian cells. Sci STKE, 2002 (147). pl13. ISSN 1525-8882 (Electronic)1525-8882 (Linking)

Lawrence, Carolyn J., Ware, Doreen (2008) Databases and data mining. In: Handbook of Maize: History and Practice of Genetics and Genomics. Springer Science + Business Media LLC, pp. 659-672. ISBN 978-0-387-77862-4

Lee, E. K., Cibrian-Jaramillo, A., Kolokotronis, S. O., Katari, M. S., Stamatakis, A., Ott, M., Chiu, J. C., Little, D. P., Stevenson, D. W., McCombie, W. R., Martienssen, R. A., Coruzzi, G., Desalle, R. (2011) A functional phylogenomic view of the seed plants. PLoS genetics, 7 (12). e1002411. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Lee, H., Schatz, M. C. (2012) Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score. Bioinformatics, 28 (16). pp. 2097-2105. ISSN 1367-4803

Lee, R. C., Hammell, C. M., Ambros, V. (2006) Interacting endogenous and exogenous RNAi pathways in Caenorhabditis elegans. RNA, 12 (4). pp. 589-597. ISSN 13558382 (ISSN)

Lee, Y. H., Ronemus, M., Kendall, J., Lakshmi, B., Leotta, A., Levy, D., Esposito, D., Grubor, V., Ye, K., Wigler, M., Yamrom, B. (2012) Reducing system noise in copy number data using principal components of self-self hybridizations. Proceedings of the National Academy of Sciences of the United States of America, 109 (3). E103-E110. ISSN 0027-8424

Lemmon, Z. H., Doebley, J. F. (2014) Genetic Dissection of a Genomic Region with Pleiotropic Effects on Domestication Traits in Maize Reveals Multiple Linked QTL. Genetics, 198 (1). pp. 345-53. ISSN 0016-6731

Leung, A., Cajigas, I., Jia, P., Ezhkova, E., Brickner, J. H., Zhao, Z., Geng, F., Tansey, W. P. (2011) Histone H2B ubiquitylation and H3 lysine 4 methylation prevent ectopic silencing of euchromatic loci important for the cellular response to heat. Mol Biol Cell, 22 (15). pp. 2741-2753. ISSN 1939-4586 (Electronic)1059-1524 (Linking)

Leung, A., Geng, F., Daulny, A., Collins, G. A., Guzzardo, P. M., Tansey, W. P. (2008) Transcriptional control and the ubiquitin-proteasome system. Ernst Schering Found Symp Proc (1). pp. 75-97.

Levine, Jesse (2013) Pluripotent Stem Cells Induced from Mouse Somatic Cells by Small- Molecule Compounds. Journal Club. (Unpublished)

Lewis, J. B., Esche, H., Smart, J. E., Stillman, B. W., Harter, M. L., Mathews, M. B. (1979) Organization and expression of the left third of the genome of adenovirus. Cold Spring Harb Symp Quant Biol, 44 (1). pp. 493-508.

Li, B. (2011) SYNAPTIC AND CIRCUITRY MECHANISMS UNDERLYING COGNITIVE ABERRATIONS IN MICE DEFICIENT IN GENES LINKED TO SCHIZOPHRENIA. Schizophrenia Bulletin, 37. p. 37. ISSN 1745-1701

Li, B., Devidze, N., Barengolts, D., Prostak, N., Sphicas, E., Apicella, A. J., Malinow, R., Emamian, E. S. (2009) NMDA Receptor Phosphorylation at a Site Affected in Schizophrenia Controls Synaptic and Behavioral Plasticity. J Neurosci, 29 (38). pp. 11965-11972.

Li, F., Huarte, M., Zaratiegui, M., Vaughn, M. W., Shi, Y., Martienssen, R., Cande, W. Z. (2008) Lid2 is required for coordinating H3K4 and H3K9 methylation of heterochromatin and euchromatin. Cell, 135 (2). pp. 272-83. ISSN 1097-4172 (Electronic)0092-8674 (Linking)

Li, L., Petsch, K., Shimizu, R., Liu, S., Xu, W. W., Ying, K., Yu, J., Scanlon, M. J., Schnable, P. S., Timmermans, M. C. P., Springer, N. M., Muehlbauer, G. J. (2013) Mendelian and Non-Mendelian Regulation of Gene Expression in Maize. PLoS Genetics, 9 (1). Article number e1003202. ISSN 15537390 (ISSN)

Li, R., Knight, J., Bream, G., Stenlund, A., Botchan, M. (1989) Specific recognition nucleotides and their DNA context determine the affinity of E2 protein for 17 binding sites in the BPV-1 genome. Genes Dev, 3 (4). pp. 510-26. ISSN 0890-9369 (Print)0890-9369 (Linking)

Li, T., Huang, J., Jiang, Y., Zeng, Y., He, F., Zhang, M. Q., Han, Z., Zhang, X. (2009) Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics, 93 (3). pp. 235-242.

Li, W., Cressy, M., Qin, H., Fulga, T., Van Vactor, D., Dubnau, J. (2013) MicroRNA-276a Functions in Ellipsoid Body and Mushroom Body Neurons for Naive and Conditioned Olfactory Avoidance in Drosophila. Journal of Neuroscience, 33 (13). pp. 5821-33. ISSN 1529-2401 (Electronic)0270-6474 (Linking)

Li, W., Prazak, L., Chatterjee, N., Gruninger, S., Krug, L., Theodorou, D., Dubnau, J. (2013) Activation of transposable elements during aging and neuronal decline in Drosophila. Nature Neuroscience, 16. pp. 529-531. ISSN 1546-1726 (Electronic)1097-6256 (Linking)

Li, W. H., Jin, Y., Prazak, L., Hammell, M., Dubnau, J. (2012) Transposable Elements in TDP-43-Mediated Neurodegenerative Disorders. PLoS ONE, 7 (9). ISSN 1932-6203

Li, W. T., Bernaola-Galvan, P., Haghighi, F., Grosse, I. (2002) Applications of recursive segmentation to the analysis of DNA sequences. Computers & Chemistry, 26 (5). pp. 491-510. ISSN 0097-8485

Li, Y., Welm, B., Podsypanina, K., Huang, S., Chamorro, M., Zhang, X., Rowlands, T., Egeblad, M., Cowin, P., Werb, Z., Tan, L. K., Rosen, J. M., Varmus, H. E. (2003) Evidence that transgenes encoding components of the Wnt signaling pathway preferentially induce mammary cancers from progenitor cells. Proceedings of the National Academy of Sciences of the United States of America, 100 (26). pp. 15853-15858. ISSN 00278424 (ISSN)

Li, H., Stillman, B. (2012) The origin recognition complex: a biochemical and structural view. In: The Eukaryotic Replisome: a Guide to Protein Structure and Function. Subcellular Biochemistry, 62 . Springer, pp. 37-58.

Liang, C., Jaiswal, P., Hebbard, C., Avraham, S., Buckler, E. S., Casstevens, T., Hurwitz, B. L., McCouch, S., Ni, J., Pujar, A., Ravenscroft, D., Ren, L., Spooner, W., Tecle, I., Thomason, J., Tung, C. W., Wei, X., Yap, I., Youens-Clark, K., Ware, D. H., Stein, L. D. (2008) Gramene: a growing plant comparative genomics resource. Nucleic Acids Res, 36 (Databa). D947-53.

Liang, C., Mao, L., Ware, D. H., Stein, L. D. (2009) Evidence-based gene predictions in plant genomes. Genome Res, 19 (10). 1912-1923 .

Lin, G., Aranda, V., Muthuswamy, S. K., Tonks, N. K. (2011) Identification of PTPN23 as a novel regulator of cell invasion in mammary epithelial cells from a loss-of-function screen of the 'PTP-ome'. Genes & Development, 25 (13). pp. 1412-1425. ISSN 0890-9369

Lin, H., Zhang, Z., Zhang, M. Q., Ma, B., Li, M. (2008) ZOOM! Zillions of oligos mapped. Bioinformatics, 24 (21). pp. 2431-7.

Lin, W., Piskol, R., Tan, M. H., Li, J. B. (2012) Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science, 335 (6074). 1302; author reply 1302. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Lindblad-Toh, K., Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., Ernst, J., Jordan, G., Mauceli, E., Ward, L. D., Lowe, C. B., Holloway, A. K., Clamp, M., Gnerre, S., Alfoldi, J., Beal, K., Chang, J., Clawson, H., Cuff, J., Di Palma, F., Fitzgerald, S., Flicek, P., Guttman, M., Hubisz, M. J., Jaffe, D. B., Jungreis, I., Kent, W. J., Kostka, D., Lara, M., Martins, A. L., Massingham, T., Moltke, I., Raney, B. J., Rasmussen, M. D., Robinson, J., Stark, A., Vilella, A. J., Wen, J., Xie, X., Zody, M. C., Baldwin, J., Bloom, T., Chin, C. W., Heiman, D., Nicol, R., Nusbaum, C., Young, S., Wilkinson, J., Worley, K. C., Kovar, C. L., Muzny, D. M., Gibbs, R. A., Cree, A., Dihn, H. H., Fowler, G., Jhangiani, S., Joshi, V., Lee, S., Lewis, L. R., Nazareth, L. V., Okwuonu, G., Santibanez, J., Warren, W. C., Mardis, E. R., Weinstock, G. M., Wilson, R. K., Delehaunty, K., Dooling, D., Fronik, C., Fulton, L., Fulton, B., Graves, T., Minx, P., Sodergren, E., Birney, E., Margulies, E. H., Herrero, J., Green, E. D., Haussler, D., Siepel, A., Goldman, N., Pollard, K. S., Pedersen, J. S., Lander, E. S., Kellis, M. (2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature, 478 (7370). pp. 476-82. ISSN 0028-0836

Lippman, Z., May, B., Yordan, C., Singer, T., Martienssen, R. (2003) Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS biology, 1 (3). pp. 420-428. ISSN 1545-7885 (Electronic)1544-9173 (Linking)

Liu, H., Niu, Y., Gonzalez-Portilla, P. J., Zhou, H., Wang, L., Zuo, T., Qin, C., Tai, S., Jansen, C., Shen, Y., Lin, H., Lee, M., Ware, D., Zhang, Z., Lubberstedt, T., Pan, G. (2015) An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize. BMC Genomics, 16 (1). p. 1078. ISSN 1471-2164 (Electronic)1471-2164 (Linking)

Liu, H., Sachidanandam, R., Stein, L. (2001) Comparative genomics between rice and Arabidopsis shows scant collinearity in gene order. Genome Research, 11 (12). pp. 2020-2026. ISSN 1088-9051

Liu, J., Valencia-Sanchez, M. A., Hannon, G. J., Parker, R. (2005) MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nature Cell Biology, 7 (7). pp. 719-23. ISSN 1465-7392

Liu, Z. J., Kumari, S., Zhang, L. F., Zheng, Y. L., Ware, D. (2012) Characterization of miRNAs in Response to Short-Term Waterlogging in Three Inbred Lines of Zea mays. PLoS ONE, 7 (6). e39786. ISSN 1932-6203

Lo Iacono, N., Mantero, S., Chiarelli, A., Garcia, E. L., Mills, A. A., Morasso, M. I., Costanzo, A., Levi, G., Guerrini, L., Merlo, G. R. (2008) Regulation of Dlx5 and Dlx6 gene expression by p63 is involved in EEC and SHFM congenital limb defects. Development, 135 (7). pp. 1377-1388. ISSN 0950-1991

Lodha, M., Marco, C. F., Timmermans, M. C. (2013) The ASYMMETRIC LEAVES complex maintains repression of KNOX homeobox genes via direct recruitment of Polycomb-repressive complex2. Genes & Development, 27 (6). pp. 596-601. ISSN 0890-9369

Lodha, M., Marco, C. F., Timmermans, M. C. P. (2008) Genetic and epigenetic regulation of stem cell homeostasis in plants. Cold Spring Harbor Symposia on Quantitative Biology, 73. pp. 243-51. ISSN 00917451 (ISSN)

Lodhi, M. A., McCombie, W. R. (1996) High-quality automated DNA sequencing primed with hexamer strings. Genome Research, 6 (1). pp. 10-18. ISSN 1054-9803

Loh, K., Deng, H., Fukushima, A., Cai, X., Boivin, B., Galic, S., Bruce, C., Shields, B. J., Skiba, B., Ooms, L. M., Stepto, N., Wu, B., Mitchell, C. A., Tonks, N. K., Watt, M. J., Febbraio, M. A., Crack, P. J., Andrikopoulos, S., Tiganis, T. (2009) Reactive Oxygen Species Enhance Insulin Sensitivity. Cell Metabolism, 10 (4). pp. 260-272.

Lopato, S., Mayeda, A., Krainer, A. R., Barta, A. (1996) Pre-mRNA splicing in plants: Characterization of Ser Arg splicing factors. Proceedings of the National Academy of Sciences of the United States of America, 93 (7). pp. 3074-3079. ISSN 0027-8424

Lorenz, P., Baker, B. F., Bennett, C. F., Spector, D. L. (1998) Phosphorothioate antisense oligonucleotides induce the formation of nuclear bodies. Molecular Biology of the Cell, 9 (5). pp. 1007-1023. ISSN 1059-1524

Lou, Y.-W., Chen, Y.-Y., Hsu, S.-F., Chen, R.-K., Lee, C.-L., Khoo, K.-H., Tonks, N. K., Meng, T.-C. (2008) Redox regulation of the protein tyrosine phosphatase PTP1B in cancer cells. FEBS Journal, 275 (1). pp. 69-88.

Lowe, S. W. (2008) Dissecting tumor suppressor gene networks in vivo. European Journal of Cancer Supplements, 6 (9). p. 7. ISSN 1359-6349

Lu, X. W., Wontakal, S. N., Kavi, H., Kim, B. J., Guzzardo, P. M., Emelyanov, A. V., Xu, N., Hannon, G. J., Zavadil, J., Fyodorov, D. V., Skoultchi, A. I. (2013) Drosophila H1 Regulates the Genetic Activity of Heterochromatin by Recruitment of Su(var)3-9. Science, 340 (6128). pp. 78-81. ISSN 0036-8075

Ludwig, M. R., Kojima, K., Bowersock, G. J., Chen, D., Jhala, N. C., Buchsbaum, D. J., Grizzle, W. E., Klug, C. A., Mobley, J. A. (2016) Surveying the serologic proteome in a tissue specific kras(G12D) knockin mouse model of pancreatic cancer. Proteomics, 16 (3). pp. 516-31. ISSN 1615-9861 (Electronic)1615-9853 (Linking)

Luo, M. C., Gu, Y. Q., You, F. M., Deal, K. R., Ma, Y., Hu, Y., Huo, N., Wang, Y., Wang, J., Chen, S., Jorgensen, C. M., Zhang, Y., McGuire, P. E., Pasternak, S., Stein, J. C., Ware, D., Kramer, M., McCombie, W. R., Kianian, S. F., Martis, M. M., Mayer, K. F. X., Sehgal, S. K., Li, W., Gill, B. S., Bevan, M. W., Šimková, H., Doležel, J., Weining, S., Lazo, G. R., Anderson, O. D., Dvorak, J. (2013) A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proceedings of the National Academy of Sciences of the United States of America, 110 (19). pp. 7940-7945. ISSN 00278424

Luo, W., Friedman, M. S., Shedden, K., Hankenson, K. D., Woolf, P. J. (2009) GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics, 10. p. 161.

Luo, W., Hankenson, K. D., Woolf, P. J. (2008) Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information. BMC Bioinformatics, 9. p. 467.

Luo, W. J., Friedman, M. S., Hankenson, K. D., Woolf, P. J. (2011) Time series gene expression profiling and temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization. BMC Systems Biology, 5 (82). ISSN 1752-0509

Lynch, T. J., Bell, D. W., Sordella, R., Gurubhagavatula, S., Okimoto, R. A., Brannigan, B. W., Harris, P. L., Haserlat, S. M., Supko, J. G., Haluska, F. G., Louis, D. N., Christiani, D. C., Settleman, J., Haber, D. A. (2004) Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. The New England Journal of Medicine, 350 (21). pp. 2129-39. ISSN 1533-4406 (Electronic)

Lyon, G. J. (2015) Discovery and genetic characterization of new neuropsychiatric syndromes from family-based studies. In: Cold Spring Harbor Laboratory: The Biology of Genomes Meeting, Cold Spring Harbor, NY. (Unpublished)

Lyon, G. J. (2015) New human genetic syndromes leading to the discovery of new biology. In: Cold Spring Harbor Laboratory: 80th CSHL Symposium on Quantitative Biology – 21st Century Genetics: Genes at Work, Cold Spring Harbor, NY. (Unpublished)

Lyon, G. J. (2012) Personalized medicine: Bring clinical standards to human-genetics research. Nature, 482 (7385). pp. 300-301. ISSN 00280836 (ISSN)

Lyon, G. J. (2012) There is nothing 'incidental' about unrelated findings. Personalized Medicine, 9 (2). pp. 163-166. ISSN 17410541 (ISSN)

Lyon, G. J. (2015) Using next generation sequencing to discover new human genetic syndromes and reveal new biology. In: GTCbio: 5th Next Generation Sequencing Conference, Boston, MA. (Unpublished)

Lyon, G. J. (2015) Variants in TAF1 are associated with a new syndrome with severe intellectual disability and characteristic dysmorphic features. In: 10th International Meeting on Copy Variants and Genes in Intellectual Disability and Autism, Troina, Italy. (Unpublished)

Lyon, G. J. (2015) Variants in TAF1 are associated with a new syndrome with severe intellectual disability and characteristic dysmorphic features. In: Cold Spring Harbor Laboratory: Wiring the Brain, Cold Spring Harbor, NY. (Unpublished)

Lyon, Gholson J. (2014) "The ARD1 Gene of Yeast Functions in the Switch between the Mitotic Cell Cycle and Alternative Developmental Pathways". Journal Club. (Unpublished)

Lyon, Gholson J. (2014) "ARD1 and NAT1 proteins from a complex that has N-terminal acetyltransferase activity". Journal Club. (Unpublished)

Lyon, Gholson J. (2013) Advancing Precision Medicine through clinical grade whole genome sequencing, return of results and deep brain stimulation. [Video] (Unpublished)

Lyon, Gholson J. (2013) Advancing Precision Medicine through clinical grade whole genome sequencing, return of results and deep brain stimulation. In: Precision Medicine: Personal Genomes & Pharmacogenomics, Nov 13th - Nov 16th 2103, Cold Spring Harbor, NY . (Unpublished)

Lyon, Gholson J. (2013) Amino-terminal acetylation of proteins: role in human disease and biology. In: Stony Brook University Department of Pharmacology Seminar Series, Oct 29th 2013, Stony Brook, NY. (Unpublished)

Lyon, Gholson J. (2015) Association of Protein Biogenesis Factors at the Yeast Ribosomal Tunnel Exit Is Affected by the Translational Status and Nascent Polypeptide Sequence. Journal Club. (Unpublished)

Lyon, Gholson J. (2015) Autoacetylation regulates differentially the roles of ARD1 variants in tumorigenesis. Journal Club. (Unpublished)

Lyon, Gholson J. (2012) Challenges of Clinical Implementation of Genomic Medicine. In: Cold Spring Harbor Laboratory In House Seminar , Nov 20th 2012, Cold Spring Harbor Laboratory. (Unpublished)

Lyon, Gholson J. (2012) Challenges of Clinical Implementation of Genomic Medicine. In: Invited Presentation at New York Genome Center, Dec 2012, New York Genome Center. (Unpublished)

Lyon, Gholson J. (2013) Childhood-­onset Neuropsychiatric Disorders. In: FarGen Summit (Faroe Genome Project), Sept 19th-20th 2013, Tórshavn, The Faroe Islands. (Unpublished)

Lyon, Gholson J. (2012) Clinical Genomics Perspective in Psychiatry. In: 3rd Annual Child and Adolescent Psychotherapy and Psychopharmacology Conference, Sept 2012, Philadelphia, PA. (Unpublished)

Lyon, Gholson J. (2014) Clinical Genomics of Neuropsychiatric Illnesses. In: Stony Brook University Division of Child and Adolescent Psychiatry, Seminar, Invited Speaker, January 2014, Stony Brook, NY. (Unpublished)

Lyon, Gholson J. (2012) Clinical Issues with the Return of Next-­Generation Sequencing Results. In: The Clinical Genome Conference, June 12th-13th 2012, San Francisco, CA. (Unpublished)

Lyon, Gholson J. (2013) Clinical genetics and other aspects of neuropsychiatric disorders. In: The International Behavioural and Neural Genetics Society (IBANGS), Genes, Brain & Behavior 15th Annual Meeting, May 20th-24th 2013, Leuven, Belgium. (Unpublished)

Lyon, Gholson J. (2013) Clinical genetics and other aspects of neuropsychiatric disorders. In: NGS Translate World Forum, May 28th-31st 2013, Boston, MA. (Unpublished)

Lyon, Gholson J. (2013) "Control of protein quality and stoichiometries by N-terminal acetylation and the N-end rule pathway". Journal Club. (Unpublished)

Lyon, Gholson J. (2013) Controversies in Giving Data Back. In: The Future of Genomic Medicine VI, March 7th-8th 2013, La Jolla, CA. (Unpublished)

Lyon, Gholson J. (2015) Cut the Hype. Accuracy and Standards Come First. Frontline Genomics, 2. pp. 19-23.

Lyon, Gholson J. (2014) Deep Brain Stimulation, Psychiatric Genetics, and iPS cell models of disease. In: CSHL In-House Seminar Series, Jan 24th 2014, Cold Spring Harbor Laboratory . (Unpublished)

Lyon, Gholson J. (2015) Different subcellular localizations and functions of human ARD1 variants. Journal Club . (Unpublished)

Lyon, Gholson J. (2013) "Epidemiology, epigenetics and the ‘Gloomy Prospect’: embracing randomness in population health research and practice". Journal Club. (Unpublished)

Lyon, Gholson J. (2012) Ethics Panel: Challenges of Clinical Implementation of Genomic Medicine. In: Personal Genomes & Medical Genomics Meeting, Nov 16th 2012, Cold Spring Harbor Laboratory. (Unpublished)

Lyon, Gholson J. (2013) Exome and Genome Sequencing. [Teaching Resource] (Unpublished)

Lyon, Gholson J. (2013) Exome and Genome Sequencing. [Teaching Resource] (Unpublished)

Lyon, Gholson J. (2013) FDA Crackdown on 23andMe Delays a Revolution in Medicine. [Audio] (Unpublished)

Lyon, Gholson J. (2013) "FDA Crackdown on 23ndMe Delays a Revolution in Medicine, says Medical Geneticist, Gholson Lyon". [Audio]

Lyon, Gholson J. (2011) Finding and Analyzing Human Genetic Variation in Neuropsychiatric Disorders. In: Faculty Recruitment Talk, Dec 2011, Cold Spring Harbor Laboratory. (Unpublished)

Lyon, Gholson J. (2014) "Genetic Complexity and Neuropsychiatric Disorders". In: Nurturing Genetics: Reflections on a Century of Scientific and Social Change - An International and Interdisciplinary Symposium, June 29th - July 2nd 2014, University of Leeds, UK. (Unpublished)

Lyon, Gholson J. (2014) "Genetic Research, and its Application in Today's Health Care System". [Audio]

Lyon, Gholson J. (2013) Genetic and Biochemical Analysis of Childhood-­Onset Idiopathic Neuropsychiatric Disorders. In: Institute for Computational Biomedicine and Department of Physiology and Biophysics Seminar Series, Feb 13th 2013, Weill Cornell Medical College, New York, NY. (Unpublished)

Lyon, Gholson J. (2012) Genetics and Genome Sequencing of Childhood-Onset Neuropsychiatric Disorders. In: Department of Psychiatry and Behavioral Science Grand Rounds, Dec 18th 2012, Stony Brook University . (Unpublished)

Lyon, Gholson J. (2013) Genome Engineering Using CRISPR. Journal Club. (Unpublished)

Lyon, Gholson J. (2014) "Genome sequencing identifies major causes of severe intellectual disability". Journal Club. (Unpublished)

Lyon, Gholson J. (2012) Guest post: Time to bring human genome sequencing into the clinic. Discussion Paper. genomesunzipped.org.

Lyon, Gholson J. (2014) Human Genetic Variation and the Genotype-Phenotype Problem. In: Lecture to Watson School Graduate Students , September 22, 2014, Cold Spring Harbor Laboratory. (Unpublished)

Lyon, Gholson J. (2014) Human Genetic Variation and the Genotype-Phenotype Problem. In: Lecture to Stony Brook University Psychology Students on "Molecular Psychology", Stony Brook University, Stony Brook, NY . (Unpublished)

Lyon, Gholson J. Human Genetic Variation and the Genotype-Phenotype Problem. [Teaching Resource] (Unpublished)

Lyon, Gholson J. (2015) Human genetic variation and the genotype-phenotype problem - part 1 of 2. In: Topical Talks: Talks of interest in the biomedical and life sciences. Henry Stewart Talks.

Lyon, Gholson J. (2012) Humanizing the Human Genome Project. In: Project Syndicate: The World's Opinion Page, August 2, 2012.

Lyon, Gholson J. (2015) (Hyper)tension release by N-terminal acetylation / Control of mammalian G protein signaling by N-terminal acetylation and the N-end rule pathway. Journal Club . (Unpublished)

Lyon, Gholson J. (2014) "Identification and characterization of genes and mutants for an N-terminal acetyltransferase from yeast". Journal Club. (Unpublished)

Lyon, Gholson J. (2014) "Identification of Methionine Na-Acetyltransferase from Saccharomyces cerevisiae". Journal Club. (Unpublished)

Lyon, Gholson J. (2012) The Implementation of Clinical Genomics: Ethical, Societal and Regulatory Considerations. In: Consumer Genetics Conference, Oct 5th 2012, Boston, MA. (Unpublished)

Lyon, Gholson J. (2012) The Implementation of Clinical Genomics: Ethical, Societal and Regulatory Considerations. In: 20th Annual International Conference on Intelligent Systems for Molecular Biology: High Throughput Sequencing Special Interest Group Meeting, July 13th-14th 2012, Long Beach, CA. (Unpublished)

Lyon, Gholson J. (2012) Implementation of Variant Calling Algorithms in Clinical Genome Sequencing. In: Bio-IT Europe The Road to the Clinic: Applying Genomics in a Clinical Setting , Oct 10th 2012, Vienna, Austria. (Unpublished)

Lyon, Gholson J. (2013) Increasing Accuracy for Exome and Whole Genome Sequencing. In: Bio-IT World and Cambridge Healthtech Institute's Inaugural- Clinical Exome Sequencing, December 4-5th 2013, Lisbon, Portugal. (Unpublished)

Lyon, Gholson J. (2013) Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. In: COMPUTATIONAL BIOLOGY & BIOINFORMATICS SEMINAR SERIES, April 10th 2013, Cold Spring Harbor Laboratory. (Unpublished)

Lyon, Gholson J. (2015) Massively parallel single-amino-acid mutagenesis. Journal Club. (Unpublished)

Lyon, Gholson J. (2014) "Model Peptides Reveal Specificity of Na-Acetyltransferase from Saccharomyces cerevisiae". Journal Club. (Unpublished)

Lyon, Gholson J. (2015) The Molecular Basis for Histone H4- and H2A Specific Amino-Terminal Acetylation by NatD. Journal Club . (Unpublished)

Lyon, Gholson J. (2014) "Molecular Cloning and Sequencing of a cDNA Encoding Na-Acetyltransferase from Saccharomyces cerevisiae". Journal Club. (Unpublished)

Lyon, Gholson J. (2013) Molecular basis for N-terminal acetylation by the heterodimeric NatA complex. Journal Club. (Unpublished)

Lyon, Gholson J. (2014) "N(α)-Acetylation of yeast ribosomal proteins and its effect on protein synthesis". Journal Club. (Unpublished)

Lyon, Gholson J. (2014) "N-Terminal Acetylation Inhibits Protein Targeting to the Endoplasmic Reticulum". Journal Club. (Unpublished)

Lyon, Gholson J. (2014) N-terminal acetyltransferases and Translation. In: Lecture to Stony Brook Chemical Biology Graduate Students, October 30, 2014 , Stony Brook University, Stony Brook, NY. (Unpublished)

Lyon, Gholson J. (2013) N=1 Human Study in Clinical Neurosciences: Genomics Guided Medicine and Deep Brain Stimulation. In: 5th Annual Consumer Genetics Conference, Sept 25th-27th 2013, Boston, MA. (Unpublished)

Lyon, Gholson J. (2015) NAA10 controls osteoblast differentiation and bone formation as a feedback regulator of Runx2. Journal Club . (Unpublished)

Lyon, Gholson J. (2014) "NAT2, an Essential Gene Encoding Methionine Na-Acetyltransferase in the Yeast Saccharomyces cerevisiae". Journal Club. (Unpublished)

Lyon, Gholson J. (2014) "Na Acetylation Is Required for Normal Growth and Mating of Saccharomyces cerevisiae". Journal Club. (Unpublished)

Lyon, Gholson J. (2012) A New Tool for Personal Genomics. [Audio]

Lyon, Gholson J. (2015) Optimized sequencing leading to new human genetic syndromes involving transcription, translation, and protein degradation. In: The 24th KOGO Annual Conference 2015 & The 10th Asian Epigenomics Meeting, The Korea Science and Technology Center, Seoul, Korea. (Unpublished)

Lyon, Gholson J. (2015) Optimized sequencing leading to new human genetic syndromes involving transcription, translation, and protein degradation. In: Seminar, Pohang University of Science and Technology (POSTECH), Pohang, South Korea. (Unpublished)

Lyon, Gholson J. (2015) An Organellar Na-Acetyltransferase, Naa60, Acetylates Cytosolic N Termini of Transmembrane Proteins and Maintains Goli Integrity. Journal Club. (Unpublished)

Lyon, Gholson J. (2011) Personal account of the discovery of a new disease using next-generation sequencing. Interview by Natalie Harrison. Pharmacogenomics, 12 (11). pp. 1519-1523. ISSN 1744-8042

Lyon, Gholson J. (2014) "Purification and Characterization of an Na-Acetyltransferase from Saccharomyces cerevisiae". Journal Club. (Unpublished)

Lyon, Gholson J. (2011) Returning Research Results from Next‐Generation Sequencing and Analysis to Patients with Idiopathic Disorders? In: Personal Genomes Meeting, Sept 30th - Oct 2nd 2011, Cold Spring Harbor Laboratory. (Unpublished)

Lyon, Gholson J. (2015) A Ribosome-Bound Quality Control Complex Triggers Degradation of Nascent Peptides and Signals Translation Stress. Journal Club. (Unpublished)

Lyon, Gholson J. (2015) Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains. Journal Club. (Unpublished)

Lyon, Gholson J. (2012) Software Considerations for Processing, Analyzing and Interpreting Exome & Genome Sequence Data in Clinical Settings. In: World Genome Data Analysis Summit: Pre Conference Workshop, Nov 27th 2012, San Francisco. (Unpublished)

Lyon, Gholson J. (2015) Sporulation in the Budding Yeast Saccharomyces cerevisiae. Journal Club . (Unpublished)

Lyon, Gholson J. (2013) Stopping 23andMe will only delay the revolution medicine needs. In: The Conversation.

Lyon, Gholson J. (2012) Summary of Efforts to Achieve and Evaluate High-Quality Exomes and Genomes. In: Bio-IT Europe Pre-Conference Short Courses: Software Considerations for Processing, Analyzing and Interpreting Sequence Data , Oct 8th 2012, Vienna, Austria. (Unpublished)

Lyon, Gholson J. (2012) Taking NGS into the Clinic. In: Cambridge Healthtech Institute Next Gen Seq Meeting, Aug 16th 2012, Providence, RI. (Unpublished)

Lyon, Gholson J. (2012) Talk from Gholson Lyon at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Lyon, Gholson J. (2013) Toward more accurate variant calling for personal genomes. In: The Clinical Genome Conference, June 25th-26th 2013, San Francisco, CA. (Unpublished)

Lyon, Gholson J. (2015) Translation inhibitors cause abnormalities in ribosome profiling experiments. Journal Club. (Unpublished)

Lyon, Gholson J. (2013) Whole Genome Sequencing Analysis of a severe Idiopathic Intellectual Disability Syndrome or "limitations of theory may not be revealed when the facts are too few" - Knox 1958. In: 20th Annual Molecular Psychiatry Meeting, Feb 3rd-5th 2013, Park City, UT. (Unpublished)

Lyon, Gholson J. (2014) "Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing". Journal Club. (Unpublished)

Lyon, Gholson J. (2014) "The Yeast ARD1 Gene Product Is Required for Repression of Cryptic Mating-Type Information at the HML Locus". Journal Club. (Unpublished)

Lyon, Gholson J. (2015) The principle of antagonism ensures protein targeting specificity at the endoplasmic reticulum. Journal Club. (Unpublished)

Lyon, Gholson J. (2016) A rare genetic “transcriptomopathy” syndrome leading to insights into more common neurologic disorders. In: New York City Wide Human Genetics Meeting 2016, Rockefeller University, New York City, NY. (Unpublished)

Lyon, Gholson J. (2013) "The ubiquitin reference technique and tandem fluorescence timers". Journal Club. (Unpublished)

Lyon, Gholson J., Bird, Lynne M., Rope, Alan (2013) X-linked Malformation and Infantile Lethality Syndrome (provisionally named Ogden Syndrome). In: Inborn errors of development. Oxford University Press, Oxford; New York. ISBN 9780195306910 (Submitted)

Lyon, Gholson J., Doerfel, Max, O'Rawe, Jason, Wu, Yiyang, Kota, Prashant (2012) Human Genetics and Genomic Medicine. Cold Spring Harbor Laboratory.

Lyon, Gholson J., Jiang, Tao, Van Wijk, Richard, Wang, Wei, Bodily, Paul Mark, Xing, Jinchuan, Tian, Lifeng, Robison, Reid J., Clement, Mark, Lin, Yang, Zhang, Peng, Liu, Ying, Moore, Barry, Glessner, Joseph T., Elia, Josephine, Reimherr, Fred, van Solinge, Wouter W., Yandell, Mark, Hakonarson, Hakon, Wang, Jun, Johnson, William Evan, Wei, Zhi, Wang, Kai (2011) Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications. Dscovery Medicine, 12 (62). pp. 41-55. ISSN 1944-7930

Lyon, Gholson J., O'Rawe, Jason (2015) Human genetics and clinical aspects of neurodevelopmental disorders. In: The Genetics of Neurodevelopmental Disorders. Wiley, pp. 289-317.

Lyon, Gholson J., O'Rawe, Jason, Wu, Yiyang, Rope, Alan, Robison, Reid J., Wang, Kai, Swensen, Jeffrey J. (2013) Whole Genome Sequencing Analysis of an Idiopathic Intellectual Disability Syndrome. In: ACMG Annual Clinical Genetics Meeting, March 19th-23rd 2013, Phoenix, AZ. (Unpublished)

Lyon, Gholson J., Robison, Reid J., Wang, Kai (2013) The Implementation of Clinical Genomics: Ethical, Societal and Regulatory Considerations. In: ACMG Annual Clinical Genetics Meeting, March 19th-23rd 2013, Phoenix, AZ. (Unpublished)

Lyon, Gholson J., Segal, Jeremy P. (2013) Practical, ethical and regulatory considerations for the evolving medical and research genomics landscape. Applied & Translational Genomics, 2 (1). pp. 34-40. ISSN 2212-0661 (In Press)

Lyon, Gholson J., Wang, Kai (2012) Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress. Genome Medicine, 4 (7). p. 58. ISSN 1756-994X (Electronic)

Lyon, Gholson J. (2011) The 2011 William Allan Award of the American Society of Human Genetics to the Right Person "J.M. Opitz"? [Teaching Resource] (Unpublished)

Lyon, Gholson J. (2014) Challenges for Clinical Implementation of Genomic Medicine. In: Ancestry.com, May 27th 2014, Provo, Utah. (Unpublished)

Lyon, Gholson J. (2014) Challenges for Clinical Implementation of Genomic Medicine. In: New York Genome Center Lecture Series, May 22nd 2014, New York Genome Center - NYC . (Unpublished)

Lyon, Gholson J. (2016) Human Genetics and Rare Diseases. In: CSHL In-House Symposium, November 21th-22nd 2016, Cold Spring Harbor Laboratory. (Unpublished)

Lyon, Gholson J. N-terminal acetyltransferases and Translation. [Teaching Resource] (Unpublished)

Lyon, Gholson J. (2014) "Ogden Syndrome and the Amino-Terminal Acetylation of Proteins". In: NIGMS Medical Scientist Training Program 50th Anniversary Symposium, July 17th 2014, NIH Campus - Bethesda, Maryland. (Unpublished)

Lyon, Gholson J., Doerfel, Max, O'Rawe, Jason, Fang, Han, Jimenez Barron, Laura (2014) Human Genetics and Genomic Medicine. Cold Spring Harbor Laboratory.

Lyon, Gholson J., Doerfel, Max, O'Rawe, Jason, Wu, Yiyang, Fang, Han, Kota, Prashant, Jimenez Barron, Laura (2013) Human Genetics and Genomic Medicine. Cold Spring Harbor Laboratory.

M

Ma, O., Cai, W. W., Zender, L., Dayaram, T., Shen, J. H., Herron, A. J., Lowe, S. W., Man, T. K., Lau, C. C., Donehower, L. A. (2009) MMP13, Birc2 (cIAP1), and Birc3 (cIAP2), Amplified on Chromosome 9, Collaborate with p53 Deficiency in Mouse Osteosarcoma Progression. Cancer Res, 69 (6). pp. 2559-2567. ISSN 0008-5472

MacAlister, C. A., Bergmann, D. C. (2011) Sequence and function of basic helix-loop-helix proteins required for stomatal development in Arabidopsis are deeply conserved in land plants. Evolution & Development, 13 (2). pp. 182-192. ISSN 1520-541X

MacAlister, C. A., Ortiz-Ramirez, C., Becker, J. D., Feijo, J. A., Lippman, Z. B. (2016) Hydroxyproline O-arabinosyltransferase mutants oppositely alter tip growth in Arabidopsis thaliana and Physcomitrella patens. Plant J, 85 (2). pp. 193-208. ISSN 1365-313X (Electronic)0960-7412 (Linking)

MacDowell, Edwin Carleton (1920) Bristle inheritance in Drosophila: III. Correlation. Journal of Experimental Zoology, 30 (4). pp. 419-460.

Machida, M., Yamazaki, S., Kunihiro, S., Tanaka, T., Kushida, N., Jinno, K., Haikawa, Y., Yamazaki, J., Yamamoto, S., Sekine, M., Oguchi, A., Nagai, Y., Sakai, M., Aoki, K., Ogura, K., Kudoh, Y., Kikuchi, H., Zhang, M. Q., Yanagida, M. (2000) A 38 kb segment containing the cdc2 gene from the left arm of fission yeast chromosome II: sequence analysis and characterization of the genomic DNA and cDNAs encoded on the segment. Yeast, 16 (1). pp. 71-80. ISSN 0749-503X

Majerciak, V., Yamanegi, K., Allemand, E., Kruhlak, M., Krainer, A. R., Zheng, Z. M. (2008) Kaposi sarcoma-associated herpesvirus ORF57 functions as a viral splicing factor and promotes the expression of intron-containing viral lytic genes in spliceosome-mediated RNA splicing. J Virol, 82 (6). pp. 2792-2801.

Malcolmson, J., Kleyner, R., Tegay, D., Adams, W., Ward, K., Coppinger, J., Nelson, L., Meisler, M. H., Wang, K., Robison, R., Lyon, G. J. (2016) SCN8A mutation in a child presenting with seizures and developmental delays. Cold Spring Harb Mol Case Stud, 2 (6). a001073. ISSN 2373-2873

Malhotra, D., McCarthy, S., Michaelson, J. J., Vacic, V., Burdick, K. E., Yoon, S., Cichon, S., Corvin, A., Gary, S., Gershon, E. S., Gill, M., Karayiorgou, M., Kelsoe, J. R., Krastoshevsky, O., Krause, V., Leibenluft, E., Levy, D. L., Makarov, V., Bhandari, A., Malhotra, A. K., McMahon, F. J., Nöthen, M. M., Potash, J. B., Rietschel, M., Schulze, T. G., Sebat, J. (2011) High frequencies of de novo cnvs in bipolar disorder and schizophrenia. Neuron, 72 (6). pp. 951-963. ISSN 08966273 (ISSN)

Malone, C. D., Falkowska, K. A., Li, A. Y., Galanti, S. E., Kanuru, R. C., LaMont, E. G., Mazzarella, K. C., Micev, A. J., Osman, M. M., Piotrowski, N. K., Suszko, J. W., Timm, A. C., Xu, M.-M., Liu, L. F., Chalker, D. L. (2008) Nucleus-Specific Importin Alpha Proteins and Nucleoporins Regulate Protein Import and Nuclear Division in the Binucleate Tetrahymena thermophila. Eukaryotic Cell, 7 (9). pp. 1487-1499.

Man, A. K., Young, L. J. T., Tynan, J. A., Lesperance, J., Egeblad, M., Werb, Z., Hauser, C. A., Muller, W. J., Cardiff, R. D., Oshima, R. G. (2003) Ets2-Dependent Stromal Regulation of Mouse Mammary Tumors. Molecular and Cellular Biology, 23 (23). pp. 8614-8625. ISSN 02707306 (ISSN)

Mardis, E., McPherson, J., Martienssen, R., Wilson, R. K., McCombie, W. R. (2002) What is finished, and why does it matter. Genome Research, 12 (5). pp. 669-671. ISSN 1088-9051

Maron, L. G., Guimaraes, C. T., Kirst, M., Albert, P. S., Birchler, J. A., Bradbury, P. J., Buckler, E. S., Coluccio, A. E., Danilova, T. V., Kudrna, D., Magalhaes, J. V., Pineros, M. A., Schatz, M. C., Wing, R. A., Kochian, L. V. (2013) Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proceedings of the National Academy of Sciences of the United States of America, 110 (13). pp. 5241-5246. ISSN 0027-8424

Marr, T. G., Yan, X., Yu, Q. (1992) Genomic mapping by single copy landmark detection: a predictive model with a discrete mathematical approach. Mamm Genome, 3 (11). pp. 644-9. ISSN 0938-8990 (Print)0938-8990 (Linking)

Marra, M., Kucaba, T., Sekhon, M., Hillier, L., Martienssen, R., Chinwalla, A., Crockett, J., Fedele, J., Grover, H., Gund, C., McCombie, W. R., McDonald, K., McPherson, J., Mudd, N., Parnell, L., Schein, J., Seim, R., Shelby, P., Waterston, R., Wilson, R. (1999) A map for sequence analysis of the Arabidopsis thaliana genome. Nature Genetics, 22 (3). pp. 265-270. ISSN 10614036 (ISSN)

Martienssen, R. (2012) Reprogramming heterochromatin and its consequences in the germline. Genes & Genetic Systems, 87 (6). p. 371. ISSN 1341-7568

Martienssen, R., Lippman, Z., May, B., Ronemus, M., Vaughn, M. (2004) Transposons, tandem repeats, and the silencing of imprinted genes. Cold Spring Harbor symposia on quantitative biology, 69. pp. 371-9. ISSN 0091-7451 (Print)0091-7451 (Linking)

Martienssen, R., McCombie, W. R. (2001) The first plant genome. Cell, 105 (5). pp. 571-574. ISSN 00928674 (ISSN)

Martienssen, R., Zaratiegui, M., Irvine, D., Goto, D., Slotkin, K., Tanurdzic, M., Lippman, Z., Vaughn, M., May, B., Cande, Z., Colot, V., Doerge, R. W. (2007) Silent running: RNA interference and heterochromatic modification. Chromosome Research, 15 (2 (Sup). pp. 20-21. ISSN 0967-3849

Martienssen, R. A. (2008) Great leap forward? Transposable elements, small interfering RNA and adaptive Lamarckian evolution. New Phytologist, 179 (3). pp. 570-572. ISSN 0028-646X

Martienssen, R. A. (2003) Maintenance of heterochromatin by RNA interference of tandem repeats. Nature Genetics, 35 (3). pp. 213-4. ISSN 1061-4036

Martienssen, R. A. (2000) Weeding out the genes: the Arabidopsis genome project. Functional & Integrative Genomics, 1 (1). pp. 2-11. ISSN 1438-793X

Martienssen, R. A., Kloc, A., Slotkin, R. K., Tanurdzic, M. (2008) Epigenetic inheritance and reprogramming in plants and fission yeast. Cold Spring Harbor symposia on quantitative biology, 73. pp. 265-71. ISSN 1943-4456 (Electronic)0091-7451 (Linking)

Martienssen, R. A., Rabinowicz, P. D., O'Shaughnessy, A., McCombie, W. R. (2004) Sequencing the maize genome. Current Opinion in Plant Biology, 7 (2). pp. 102-107. ISSN 13695266 (ISSN)

Martin-Gallardo, A., Marchuk, D. A., Gocayne, J., Kerlavage, A. R., McCombie, W. R., Venter, J. C., Collins, F. S., Wallace, M. R. (1992) Sequencing and analysis of genomic fragments from the NF1 locus. DNA sequence : The journal of DNA sequencing and mapping, 3 (4). pp. 237-243. ISSN 10425179 (ISSN)

Martin-Gallardo, A., McCombie, W. R., Gocayne, J. D., FitzGerald, M. G., Wallace, S., Lee, B. M. B., Lamerdin, J., Trapp, S., Kelley, J. M., Liu, L. I., Dubnick, M., Johnston-Dow, L. A., Kerlavage, A. R., De Jong, P., Carrano, A., Fields, C., Venter, J. C. (1992) Automated DNA sequencing and analysis of 106 kilobases from human chromosome 19q13.3. Nature Genetics, 1 (1). pp. 34-39. ISSN 10614036 (ISSN)

Masuda, H. P., Cabral, L. M., De Veylder, L., Tanurdzic, M., de Almeida Engler, J., Geelen, D., Inze, D., Martienssen, R. A., Ferreira, P. C., Hemerly, A. S. (2008) ABAP1 is a novel plant Armadillo BTB protein involved in DNA replication and transcription. EMBO Journal, 27 (20). pp. 2746-56. ISSN 1460-2075 (Electronic)0261-4189 (Linking)

Matasci, N., McKay, S. (2013) Phylogenetic analysis with the iPlant discovery environment. Current protocols in bioinformatics (SUPPL.). 6.13.1-6.13.13. ISSN 19343396 (ISSN)

Matise, T. C., Sachidanandam, R., Clark, A. G., Kruglyak, L., Wijsman, E., Kakol, J., Buyske, S., Chui, B., Cohen, P., de Toma, C., Ehm, M., Glanowski, S., He, C. S., Heil, J., Markianos, K., McMullen, I., Pericak-Vance, M. A., Silbergleit, A., Stein, L., Wagner, M., Wilson, A. F., Winick, J. D., Winn-Deen, E. S., Yamashiro, C. T., Cann, H. M., Lai, E., Holden, A. L. (2003) A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. American Journal of Human Genetics, 73 (2). pp. 271-284. ISSN 0002-9297

Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., de Bono, B., Garapati, P., Hemish, J., Hermjakob, H., Jassal, B., Kanapin, A., Lewis, S., Mahajan, S., May, B., Schmidt, E., Vastrik, I., Wu, G., Birney, E., Stein, L. D., D'Eustachio, P. (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res, 37. D619-22.

Maulik, U., Mukhopadhyay, A., Bandyopadhyay, S., Zhang, M. Q., Zhang, X. (2008) Multiobjective fuzzy biclustering in microarray data: Method and a new performance measure. Evolutionary Computation, 2008. CEC 2008. (IEEE World Congress on Computational Intelligence). pp. 1536-1543.

Mavrakis, K. J., Zhu, H., Silva, R. L., Mills, J. R., Teruya-Feldstein, J., Lowe, S. W., Tam, W., Pelletier, J., Wendel, H. G. (2008) Tumorigenic activity and therapeutic inhibition of Rheb GTPase. Genes Dev, 22 (16). pp. 2178-88.

May, B. P., Martienssen, R. A. (2003) Transposon mutagenesis in the study of plant development. Critical Reviews in Plant Sciences, 22 (1). pp. 1-35. ISSN 0735-2689

May, P., Liao, W., Wu, Y., Shuai, B., McCombie, W. R., Zhang, M. Q., Liu, Q. A. (2013) The effects of carbon dioxide and temperature on microRNA expression in Arabidopsis development. Nature Communications, 4. ISSN 20411723

Mayeda, A., Munroe, S. H., Xu, R. M., Krainer, A. R. (1998) Distinct functions of the closely related tandem RNA-recognition motifs of hnRNP A1. RNA, 4 (9). pp. 1111-1123. ISSN 1355-8382

Mayeda, A., Zahler, A. M., Krainer, A. R., Roth, M. B. (1992) Two members of a conserved family of nuclear phosphoproteins are involved in pre-mRNA splicing. Proceedings of the National Academy of Sciences of the United States of America, 89 (4). pp. 1301-1304. ISSN 0027-8424

Mazurek, A., Luo, W., Krasnitz, A., Hicks, J., Powers, R. S., Stillman, B. (2012) DDX5 regulates DNA replication and is required for cell proliferation in a subset of breast cancer cells. Cancer Discovery, 2 (9). pp. 812-825. ISSN 21598274 (ISSN)

McCarthy, S. E., Makarov, V., Kirov, G., Addington, A. M., McClellan, J., Yoon, S., Perkins, D. O., Dickel, D. E., Kusenda, M., Krastoshevsky, O., Krause, V., Kumar, R. A., Grozeva, D., Malhotra, D., Walsh, T., Zackai, E. H., Kaplan, P., Ganesh, J., Krantz, I. D., Spinner, N. B., Roccanova, P., Bhandari, A., Pavon, K., Lakshmi, B., Leotta, A., Kendall, J. T., Lee, Y. H., Vacic, V., Gary, S., Iakoucheva, L. M., Crow, T. J., Christian, S. L., Lieberman, J. A., Stroup, T. S., Lehtimaki, T., Puura, K., Haldeman-Englert, C., Pearl, J., Goodell, M., Willour, V. L., DeRosse, P., Steele, J., Kassem, L., Wolff, J., Chitkara, N., McMahon, F. J., Malhotra, A. K., Potash, J. B., Schulze, T. G., Nothen, M. M., Cichon, S., Rietschel, M., Leibenluft, E., Kustanovich, V., Lajonchere, C. M., Sutcliffe, J. S., Skuse, D., Gill, M., Gallagher, L., Mendell, N. R., Craddock, N., Owen, M. J., O'Donovan, M. C., Shaikh, T. H., Susser, E., DeLisi, L. E., Sullivan, P. F., Deutsch, C. K., Rapoport, J., Levy, D. L., King, M. C., Sebat, J. (2009) Microduplications of 16p11.2 are associated with schizophrenia. Nature Genetics, 41 (11). pp. 1223-1227. ISSN 1061-4036

McClellan, J. M., Walsh, T., McCarthy, S. E., King, M. C., Sebat, J. (2008) Gene mutations and cognitive delay - Response. Science, 321 (5889). p. 640. ISSN 0036-8075

McClintock, Barbara (1978) Mechanisms that rapidly reorganize the genome. In: Stadler genetics symposium , University of Missouri.

McCombie, W. R. (2012) Talk from Dick McCombie at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

McCombie, W. R., Adams, M. D., Kelley, J. M., FitzGerald, M. G., Utterback, T. R., Khan, M., Dubnick, M., Kerlavage, A. R., Venter, J. C., Fields, C. (1992) Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologues. Nature Genetics, 1 (2). pp. 124-131. ISSN 10614036 (ISSN)

McCombie, W. R., De la Bastide, M., Habermann, K., Parnell, L., Dedhia, N., Gnoj, L., Schutz, K., Huang, E., Spiegel, L., Yordan, C., Sehkon, M., Murray, J., Sheet, P., Cordes, M., Threideh, J., Stoneking, T., Kalicki, J., Graves, T., Harmon, G., Edwards, J., Latreille, P., Courtney, L., Cloud, J., Abbott, A., Scott, K., Johnson, D., Minx, P., Bentley, D., Fulton, B., Miller, N., Greco, T., Kemp, K., Kramer, J., Fulton, L., Mardis, E., Dante, M., Pepin, K., Hillier, L., Nelson, J., Spieth, J., Simorowski, J., May, B., Ma, P., Preston, R., Vil, D., Lei, H. S., Shekher, M., Matero, A., Shah, R., Swaby, I., O'Shaughnessy, A., Rodriguez, M., Hoffman, J., Till, S., Granat, S., Shohdy, N., Hasegawa, A., Hameed, A., Lodhi, M., Johnson, A., Chen, E., Marra, M., Wilson, R. K., Martienssen, R. (2000) The complete sequence of a heterochromatic island from a higher eukaryote. Cell, 100 (3). pp. 377-386. ISSN 00928674 (ISSN)

McCombie, W. R., Hansen, J. B., Zylstra, G. J., Maurer, B., Olsen, R. H. (1983) Pseudomonas Streptomycin Resistance Transposon Associated with R-Plasmid Mobilization. Journal of Bacteriology, 155 (1). pp. 40-48. ISSN 0021-9193

McCombie, W. R., Kieleczawa, J. (1994) Automated DNA sequencing using 4-color fluorescent detection of reactions primed with hexamer strings. Biotechniques, 17 (3). pp. 574-579. ISSN 07366205 (ISSN)

McCombie, W. R., Martin-Gallardo, A., Gocayne, J. D., FitzGerald, M., Dubnick, M., Kelley, J. M., Castilla, L., Liu, L. I., Wallace, S., Trapp, S., Tagle, D., Whaley, W. L., Cheng, S., Gusella, J., Frischauf, A. M., Poustka, A., Lehrach, H., Collins, F. S., Kerlavage, A. R., Fields, C., Venter, J. C. (1992) Expressed genes, Alu repeats and polymorphisms in cosmids sequenced from chromosome 4p16.3. Nature Genetics, 1 (5). pp. 348-353. ISSN 10614036 (ISSN)

McEachern, M. J., Hicks, J. B. (1993) Unusually large telomeric repeats in the yeast Candida albicans. Molecular and Cellular Biology, 13 (1). pp. 551-560. ISSN 02707306 (ISSN)

McFadden, D. G., Politi, K., Bhutkar, A., Chen, F. K., Song, X., Pirun, M., Santiago, P. M., Kim-Kiselak, C., Platt, J. T., Lee, E., Hodges, E., Rosebrock, A. P., Bronson, R. T., Socci, N. D., Hannon, G. J., Jacks, T., Varmus, H. (2016) Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma. Proc Natl Acad Sci U S A, 113 (42). E6409-E6417. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

McKain, M. R., Wickett, N., Zhang, Y., Ayyampalayam, S., McCombie, W. R., Chase, M. W., Pires, J. C., dePamphilis, C. W., Leebens-Mack, J. (2012) Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). American Journal of Botany, 99 (2). pp. 397-406. ISSN 0002-9122

McKay, S. J., Vergara, I. A., Stajich, J. E. (2010) Using the Generic Synteny Browser (GBrowse_syn). Curr Protoc Bioinformatics, Chapte. Unit 9 12. ISSN 1934-340X (Electronic) 1934-3396 (Linking)

McMullen, M. D., Kresovich, S., Villeda, Hector S., Bradbury, P. J., Li, H., Sun, Q., Flint-Garcia, S., Thornsberry, J., Acharya, C. B., Bottoms, C., Brown, P. J., Browne, C., Eller, M., Guill, K., Harjes, C., Kroon, D. E., Lepak, N.., Mitchell, S. E., Peterson, B., Pressoir, G., Romero, S., Rosas, M. O., Salvo, S., Yates, H., Hanson, M., Jones, E. G., Smith, S., Glaubitz, J. C., Goodman, M. M., Ware, D. H., Holland, J. B., Buckler, E. S. (2009) Genetic Properties of the Maize Nested Association Mapping Population. Science, 325 (5941). pp. 737-740.

Mefford, H. C., Sharp, A. J., Baker, C., Itsara, A., Jiang, Z., Buysse, K., Huang, S., Maloney, V. K., Crolla, J. A., Baralle, D., Collins, A., Mercer, C., Norga, K., de Ravel, T., Devriendt, K., Bongers, E. M., de Leeuw, N., Reardon, W., Gimelli, S., Bena, F., Hennekam, R. C., Male, A., Gaunt, L., Clayton-Smith, J., Simonic, I., Park, S. M., Mehta, S. G., Nik-Zainal, S., Woods, C. G., Firth, H. V., Parkin, G., Fichera, M., Reitano, S., Lo Giudice, M., Li, K. E., Casuga, I., Broomer, A., Conrad, B., Schwerzmann, M., Raber, L., Gallati, S., Striano, P., Coppola, A., Tolmie, J. L., Tobias, E. S., Lilley, C., Armengol, L., Spysschaert, Y., Verloo, P., De Coene, A., Goossens, L., Mortier, G., Speleman, F., van Binsbergen, E., Nelen, M. R., Hochstenbach, R., Poot, M., Gallagher, L., Gill, M., McClellan, J., King, M. C., Regan, R., Skinner, C., Stevenson, R. E., Antonarakis, S. E., Chen, C., Estivill, X., Menten, B., Gimelli, G., Gribble, S., Schwartz, S., Sutcliffe, J. S., Walsh, T., Knight, S. J., Sebat, J., Romano, C., Schwartz, C. E., Veltman, J. A., de Vries, B. B., Vermeesch, J. R., Barber, J. C., Willatt, L., Tassabehji, M., Eichler, E. E. (2008) Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. New England Journal of Medicine , 359 (16). pp. 1685-99.

Mehta, M. S., Vazquez, A., Kulkarni, D. A., Kerrigan, J. E., Atwal, G. S., Metsugi, S., Toppmeyer, D. L., Levine, A. J., Hirshfield, K. M. (2011) Polymorphic variants in TSC1 and TSC2 and their association with breast cancer phenotypes. Breast Cancer Research and Treatment, 125 (3). pp. 861-868.

Meier, I., Xu, X. M., Brkljacic, J., Zhao, Q., Wang, H. J. (2008) Going green: plants' alternative way to position the Ran gradient. Journal of Microscopy-Oxford, 231 (2). pp. 225-233. ISSN 0022-2720

Meissner, B., Warner, A., Wong, K., Dube, N., Lorch, A., McKay, S. J., Khattra, J., Rogalski, T., Somasiri, A., Chaudhry, I., Fox, R. M., Miller Iii, D. M., Baillie, D. L., Holt, R. A., Jones, S. J. M., Marra, M. A., Moerman, D. G. (2009) An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans. PLoS Genet, 5 (6). e1000537.

Melka, M. G., Gillis, J., Bernard, M., Abrahamowicz, M., Chakravarty, M. M., Leonard, G. T., Perron, M., Richer, L., Veillette, S., Banaschewski, T., Barker, G. J., BüChel, C., Conrod, P., Flor, H., Heinz, A., Garavan, H., Brühl, R., Mann, K., Artiges, E., Lourdusamy, A., Lathrop, M., Loth, E., Schwartz, Y., Frouin, V., Rietschel, M., Smolka, M. N., hle, A., Gallinat, J., Struve, M., Lattka, E., Waldenberger, M., Schumann, G., Pavlidis, P., Gaudet, D., Paus, T., Pausova, Z. (2013) FTO, obesity and the adolescent brain. Human Molecular Genetics, 22 (5). pp. 1050-1058. ISSN 09646906 (ISSN)

Meng, T. C., Tonks, N. K. (2003) Analysis of the regulation of protein tyrosine phosphatases in vivo by reversible oxidation. In: Protein Phosphatases. Methods in Enzymology, 366 . Academic Press Inc, San Diego, pp. 304-318. ISBN 0076-6879

Menges, F., Narzisi, G., Mishra, B. (2011) TotalReCaller: improved accuracy and performance via integrated alignment and base-calling. Bioinformatics, 27 (17). pp. 2330-2337. ISSN 1367-4803

Metz, Charles William (1920) Correspondence between chromosome number and linkage groups in Drosophila virilis. Science, 51 (1321). pp. 417-418.

Meyers, B. C., Axtell, M. J., Bartel, B., Bartel, D. P., Baulcombe, D., Bowman, J. L., Cao, X., Carrington, J. C., Chen, X., Green, P. J., Griffiths-Jones, S., Jacobsen, S. E., Mallory, A. C., Martienssen, R. A., Poethig, R. S., Qi, Y., Vaucheret, H., Voinnet, O., Watanabe, Y., Weigel, D., Zhu, J. K. (2008) Criteria for annotation of plant MicroRNAs. The Plant cell, 20 (12). pp. 3186-90. ISSN 1040-4651 (Print)1040-4651 (Linking)

Miller, W., Rosenbloom, K., Hardison, R. C., Hou, M., Taylor, J., Raney, B., Burhans, R., King, D. C., Baertsch, R., Blankenberg, D., Kosakovsky Pond, S. L., Nekrutenko, A., Giardine, B., Harris, R. S., Tyekucheva, S., Diekhans, M., Pringle, T. H., Murphy, W. J., Lesk, A., Weinstock, G. M., Lindblad-Toh, K., Gibbs, R. A., Lander, E. S., Siepel, A., Haussler, D., Kent, W. J. (2007) 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research, 17 (12). pp. 1797-808. ISSN 1088-9051

Mills, A. (2002) Conducting the exploration of gene function. Seminars in Cell & Developmental Biology, 13 (2). p. 107. ISSN 1084-9521

Mills, A. A. (2001) Changing colors in mice: an inducible system that delivers. Genes & Development, 15 (12). pp. 1461-1467. ISSN 0890-9369

Mills, A. A. (2017) The Chromodomain Helicase DNA-Binding Chromatin Remodelers: Family Traits that Protect from and Promote Cancer. Cold Spring Harb Perspect Med. ISSN 2157-1422 (Electronic)2157-1422 (Linking)

Mills, A. A., Bradley, A. (2001) From mouse to man: generating megabase chromosome rearrangements. Trends in Genetics, 17 (6). pp. 331-339. ISSN 0168-9525

Mills, A. A., Mills, M. J., Gardiner, D. M., Bryant, S. V., Stanbridge, E. J. (1999) Analysis of the pattern of QM expression during mouse development. Differentiation, 64 (3). pp. 161-171. ISSN 03014681 (ISSN)

Mills, A. A., Qi, Y., Bradley, A. (2002) Conditional inactivation of p63 by Cre-mediated excision. Genesis, 32 (2). pp. 138-141. ISSN 1526-954X

Mills, A. A., Zheng, B., Wang, X. J., Vogel, H., Roop, D. R., Bradley, A. (1999) p63 is a p53 homologue required for limb and epidermal morphogenesis. Nature, 398 (6729). pp. 708-713. ISSN 00280836 (ISSN)

Mills, J. R., Hippo, Y., Robert, F., Chen, S. M. H., Malina, A., Lin, C. J., Trojahn, U., Wendel, H. G., Charest, A., Bronson, R. T., Kogan, S. C., Nadon, R., Housman, D. E., Lowe, S. W., Pelletier, J. (2008) mTORC1 promotes survival through translational control of Mcl-1. Proc Natl Acad Sci U S A, 105 (31). pp. 10853-10858.

Min, J. R., Zhang, X., Cheng, X. D., Grewal, S. I. S., Xu, R. M. (2002) Structure of the SET domain histone lysine methyltransferase Clr4. Nature Structural Biology, 9 (11). pp. 828-832. ISSN 1072-8368

Min, J. R., Zhang, Y., Xu, R. M. (2003) Structural basis for specific binding of polycomb chromodomain to histone H3 methylated at Lys 27. Genes & Development, 17 (15). pp. 1823-1828. ISSN 0890-9369

Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., Saw, J. H., Senin, P., Wang, W., Ly, B. V., Lewis, K. L. T., Salzberg, S. L., Feng, L., Jones, M. R., Skelton, R. L., Murray, J. E., Chen, C., Qian, W., Shen, J., Du, P., Eustice, M., Tong, E., Tang, H., Lyons, E., Paull, R. E., Michael, T. P., Wall, K., Rice, D. W., Albert, H., Wang, M. L., Zhu, Y. J., Schatz, M., Nagarajan, N., Acob, R. A., Guan, P., Blas, A., Wai, C. M., Ackerman, C. M., Ren, Y., Liu, C., Wang, J., Na, J. K., Shakirov, E. V., Haas, B., Thimmapuram, J., Nelson, D., Wang, X., Bowers, J. E., Gschwend, A. R., Delcher, A. L., Singh, R., Suzuki, J. Y., Tripathi, S., Neupane, K., Wei, H., Irikura, B., Paidi, M., Jiang, N., Zhang, W., Presting, G., Windsor, A., Navajas-Pérez, R., Torres, M. J., Feltus, F. A., Porter, B., Li, Y., Burroughs, A. M., Luo, M. C., Liu, L., Christopher, D. A., Mount, S. M., Moore, P. H., Sugimura, T., Jiang, J., Schuler, M. A., Friedman, V., Mitchell-Olds, T., Shippen, D. E., Depamphilis, C. W., Palmer, J. D., Freeling, M., Paterson, A. H., Gonsalves, D., Wang, L., Alam, M. (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature, 452 (7190). pp. 991-996. ISSN 00280836 (ISSN)

Ming, R., VanBuren, R., Liu, Y. L., Yang, M., Han, Y. P., Li, L. T., Zhang, Q., Kim, M. J., Schatz, M. C., Campbell, M., Li, J. P., Bowers, J. E., Tang, H. B., Lyons, E., Ferguson, A. A., Narzisi, G., Nelson, D. R., Blaby-Haas, C. E., Gschwend, A. R., Jiao, Y. N., Der, J. P., Zeng, F. C., Han, J., Min, X. J., Hudson, K. A., Singh, R., Grennan, A. K., Karpowicz, S. J., Watling, J. R., Ito, K., Robinson, S. A., Hudson, M. E., Yu, Q. Y., Mockler, T. C., Carroll, A., Zheng, Y., Sunkar, R., Jia, R. Z., Chen, N., Arro, J., Wai, C. M., Wafula, E., Spence, A., Han, Y. N., Xu, L. M., Zhang, J. S., Peery, R., Haus, M. J., Xiong, W. W., Walsh, J. A., Wu, J., Wang, M. L., Zhu, Y. J., Paull, R. E., Britt, A. B., Du, C. G., Downie, S. R., Schuler, M. A., Michael, T. P., Long, S. P., Ort, D. R., Schopf, J. W., Gang, D. R., Jiang, N., Yandell, M., dePamphilis, C. W., Merchant, S. S., Paterson, A. H., Buchanan, B. B., Li, S. H., Shen-Miller, J. (2013) Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology, 14 (5). ISSN 1465-6906

Mintz, P. J., Patterson, S. D., Neuwald, A. F., Spahr, C. S., Spector, D. L. (1999) Purification and biochemical characterization of interchromatin granule clusters. Embo Journal, 18 (15). pp. 4308-4320. ISSN 0261-4189

Mintz, P. J., Spector, D. L. (2000) Compartmentalization of RNA processing factors within nuclear speckles. Journal of Structural Biology, 129 (2-3). pp. 241-251. ISSN 1047-8477

Mishra, B. (2003) Life's duplicities: Sex, death, and Valis. In: High Performance Computing - HiPC 2003. Lecture Notes in Computer Science, 2913 . Springer-Verlag Berlin, Berlin, p. 1. ISBN 978-3-540-20626-2

Misteli, T., Cáceres, J. F., Clement, J. Q., Krainer, A. R., Wilkinson, M. F., Spector, D. L. (1998) Serine phosphorylation of SR proteins is required for their recruitment to sites of transcription in vivo. Journal of Cell Biology, 143 (2). pp. 297-307. ISSN 0021-9525

Misteli, T., Spector, D. L. (1997) Protein phosphorylation and the nuclear organization of pre-mRNA splicing. Trends In Cell Biology, 7 (4). pp. 135-138. ISSN 0962-8924

Misteli, T., Spector, D. L. (1996) Serine/threonine phosphatase 1 modulates the subnuclear distribution of pre-mRNA splicing factors. Molecular Biology of the Cell, 7. pp. 1559-1572. ISSN 1059-1524

Mistry, M., Gillis, J., Pavlidis, P. (2013) Data and design files for 6 public datasets used in "Genome-wide expression profiling of schizophrenia using a large combined cohort" Mistry, M. and Gillis, J. and Pavlidis, P. (2013) Molecular Psychiatry, 18 (2). pp. 215-225. [Dataset]

Mistry, M., Gillis, J., Pavlidis, P. (2013) Genome-wide expression profiling of schizophrenia using a large combined cohort. Molecular Psychiatry, 18 (2). pp. 215-225. ISSN 13594184 (ISSN)

Mizuno, H., Atwal, G. S., Wang, H., Levine, A. J., Vazquez, A. (2010) Fine-scale detection of population-specific linkage disequilibrium using haplotype entropy in the human genome. BMC Genet, 11. p. 27. ISSN 1471-2156 (Electronic) 1471-2156 (Linking)

Mo, Q., Wang, S., Seshan, V. E., Olshen, A. B., Schultz, N., Sander, C., Powers, R. S., Ladanyi, M., Shen, R. (2013) Pattern discovery and cancer gene identification in integrated cancer genomic data. Proceedings of the National Academy of Sciences of the United States of America, 110 (11). pp. 4245-4250. ISSN 00278424 (ISSN)

Monaco, M. K., Sen, T. Z., Dharmawardhana, P. D., Ren, L., Schaeffer, M., Naithani, S., Amarasinghe, V., Thomason, J., Harper, L., Gardiner, J., Cannon, E. K. S., Lawrence, C. J., Ware, D., Jaiswal, P. (2013) Maize Metabolic Network Construction and Transcriptome Analysis. Plant Genome, 6 (1). ISSN 1940-3372

Monaco, M. K., Stein, J., Naithani, S., Wei, S., Dharmawardhana, P., Kumari, S., Amarasinghe, V., Youens-Clark, K., Thomason, J., Preece, J., Pasternak, S., Olson, A., Jiao, Y., Lu, Z., Bolser, D., Kerhornou, A., Staines, D., Walts, B., Wu, G., D'Eustachio, P., Haw, R., Croft, D., Kersey, P. J., Stein, L., Jaiswal, P., Ware, D. (2014) Gramene 2013: comparative plant genomics resources. Nucleic Acids Research, 42 (Databa). D1193-9. ISSN 0305-1048

Monardo, P. J., Boutell, T., Garrels, J. I., Latter, G. I. (1994) A distributed system for two-dimensional gel analysis. Comput Appl Biosci, 10 (2). pp. 137-43.

Moreno-Lopez, J., Ahola, H., Stenlund, A., Osterhaus, A., Pettersson, U. (1984) Genome of an avian papillomavirus. J Virol, 51 (3). pp. 872-5. ISSN 0022-538X (Print)0022-538X (Linking)

Moretti, F., Marinari, B., Iacono, N. L., Botti, E., Giunta, A., Spallone, G., Garaffo, G., Vernersson-Lindahl, E., Merlo, G., Mills, A. A., Ballaro, C., Alema, S., Chimenti, S., Guerrini, L., Costanzo, A. (2010) A regulatory feedback loop involving p63 and IRF6 links the pathogenesis of 2 genetically different human ectodermal dysplasias. Journal of Clinical Investigation, 120 (5). pp. 1570-1577.

Moretti, F., Spallone, G., Botti, E., Giunta, A., Lo Iacono, N., Merlo, G., Mills, A. A., Alema, S., Chimenti, S., Guerrini, L., Costanzo, A. (2010) p63 and IRF6 are components of a common molecular pathway disrupted in ectodermal dysplasias. Journal of Investigative Dermatology, 130. p. 626. ISSN 0022-202X

Muerdter, F., Guzzardo, P. M., Gillis, J., Luo, Y., Yu, Y., Chen, C., Fekete, R., Hannon, G.J. (2013) A Genome-wide RNAi Screen Draws a Genetic Framework for Transposon Control and Primary piRNA Biogenesis in Drosophila. Molecular Cell, 50 (5). pp. 736-748. ISSN 1097-4164

Mukhopadhyay, S., Schedl, P., Studitsky, V. M., Sengupta, A. M. (2011) Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators. Proceedings of the National Academy of Sciences of the United States of America, 108 (50). pp. 19919-19924. ISSN 0027-8424

Mukhopadhyay, S., Sengupta, A. M. (2013) The role of multiple marks in epigenetic silencing and the emergence of a stable bivalent chromatin state. PLoS Computational Biology, 9 (7). e1003121. ISSN 1553-7358 (Electronic)1553-734X (Linking)

Mulder, K. W., Wang, X., Escriu, C., Ito, Y., Schwarz, R. F., Gillis, J., Sirokmany, G., Donati, G., Uribe-Lewis, S., Pavlidis, P., Murrell, A., Markowetz, F., Watt, F. M. (2012) Diverse epigenetic strategies interact to control epidermal differentiation. Nature Cell Biology, 14 (7). pp. 753-763. ISSN 1465-7392

Muratani, M., Gerlich, D., Janicki, S. M., Gebhard, M., Eils, R., Spector, D. L. (2002) Metabolic-energy-dependent movement of PML bodies within the mammalian cell nucleus. Nature Cell Biology, 4. pp. 106-110. ISSN 1465-7392

Murn, J., Mlinaric-Rascan, I., Vaigot, P., Alibert, O., Frouin, V., Gidrol, X. (2009) A Myc-regulated transcriptional network controls B-cell fate in response to BCR triggering. BMC Genomics, 10. p. 323.

Muthuswamy, S. K. (2009) A New Tumor Suppressor That Regulates Tissue Architecture. PLoS Medicine, 6 (5). e1000073.

Muzzin, P., Revelli, J. P., Kuhne, F., Gocayne, J. D., McCombie, W. R., Venter, J. C., Giacobino, J. P., Fraser, C. M. (1991) An adipose tissue-specific β-adrenergic receptor. Molecular cloning and down-regulation in obesity. Journal of Biological Chemistry, 266 (35). pp. 24053-24058. ISSN 00219258 (ISSN)

Myklebust, L. M., Van Damme, P., Stove, S. I., Dorfel, M. J., Abboud, A., Kalvik, T. V., Grauffel, C., Jonckheere, V., Wu, Y., Swensen, J., Kaasa, H., Liszczak, G., Marmorstein, R., Reuter, N., Lyon, G. J., Gevaert, K., Arnesen, T. (2014) Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects. Human Molecular Genetics, 24 (7). pp. 1956-1976. ISSN 0964-6906

Myles, S., Boyko, A. R., Owens, C. L., Brown, P. J., Grassi, F., Aradhya, M. K., Prins, B., Reynolds, A., Chia, J. M., Ware, D. H., Bustamante, C. D., Buckler, E. S. (2011) Genetic structure and domestication history of the grape. Proceedings of the National Academy of Sciences of the United States of America, 108 (9). pp. 3530-3535. ISSN 0027-8424

Määttä, J. A., Sundvall, M., Junttila, T. T., Peri, L., Laine, V. J. O., Isola, J., Egeblad, M., Elenius, K. (2006) Proteolytic cleavage and phosphorylation of a tumor-associated ErbB4 isoform promote ligand-independent survival and cancer cell growth. Molecular Biology of the Cell, 17 (1). pp. 67-79. ISSN 10591524 (ISSN)

N

Nadif Kasri, N., Nakano-Kobayashi, A., Malinow, R., Li, B., Van Aelst, L. (2009) The Rho-linked mental retardation protein oligophrenin-1 controls synapse maturation and plasticity by stabilizing AMPA receptors. Genes Dev, 23 (11). pp. 1289-1302. ISSN 0890-9369

Nadif Kasri, N., Nakano-Kobayashi, A., Van Aelst, L. (2011) Rapid Synthesis of the X-Linked Mental Retardation Protein OPHN1 Mediates mGluR-Dependent LTD through Interaction with the Endocytic Machinery. Neuron, 72 (2). pp. 300-315. ISSN 1097-4199 (Electronic)0896-6273 (Linking)

Nadif Kasri, N., Van Aelst, L. (2008) Rho-linked genes and neurological disorders. Pflügers Archiv European Journal of Physiology, 455 (5). pp. 787-797.

Nahle, Z., Hsieh, M., Pietka, T., Coburn, C. T., Grimaldi, P. A., Zhang, M. Q., Das, D., Abumrad, N. A. (2008) CD36-dependent Regulation of Muscle FoxO1 and PDK4 in the PPAR{delta}/{beta}-mediated Adaptation to Metabolic Stress. J Biol Chem, 283 (21). pp. 14317-26.

Nakayama, J., Xiao, G., Noma, K., Malikzay, A., Bjerling, P., Ekwall, K., Kobayashi, R., Grewal, S. I. (2003) Alp13, an MRG family protein, is a component of fission yeast Clr6 histone deacetylase required for genomic integrity. Embo Journal, 22 (11). pp. 2776-87. ISSN 0261-4189

Narzisi, G., O'Rawe, Jason, Iossifov, I., Fang, Han, Lee, Y. H., Wang, Zihua, Wu, Yiyang, Lyon, Gholson J., Wigler, M. H., Schatz, M. C. (2014) Accurate de novo and transmitted indel detection in exome-capture data using microassembly. Nature Methods, 11 (10). pp. 1033-1036.

Nattestad, M., Schatz, M. C. (2016) Assemblytics: a web analytics tool for the detection of variants from an assembly. Bioinformatics, 32 (19). pp. 3021-3023. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

Navin, N. E., Krasnitz, A., Rodgers, L., Cook, K., Meth, J. L., Kendall, J. T., Riggs, M., Eberling, Y., Troge, J. E., Grubor, V., Levy, D., Lundin, P., Månér, S., Zetterberg, A., Hicks, J. B., Wigler, M. H. (2010) Inferring tumor progression from genomic heterogeneity. Genome Research, 20 (1). pp. 68-80.

Nawy, T., Lukowitz, W., Bayer, M. (2008) Talk global, act local - patterning the Arabidopsis embryo. Current Opinion in Plant Biology, 11 (1). pp. 28-33. ISSN 1369-5266

Nene, V., Wortman, J. R., Lawson, D., Haas, B., Kodira, C., Tu, Z., Loftus, B., Xi, Z., Megy, K., Grabherr, M., Ren, Q., Zdobnov, E. M., Lobo, N. F., Campbell, K. S., Brown, S. E., Bonaldo, M. F., Zhu, J., Sinkins, S. P., Hogenkamp, D. G., Amedeo, P., Arensburger, P., Atkinson, P. W., Bidwell, S., Biedler, J., Birney, E., Bruggner, R. V., Costas, J., Coy, M. R., Crabtree, J., Crawford, M., DeBruyn, B., DeCaprio, D., Eiglmeier, K., Eisenstadt, E., El-Dorry, H., Gelbart, W. M., Gomes, S. L., Hammond, M., Hannick, L. I., Hogan, J. R., Holmes, M. H., Jaffe, D., Johnston, J. S., Kennedy, R. C., Koo, H., Kravitz, S., Kriventseva, E. V., Kulp, D., LaButti, K., Lee, E., Li, S., Lovin, D. D., Mao, C., Mauceli, E., Menck, C. F. M., Miller, J. R., Montgomery, P., Mori, A., Nascimento, A. L., Naveira, H. F., Nusbaum, C., O'Leary, S., Orvis, J., Pertea, M., Quesneville, H., Reidenbach, K. R., Rogers, Y. H., Roth, C. W., Schneider, J. R., Schatz, M., Shumway, M., Stanke, M., Stinson, E. O., Tubio, J. M. C., VanZee, J. P., Verjovski-Almeida, S., Werner, D., White, O., Wyder, S., Zeng, Q., Zhao, Q., Zhao, Y., Hill, C. A., Raikhel, A. S., Soares, M. B., Knudson, D. L., Lee, N. H., Galagan, J., Salzberg, S. L., Paulsen, I. T., Dimopoulos, G., Collins, F. H., Birren, B., Fraser-Liggett, C. M., Severson, D. W. (2007) Genome sequence of Aedes aegypti, a major arbovirus vector. Science, 316 (5832). pp. 1718-1723. ISSN 00368075 (ISSN)

Nestler, H. P., Doseff, A. (1997) A two-dimensional, diagonal sodium dodecyl sulfate-polyacrylamide gel electrophoresis technique to screen for protease substrates in protein mixtures. Analytical Biochemistry, 251 (1). pp. 122-5. ISSN 0003-2697 (Print)

Neuwald, A. F. (2003) Evolutionary clues to DNA polymerase III beta clamp structural mechanisms. Nucleic Acids Research, 31 (15). pp. 4503-4516. ISSN 0305-1048

Neuwald, A. F., Aravind, L., Spouge, J. L., Koonin, E. V. (1999) AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Research, 9 (1). pp. 27-43. ISSN 1088-9051 (Print)

Neuwald, A. F., Poleksic, A. (2000) PSI-BLAST searches using hidden Markov models of structural repeats: prediction of an unusual sliding DNA clamp and of beta-propellers in UV-damaged DNA-binding protein. Nucleic Acids Research, 28 (18). pp. 3570-3580. ISSN 0305-1048

Nguyen, Y. H., Mills, A. A., Stanbridge, E. J. (1998) Assembly of the QM protein onto the 60S ribosomal subunit occurs in the cytoplasm. Journal of Cellular Biochemistry, 68 (2). pp. 281-285. ISSN 07302312 (ISSN)

Ni, J., Pujar, A., Youens-Clark, K., Yap, I. V., Jaiswal, P., Tecle, I., Tung, C.-W., Ren, L. , Spooner, W., Wei, X, Avraham, S, Ware, D. H., Stein, L. D., McCouch, S. (2009) Gramene QTL database: development, content and applications. Database, 2009. bap005.

Nieto, A., Goldfarb, L. G., Brown, P., McCombie, W. R., Trapp, S., Asher, D. M., Gajdusek, D. C. (1991) Codon 178 mutation in ethnically diverse Creutzfeldt-Jakob disease families [29]. Lancet, 337 (8741). pp. 622-623. ISSN 01406736 (ISSN)

Niida, A., Smith, A. D., Imoto, S., Aburatani, H., Zhang, M. Q., Akiyama, T. (2009) Gene set-based module discovery in the breast cancer transcriptome. BMC Bioinformatics, 10. p. 71. ISSN 1471-2105

Niida, A., Smith, A. D., Imoto, S., Tsutsumi, S., Aburatani, H., Zhang, M. Q., Akiyama, T. (2008) Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. BMC Bioinformatics, 9. p. 404.

Nishijima, I., Mills, A., Qi, Y., Mills, M., Bradley, A. (2003) Two new balancer chromosomes on mouse chromosome 4 to facilitate functional annotation of human chromosome 1p. Genesis, 36 (3). pp. 142-148. ISSN 1526-954X

Nogueira, F. T. S., Chitwood, D. H., Madi, S., Ohtsu, K., Schnable, P. S., Scanlon, M. J., Timmermans, M. C. P. (2009) Regulation of Small RNA Accumulation in the Maize Shoot Apex. Plos Genetics, 5 (1). e1000320. ISSN 1553-7390

Nolan, M. E., Aranda, V., Lee, S., Lakshmi, B., Basu, S., Allred, D. C., Muthuswamy, S. K. (2008) The polarity protein Par6 induces cell proliferation and is overexpressed in breast cancer. Cancer Res, 68 (20). pp. 8201-9.

Nord, A. S., Roeb, W., Dickel, D. E., Walsh, T., Kusenda, M., O'Connor, K. L., Malhotra, D., McCarthy, S. E., Stray, S. M., Taylor, S. M., Sebat, J., King, B., King, M. C., McClellan, J. M. (2011) Reduced transcript expression of genes affected by inherited and de novo CNVs in autism. European Journal of Human Genetics, 19 (6). pp. 727-731. ISSN 10184813 (ISSN)

Noutsos, C., Perera, A. M., Nikolau, B. J., Seaver, S. M., Ware, D. H. (2015) Metabolomic Profiling of the Nectars of Aquilegia pubescens and A. Canadensis. PLoS One, 10 (5). e0124501. ISSN 1932-6203 (Electronic)1932-6203 (Linking)

Nowack, Moritz K., Harashima, Hirofumi, Dissmeyer, Nico, Zhao, Xin'Ai, Bouyer, Daniel, Weimer, Annika K., De Winter, Freya, Yang, Fang, Schnittger, Arp (2012) Genetic Framework of Cyclin-Dependent Kinase Function in Arabidopsis. Developmental Cell, 22 (5). pp. 1030-1040. ISSN 1534-5807

Nurenberg, A., Kitzing, T. M., Grosse, R. (2011) Nucleating actin for invasion. Nature Reviews Cancer, 11 (3). pp. 177-187. ISSN 1474-175X

O

O'Connor, B. D., Day, A., Cain, S., Arnaiz, O., Sperling, L., Stein, L. D. (2008) GMODWeb: a web framework for the generic model organism database. Genome Biol, 9 (6). R102.

O'Keefe, R. T., Henderson, S. C., Spector, D. L. (1992) Dynamic organization of DNA replication in mammalian cell nuclei: spatially and temporally defined replication of chromosome-specific alpha-satellite DNA sequences. Journal of Cell Biology, 116 (5). pp. 1095-1110. ISSN 0021-9525

O'Keefe, R. T., Mayeda, A., Sadowski, C. L., Krainer, A. R., Spector, D. L. (1994) Disruption of pre-mRNA splicing in vivo results in reorganization of splicing factors. Journal of Cell Biology, 124 (3). pp. 249-260. ISSN 0021-9525

O'Meara, M. J., Ballouz, S., Shoichet, B. K., Gillis, J. (2016) Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction. PLoS One, 11 (7). e0160098. ISSN 1932-6203 (Electronic)1932-6203 (Linking)

O'Rawe, J., Jiang, T., Sun, G., Wu, Y., Wang, W., Hu, J., Bodily, P., Tian, L., Hakonarson, H., Johnson, W. E., Wei, Z., Wang, K., Lyon, G. J. (2013) Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med, 5 (3). p. 28. ISSN 1756-994X (Print)

O'Rawe, Jason, Fang, Han, Rynearson, Shawn, Robison, Reid J., Kiruluta, Edward S., Higgins, Gerald, Eilbeck, Karen, Reese, Martin G., Lyon, Gholson J. Supplementary video of subject M.A for Integrating precision medicine in the study and clinical treatment of a severely mentally ill person. PeerJ 1:e177. [Video]

O'Rawe, Jason, Fang, Han, Rynearson, Shawn, Robison, Reid J., Kiruluta, Edward S., Higgins, Gerald, Eilbeck, Karen, Reese, Martin G., Lyon, Gholson J. (2013) Integrating precision medicine in the study and clinical treatment of a severely mentally ill person. PeerJ, 1. e177.

O'Rawe, Jason, Jiang, Tao, Sun, Guangqing, Wu, Yiyang, Wang, Wei, Hu, Jingchu, Bodily, Paul, Tian, Lifeng, Hakonarson, Hakon, Johnson, W. Evan, Robison, Reid J., Wei, Zhi, Wang, Kai, Lyon, Gholson J. (2013) Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. In: The Biology of Genomes , May 2013, Cold Spring Harbor Laboratory. (Unpublished)

O'Rawe, Jason, Jiang, Tao, Sun, Guangqing, Wu, Yiyang, Wang, Wei, Hu, Jingchu, Bodily, Paul, Tian, Lifeng, Harkonarson, Hakon, Johnson, W. Evan, Robison, Reid J., Wei, Zhi, Wang, Kai, Lyon, Gholson J. (2013) Toward more accurate variant calling for “personal genomes”. In: ACMG Annual Clinical Genetics Meeting, March 19th-23rd 2013, Phoenix, AZ. (Unpublished)

O'Rawe, Jason, Lyon, Gholson J. (2014) Large pedigrees in human sequencing studies: toward a more resolved and accurate picture of genetic disease. In: 64th Annual Meeting of the American Society of Human Genetics (ASHG), October 2014, San Diego, California. (Unpublished)

O'Rawe, Jason, Lyon, Gholson J. (2014) Large pedigrees in human sequencing studies: toward a more resolved and accurate picture of genetic disease. In: Cold Spring Harbor Laboratory Personal Genomes Meeting, November 2014, Cold Spring Harbor, NY. (Unpublished)

O'Rawe, Jason, Wu, Yiyang, Mittelman, David, Fang, Han, Lyon, Gholson J. (2013) Uncovering genetic components of a previously un-described syndrome. In: Cold Spring Harbor Laboratory: Precision Medicine Meeting, November 2013, Cold Spring Harbor, New York. (Unpublished)

Obad, S., Dos Santos, C. O., Petri, A., Heidenblad, M., Broom, O., Ruse, C., Fu, C., Lindow, M., Stenvang, J., Straarup, E. M., Hansen, H. F., Koch, T., Pappin, D., Hannon, G. J., Kauppinen, S. (2011) Silencing of microRNA families by seed-targeting tiny LNAs. Nature Genetics, 43 (4). pp. 371-380. ISSN 10614036 (ISSN)

Okada, H., Suh, W. K., Jin, J., Woo, M., Du, C., Elia, A., Duncan, G. S., Wakeham, A., Itie, A., Lowe, S. W., Wang, X., Mak, T. W. (2002) Generation and characterization of Smac/DIABLO-deficient mice. Molecular and Cellular Biology, 22 (10). pp. 3509-3517. ISSN 0270-7306

Okunola, H. L., Krainer, A. R. (2009) Cooperative-binding and splicing-repressive properties of hnRNP A1. Mol Cell Biol, 29 (20). pp. 5620-5631.

Oliver, S. L., Lenards, A. J., Barthelson, R. A., Merchant, N., McKay, S. J. (2013) Using the iplant collaborative discovery environment. Current protocols in bioinformatics (SUPPL.). 1.22. ISSN 19343396 (ISSN)

Olsen, R. H., Debusscher, G., McCombie, W. R. (1982) Development of broad-host-range vectors and gene banks: self-cloning of the Pseudomonas aeruginosa PAO chromosome. Journal of Bacteriology, 150 (1). pp. 60-69. ISSN 0021-9193

Olson, A., Klein, R. R., Dugas, D. V., Lu, Z. Y., Regulski, M., Klein, P. E., Ware, D. (2014) Expanding and Vetting Sorghum bicolor Gene Annotations through Transcriptome and Methylome Sequencing. Plant Genome, 7 (2). p. 20. ISSN 1940-3372

Olson, A. J., Brennecke, J., Aravin, A. A., Hannon, G. J., Sachidanandam, R. (2008) Analysis of large-scale sequencing of small RNAs. Pacific Symposium on Biocomputing. pp. 126-136. ISSN 17935091 (ISSN)

Onai, T., FitzGerald, M. G., Arakawa, S., Gocayne, J. D., Urquhart, D. A., Hall, L. M., Fraser, C. M., McCombie, W. R., Venter, J. C. (1989) Cloning, sequence analysis and chromosome localization of a Drosophila muscarinic acetylcholine receptor. FEBS Letters, 255 (2). pp. 219-225. ISSN 00145793 (ISSN)

Ono, T., Losada, A., Hirano, M., Myers, M. P., Neuwald, A. F., Hirano, T. (2003) Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells. Cell, 115 (1). pp. 109-121. ISSN 0092-8674

Ordway, J. M., Bedell, J. A., Citek, R. W., Nunberg, A., Garrido, A., Kendall, R., Stevens, J. R., Cao, D., Doerge, R. W., Korshunova, Y., Holemon, H., McPherson, J. D., Lakey, N., Leon, J., Martienssen, R. A., Jeddeloh, J. A. (2006) Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets. Carcinogenesis, 27 (12). pp. 2409-23. ISSN 0143-3334 (Print)0143-3334 (Linking)

P

Paddison, P. J. (2008) RNA interference in mammalian cell systems. In: RNA Interference. Curr Top Microbiol Immunol, 320 . Springer Verlag, Berlin; New York, pp. 1-19. ISBN 978-3-540-75156-4

Paddison, Patrick J., Hannon, Gregory J. (2004) RNA Interference in Mammals: Journey to the Center of Human Disease. In: Molecular Cancer Therapeutics. John Wiley & Sons, Inc., Hoboken, NJ, pp. 55-72. ISBN 9780471656166

Palmer, L. E., McCombie, W. R. (2002) On the importance of being finished. Genome Biology, 3 (10). 2010.1-2010.4. ISSN 14656906 (ISSN)

Palmer, L. E., Rabinowicz, P. D., O'Shaughnessy, A. L., Balija, V. S., Nascimento, L. U., Dike, S., de la Bastide, M., Martienssen, R. A., McCombie, W. R. (2003) Maize genome sequencing by methylation filtrations. Science, 302 (5653). pp. 2115-2117. ISSN 0036-8075

Pan, X. K., Liu, H., Clarke, J., Jones, J., Bevan, M., Stein, L. (2003) ATIDB: Arabidopsis thaliana insertion database. Nucleic Acids Research, 31 (4). pp. 1245-1251. ISSN 0305-1048

Pappin, D. J. (2012) Talk from Darryl Pappin at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Passini, M. A., Bu, J., Richards, A. M., Kinnecom, C., Sardi, S. P., Stanek, L. M., Hua,  Y., Rigo, F., Matson, J., Hung, G., Kaye, E. M., Shihabuddin, L. S., Krainer, A. R., Bennett, C. F., Cheng, S. H. (2011) Antisense oligonucleotides delivered to the mouse CNS ameliorate symptoms of severe spinal muscular atrophy. Science Translational Medicine, 3 (72). ISSN 19466234 (ISSN)

Paterson, A. H., Bowers, J. E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., Haberer, G., Hellsten, U., Mitros, T., Poliakov, A., Schmutz, J., Spannagl, M., Tang, H., Wang, X., Wicker, T., Bharti, A. K., Chapman, J., Feltus, F. A., Gowik, U., Grigoriev, I. V., Lyons, E., Maher, C. A., Martis, M., Narechania, A., Otillar, R. P., Penning, B. W., Salamov, A. A., Wang, Y., Zhang, L., Carpita, N. C., Freeling, M., Gingle, A. R., Hash, C. T., Keller, B., Klein, P., Kresovich, S., McCann, M. C., Ming, R., Peterson, D. G., Mehboob ur, R., Ware, D. H., Westhoff, P., Mayer, K. F. X., Messing, J., Rokhsar, D. S. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature, 457 (7229). pp. 551-556.

Paul, A., Cai, Y., Atwal, G. S., Huang, Z. J. (2012) Developmental Coordination of Gene Expression between Synaptic Partners During GABAergic Circuit Assembly in Cerebellar Cortex. Frontiers in Neural Circuits, 6. p. 37. ISSN 1662-5110 (Electronic)1662-5110 (Linking)

Paul, S., Kuo, A., Schalch, T., Vogel, H., Joshua-Tor, L., McCombie, W. R., Gozani, O., Hammell, M., Mills, A. A. (2013) Chd5 Requires PHD-Mediated Histone 3 Binding for Tumor Suppression. Cell Reports, 3 (1). pp. 92-102. ISSN 2211-1247

Paus, T., Bernard, M., Chakravarty, M. M., Davey Smith, G., Gillis, J., Lourdusamy, A., Melka, M. G., Leonard, G., Pavlidis, P., Perron, M., Pike, G. B., Richer, L., Schumann, G., Timpson, N., Toro, R., Veillette, S., Pausova, Z. (2012) KCTD8 gene and brain growth in adverse intrauterine environment: A genome-wide association study. Cerebral Cortex, 22 (11). pp. 2634-2642. ISSN 10473211 (ISSN)

Pavlidis, P., Gillis, J. (2012) Progress and challenges in the computational prediction of gene function using networks. F1000 Research, 1. ISSN 20461402 (ISSN)

Pavlovsky, A. G., Liu, X., Faehnle, C. R., Potente, N., Viola, R. E. (2012) Structural characterization of inhibitors with selectivity against members of a homologous enzyme family. Chemical Biology and Drug Design, 79 (1). pp. 128-136. ISSN 17470277 (ISSN)

Pearson, H. B., Perez-Mancera, P. A., Dow, L. E., Ryan, A., Tennstedt, P., Bogani, D., Elsum, I., Greenfield, A., Tuveson, D. A., Simon, R., Humbert, P. O. (2011) SCRIB expression is deregulated in human prostate cancer, and its deficiency in mice promotes prostate neoplasia. Journal of Clinical Investigation, 121 (11). pp. 4257-4267. ISSN 0021-9738

Pedersen, J. S., Bejerano, G., Siepel, A., Rosenbloom, K., Lindblad-Toh, K., Lander, E. S., Kent, J., Miller, W., Haussler, D. (2006) Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol, 2 (4). e33. ISSN 1553-734x

Pendergrast, P. S., Wang, C., Hernandez, N., Huang, S. (2002) FBI-1 can stimulate HIV-1 Tat activity and is targeted to a novel subnuclear domain that includes the Tat-P-TEFb-containing nuclear speckles. Molecular Biology of the Cell, 13 (3). pp. 915-929. ISSN 1059-1524

Pendleton, R. G., Rasheed, A., Sardina, T., Tully, T., Hillman, R. (2002) Effects of tyrosine hydroxylase mutants on locomotor activity in Drosophila: A study in functional genomics. Behavior Genetics, 32 (2). pp. 89-94. ISSN 0001-8244

Penning, B. W., Hunter, C. T., Tayengwa, R., Eveland, A. L., Dugard, C. K., Olek, A. T., Vermerris, W., Koch, K. E., McCarty, D. R., Davis, M. F., Thomas, S. R., McCann, M. C., Carpita, N. C. (2009) Genetic resources for maize cell wall biology. Plant Physiology, 151 (4). pp. 1703-1728.

Perez-Mancera, P. A., Rust, A. G., van der Weyden, L., Kristiansen, G., Li, A., Sarver, A. L., Silverstein, K. A., Grutzmann, R., Aust, D., Rummele, P., Knosel, T., Herd, C., Stemple, D. L., Kettleborough, R., Brosnan, J. A., Li, A., Morgan, R., Knight, S., Yu, J., Stegeman, S., Collier, L. S., ten Hoeve, J. J., de Ridder, J., Klein, A. P., Goggins, M., Hruban, R. H., Chang, D. K., Biankin, A. V., Grimmond, S. M., Wessels, L. F., Wood, S. A., Iacobuzio-Donahue, C. A., Pilarsky, C., Largaespada, D. A., Adams, D. J., Tuveson, D. A. (2012) The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma. Nature, 486 (7402). pp. 266-70. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Perna, D., Karreth, F. A., Rust, A. G., Perez-Mancera, P. A., Rashid, M., Iorio, F., Alifrangis, C., Arends, M. J., Bosenberg, M. W., Bollag, G., Tuveson, D. A., Adams, D. J. (2015) BRAF inhibitor resistance mediated by the AKT pathway in an oncogenic BRAF mouse melanoma model. Proceedings of the National Academy of Sciences of the United States of America, 112 (6). E536-E545. ISSN 0027-8424

Pettersson, U., Ahola, H., Stenlund, A., Bergman, P., Ustav, M., Moreno-Lopez, J. (1986) Organization and expression of the genome of bovine papillomavirus type 1. Ciba Found Symp, 120. pp. 23-38. ISSN 0300-5208 (Print)0300-5208 (Linking)

Phillippy, A. M., Schatz, M. C., Pop, M. (2008) Genome assembly forensics: Finding the elusive mis-assembly. Genome Biology, 9 (3). ISSN 14747596 (ISSN)

Pierce-Shimomura, J. T. , Chen, B. L. , Mun, J. J. , Ho, R., Sarkis, R., McIntire, S. L. (2008) Genetic analysis of crawling and swimming locomotory patterns in C. elegans. Proc Natl Acad Sci U S A, 105 (52). pp. 20982-20987.

Piirsoo, M., Ustav, E., Mandel, T., Stenlund, A., Ustav, M. (1996) Cis and trans requirements for stable episomal maintenance of the BPV-1 replicator. EMBO J, 15 (1). pp. 1-11. ISSN 0261-4189 (Print)0261-4189 (Linking)

Pinard, R., Lambert, D., Heckman, J. E., Esteban, J. A., Gundlach, C. W., Hampel, K. J., Glick, G. D., Walter, N. G., Major, F., Burke, J. M. (2001) The hairpin ribozyme substrate binding-domain: A highly constrained D-shaped conformation. Journal of Molecular Biology, 307 (1). pp. 51-65. ISSN 0022-2836

Pinon, V., Etchells, J. P., Rossignol, P., Collier, S. A., Arroyo, J. M., Martienssen, R. A., Byrne, M. E. (2008) Three PIGGYBACK genes that specifically influence leaf patterning encode ribosomal proteins. Development, 135 (7). pp. 1315-24. ISSN 0950-1991 (Print)0950-1991 (Linking)

Plavskin, Y., Timmermans, M. C. (2013) Small RNA-Regulated Networks and the Evolution of Novel Structures in Plants. Cold Spring Harbor Symposia on Quantitative Biology, 77. ISSN 00917451 (ISSN)

Plummer, P. N., Freeman, R., Taft, R. J., Vider, J., Sax, M., Umer, B. A., Gao, D. C., Johns, C., Mattick, J. S., Wilto, S. D., Ferro, V., McMillan, N. A. J., Swarbrick, A., Mittal, V., Mellick, A. S. (2013) MicroRNAs Regulate Tumor Angiogenesis Modulated by Endothelial Progenitor Cells. Cancer Research, 73 (1). pp. 341-352. ISSN 0008-5472

Png, K. J., Yoshida, M., Zhang, X. H. F., Shu, W., Lee, H., Rimner, A., Chan, T. A., Comen, E., Andrade, V. P., Kim, S. W., King, T. A., Hudis, C. A., Norton, L., Hicks, J. B., Massagué, J., Tavazoie, S. F. (2011) MicroRNA-335 inhibits tumor reinitiation and is silenced through genetic and epigenetic mechanisms in human breast cancer. Genes and Development, 25 (3). pp. 226-231. ISSN 08909369

Popescu, G. V., Noutsos, C., Popescu, S. C. (2016) Big Data in Plant Science: Resources and Data Mining Tools for Plant Genomics and Proteomics. Methods Mol Biol, 1415. pp. 533-547. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Potashkin, J. A., Derby, R. J., Spector, D. L. (1990) Differential distribution of factors involved in pre-mRNA processing in the yeast cell nucleus. Molecular and Cellular Biology, 10 (7). pp. 3524-3534. ISSN 0270-7306

Powell, R. D., Halsey, C. M., Spector, D. L., Kaurin, S. L., McCann, J., Hainfeld, J. F. (1997) A covalent fluorescent-gold immunoprobe: simultaneous detection of a pre-mRNA splicing factor by light and electron microscopy. Journal of Histochemistry and Cytochemistry, 45 (7). pp. 947-956. ISSN 0022-1554

Powers, S., Mu, D. (2008) Genetic similarities between organogenesis and tumorigenesis of the lung. Cell Cycle, 7 (2). 200 - 204 .

Prasanth, S. G., Mendez, J., Prasanth, K. V. , Stillman, B. (2004) Dynamics of pre-replication complex proteins during the cell division cycle. Philos Trans R Soc Lond B Biol Sci, 359 (1441). pp. 7-16. ISSN 0962-8436 (Print)

Premsrirut, P. K., Miething, C., Zuber, J., Yong, K. S., Hannon, G. J., Lowe, S. W. (2009) Conditional Regulation of Tumor Suppressor Genes in Vivo Using Rna Interference. Journal of Investigative Medicine, 57 (3). ISSN 1081-5589

Prior, T. W., Krainer, A. R., Hua, Y., Swoboda, K. J., Snyder, P. C., Bridgeman, S. J., Burghes, A. H. M., Kissel, J. T. (2009) A Positive Modifier of Spinal Muscular Atrophy in the SMN2 Gene. The American Journal of Human Genetics, 85 (3). pp. 408-413.

Prokopenko, I., Zeggini, E., Hanson, R. L., Mitchell, B. D., Rayner, N. W., Akan, P., Baier, L., Das, S. K., Elliott, K. S., Fu, M., Frayling, T. M., Groves, C. J., Gwilliam, R., Scott, L. J., Voight, B. F., Hattersley, A. T., Hu, C., Morris, A. D., Ng, M., Palmer, C. N. A., Tello-Ruiz, M., Vaxillaire, M., Wang, C. R., Stein, L. D., Chan, J., Jia, W. P., Froguel, P., Elbein, S. C., Deloukas, P., Bogardus, C., Shuldiner, A. R., McCarthy, M. I. (2009) Linkage Disequilibrium Mapping of the Replicated Type 2 Diabetes Linkage Signal on Chromosome 1q. Diabetes, 58 (7). pp. 1704-1709. ISSN 0012-1797

Pruitt, R. E., Bowman, J. L., Grossniklaus, U. (2003) Plant genetics: a decade of integration. Nature Genetics, 33. pp. 294-304. ISSN 1061-4036

Q

Quadrana, L., Bortolini Silveira, A., Mayhew, G. F., LeBlanc, C., Martienssen, R. A., Jeddeloh, J. A., Colot, V. (2016) The Arabidopsis thaliana mobilome and its impact at the species level. Elife, 5. ISSN 2050-084X (Electronic)2050-084X (Linking)

R

Rabinowicz, P. D. (2001) Genomics in Latin America: Reaching the Frontiers. Genome Research, 11 (3). pp. 319-322. ISSN 1088-9051

Rabinowicz, P. D., Byrne, M. E. (2001) Follow that plant! Genome Biology, 2 (2). ISSN 1474-7596

Rabinowicz, P. D., Citek, R., Budiman, M. A., Nunberg, A., Bedell, J. A., Lakey, N., O'Shaughnessy, A. L., Nascimento, L. U., McCombie, W. R., Martienssen, R. A. (2005) Differential methylation of genes and repeats in land plants. Genome Research, 15 (10). pp. 1431-1440. ISSN 1088-9051

Rabinowicz, P. D., McCombie, W. R., Martienssen, R. A. (2003) Gene enrichment in plant genomic shotgun libraries. Current Opinion in Plant Biology, 6 (2). pp. 150-156. ISSN 13695266 (ISSN)

Rabinowicz, P. D., Palmer, L. E., May, B. P., Hemann, M. T., Lowe, S. W., McCombie, W. R., Martienssen, R. A. (2003) Genes and transposons are differentially methylated in plants, but not in mammals. Genome Research, 13 (12). pp. 2658-64. ISSN 1088-9051

Rabinowicz, P. D., Scahidanandam, R. (2002) Genomics: More than the sum of the parts. Genome Research, 12 (7). pp. 1015-1016. ISSN 1088-9051

Rabinowicz, P. D., Schutz, K., Dedhia, N., Yordan, C., Parnell, L. D., Stein, L., McCombie, W. R., Martienssen, R. A. (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nature Genetics, 23 (3). pp. 305-308. ISSN 10614036 (ISSN)

Rabinowicz, Pablo D. (2003) Constructing gene-enriched plant genomic libraries using methylation filtration technology. In: Plant functional genomics: methods and protocols. Methods in Molecular Biology, 236 . Humana Press, pp. 21-36.

Ragno, S., Romano, M., Howell, S., Pappin, D. J., Jenner, P. J., Colston, M. J. (2001) Changes in gene expression in macrophages infected with Mycobacterium tuberculosis: a combined transcriptomic and proteomic approach. Immunology, 104 (1). pp. 99-108. ISSN 0019-2805 (Print)0019-2805 (Linking)

Rajan, P., Dalgliesh, C., Carling, P. J., Buist, T., Zhang, C. L., Grellscheid, S. N., Armstrong, K., Stockley, J., Simillion, C., Gaughan, L., Kalna, G., Zhang, M. Q., Robson, C. N., Leung, H. Y., Elliott, D. J. (2011) Identification of Novel Androgen-Regulated Pathways and mRNA Isoforms through Genome-Wide Exon-Specific Profiling of the LNCaP Transcriptome. PLoS ONE, 6 (12). ISSN 1932-6203

Rajaram, M., Li, J., Egeblad, M., Powers, R. S. (2013) System-wide analysis reveals a complex network of tumor-fibroblast interactions involved in tumorigenicity. PLoS Genetics, 9 (9). e1003789. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Rajaram, M., Zhang, J., Wang, T., Li, J., Kuscu, C., Qi, H., Kato, M., Grubor, V., Weil, R. J., Helland, A., Borrenson-Dale, A. L., Cho, K. R., Levine, D. A., Houghton, A. N., Wolchok, J. D., Myeroff, L., Markowitz, S. D., Lowe, S. W., Zhang, M., Krasnitz, A., Lucito, R., Mu, D., Powers, R. S. (2013) Two Distinct Categories of Focal Deletions in Cancer Genomes. PLoS ONE, 8 (6). e66264. ISSN 1932-6203 (Electronic)1932-6203 (Linking)

Ramaswami, G., Lin, W., Piskol, R., Tan, M. H., Davis, C., Li, J. B. (2012) Accurate identification of human Alu and non-Alu RNA editing sites. Nature Methods, 9 (6). 579-+. ISSN 1548-7091

Rasmussen, M. D., Hubisz, M. J., Gronau, I., Siepel, A. (2014) Genome-wide inference of ancestral recombination graphs. PLoS Genetics, 10 (5). e1004342. ISSN 15537390 (ISSN)

Ren, J., Martienssen, R. A. (2012) Silent decision: HP1 protein escorts heterochromatic RNAs to their destiny. Embo Journal, 31 (15). pp. 3237-8. ISSN 0261-4189

Revill, Kate, Wang, Tim, Lachenmayer, Anja, Kojima, Kensuke, Harrington, Andrew, Li, Jinyu, Hoshida, Yujin, Llovet, Josep M., Powers, R. Scott (2013) Genome-wide Methylation Analysis and Epigenetic Unmasking Identify Tumor Suppressor Genes in Hepatocellular Carcinoma. Gastroenterology, 145 (6). pp. 1424-1435. ISSN 0016-5085

Revyakin, A., Allemand, J. F., Croquette, V., Ebright, R. H., Strick, T. R. (2003) Single-molecule DNA nanomanipulation: Detection of promoter-unwinding events by RNA polymerase. In: Rna Polymerases and Associated Factors, Part C. Methods in Enzymology, 370 . Academic Press Inc, San Diego, pp. 577-598. ISBN 0076-6879

Rhind, N., Chen, Z., Yassour, M., Thompson, D. A., Haas, B. J., Habib, N., Wapinski, I., Roy, S., Lin, M. F., Heiman, D. I., Young, S. K., Furuya, K., Guo, Y., Pidoux, A., Chen, H. M., Robbertse, B., Goldberg, J. M., Aoki, K., Bayne, E. H., Berlin, A. M., Desjardins, C. A., Dobbs, E., Dukaj, L., Fan, L., FitzGerald, M. G., French, C., Gujja, S., Hansen, K., Keifenheim, D., Levin, J. Z., Mosher, R. A., Muller, C. A., Pfiffner, J., Priest, M., Russ, C., Smialowska, A., Swoboda, P., Sykes, S. M., Vaughn, M., Vengrova, S., Yoder, R., Zeng, Q., Allshire, R., Baulcombe, D., Birren, B. W., Brown, W., Ekwall, K., Kellis, M., Leatherwood, J., Levin, H., Margalit, H., Martienssen, R., Nieduszynski, C. A., Spatafora, J. W., Friedman, N., Dalgaard, J. Z., Baumann, P., Niki, H., Regev, A., Nusbaum, C. (2011) Comparative functional genomics of the fission yeasts. Science, 332 (6032). pp. 930-6. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Rigo, F., Hua, Y. M., Chun, S. J., Prakash, T. P., Krainer, A. R., Bennett, C. F. (2012) Synthetic oligonucleotides recruit ILF2/3 to RNA transcripts to modulate splicing. Nature Chemical Biology, 8 (6). pp. 555-561. ISSN 1552-4450

Rigo, F., Hua, Y. M., Krainer, A. R., Bennett, C. F. (2012) Antisense-based therapy for the treatment of spinal muscular atrophy. Journal of Cell Biology, 199 (1). pp. 21-25. ISSN 0021-9525

Robert, F., Carrier, M., Rawe, S., Chen, S., Lowe, S. W., Pelletier, J. (2009) Altering chemosensitivity by modulating translation elongation. PLoS ONE, 4 (5). e5428.

Robinson, S., Tang, L., Mooney, B., McKay, S. J., Clarke, W., Links, M., Karcz, S., Regan, S., Wu, Y.-Y., Gruber, M., Cui, D., Yu, M., Parkin, I. (2009) An archived activation tagged population of Arabidopsis thaliana to facilitate forward genetics approaches. BMC Plant Biology, 9 (1). p. 101. ISSN 1471-2229

Robledo, R., Orru, S., Sidoti, A., Muresu, R., Esposito, D., Grimaldi, M. C., Carcassi, C., Rinaldi, A., Bernini, L., Contu, L., Romani, M., Roe, B., Siniscalco, M. (2002) A 9.1-kb gap in the genome reference map is shown to be a stable deletion/insertion polymorphism of ancestral origin. Genomics, 80 (6). pp. 585-592. ISSN 0888-7543

Roca, X., Akerman, M., Gaus, H., Berdeja, A., Bennett, C. F., Krainer, A. R. (2012) Widespread recognition of 5' splice sites by noncanonical base-pairing to U1 snRNA involving bulged nucleotides. Genes & Development, 26 (10). pp. 1098-109. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Roca, X., Karginov, F. V. (2012) RNA biology in a test tubeuan overview of in vitro systems/assays. Wiley Interdisciplinary Reviews-Rna, 3 (4). pp. 509-527. ISSN 1757-7004

Roca, X., Krainer, A. R. (2009) Recognition of atypical 5' splice sites by shifted base-pairing to U1 snRNA. Nat Struct Mol Biol, 16 (2). pp. 176-182.

Roca, X., Krainer, A. R. (2009) A splicing component adapted to gene silencing. Nat Biotechnol, 27 (3). pp. 250-1. ISSN 1546-1696 (Electronic)1087-0156 (Linking)

Roca, X., Krainer, A. R., Eperon, I. C. (2013) Pick one, but be quick: 5′ splice sites and the problems of too many choices. Genes and Development, 27 (2). pp. 129-144. ISSN 08909369 (ISSN)

Roca, X., Olson, A. J., Rao, A. R., Enerly, E., Kristensen, V. N., Borresen-Dale, A. L., Andresen, B. S., Krainer, A. R., Sachidanandam, R. (2008) Features of 5'-splice-site efficiency derived from disease-causing mutations and comparative genomics. Genome Res, 18 (1). pp. 77-87.

Roca, X., Sachidanandam, R., Krainer, A. R. (2003) Intrinsic differences between authentic and cryptic 5 ' splice sites. Nucleic Acids Research, 31 (21). pp. 6321-6333. ISSN 0305-1048

Rogers, A., Antoshechkin, I., Bieri, T., Blasiar, D., Bastiani, C., Canaran, P., Chan, J., Chen, W. J., Davis, P., Fernandes, J., Fiedler, T. J., Han, M. , Harris, T. , Kishore, R., Lee, R., McKay, S. J., Muller, H. M., Nakamura, C., Ozersky, P., Petcherski, A., Schindelman, G., Schwarz, E. M., Spooner, W., Tuli, M. A., Auken, K. V., Wang, D., Wang, X., Williams, G., Yook, K., Durbin, R., Stein, L. D., Spieth, J., Sternberg, P. W. (2008) WormBase 2007. Nucl. Acids Res., 36 (Databa). D612-7.

Rogers, J., Rubin, E., Stewart, D., Stillman, B. (2003) The Genome of Homo Sapiens. In: Cold Spring Harbor Symposia on Quantitative Biology LXVIII: The Genome of Homo Sapiens, Cold Spring Harbor.

Rosenfeld, J. A., Wang, Z., Schones, D. E., Zhao, K., DeSalle, R., Zhang, M. Q. (2009) Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics, 10 (1). p. 143. ISSN 1471-2164

Rosenfeld, J. A., Xuan, Z., Desalle, R. (2009) Investigating repetitively matching short sequencing reads: The enigmatic nature of H3K9me3. Epigenetics, 4 (7).

Rossmann, M. P., Stillman, B. (2013) Immunoblotting histones from yeast whole-cell protein extracts. Cold Spring Harbor Protocols, 2013 (7). ISSN 1559-6095

Rothstein, J. L., Johnson, D., Jessee, J., Skowronski, J., Deloia, J. A., Solter, D., Knowles, B. B. (1993) Construction of Primary and Subtracted Cdna Libraries from Early Embryos. In: Guide to Techniques in Mouse Development (Methods in Enzymology. Methods in Enzymology, 225 . Academic Press Inc, San Diego, pp. 587-610. ISBN 0076-6879

Rozhkov, N. V., Hammell, M., Hannon, G. J. (2013) Multiple roles for Piwi in silencing Drosophila transposons. Genes and Development, 27 (4). pp. 400-412. ISSN 08909369 (ISSN)

Rozhkov, N. V., Schostak, N. G., Zelentsova, E. S., Yushenova, I. A., Zatsepina, O. G., Evgen'ev, M. B. (2013) Evolution and Dynamics of Small RNA Response to a Retroelement Invasion in Drosophila. Molecular Biology and Evolution, 30 (2). pp. 397-408. ISSN 0737-4038

Ruiz, C., Li, J., Luttgen, M. S., Kolatkar, A., Kendall, J. T., Flores, E., Topp, Z., Samlowski, W. E., McClay, E., Bethel, K., Ferrone, S., Hicks, J., Kuhn, P. (2015) Limited genomic heterogeneity of circulating melanoma cells in advanced stage patients. Physical biology, 12 (1). 016008. ISSN 1478-3967

Ruse, C. I., Peacock, S., Ghiban, C., Rivera, K., Pappin, D. J., Leopold, P. (2013) A tool to evaluate correspondence between extraction ion chromatographic peaks and peptide-spectrum matches in shotgun proteomics experiments. Proteomics, 13 (16). pp. 2386-2397. ISSN 1615-9861 (Electronic)1615-9853 (Linking)

Rustchenko-Bulgac, E. P., Sherman, F., Hicks, J. B. (1990) Chromosomal rearrangements associated with morphological mutants provide a means for genetic variation of Candida albicans. Journal of Bacteriology, 172 (3). pp. 1276-1283. ISSN 00219193 (ISSN)

Ruzinova, M. B., Schoer, R. A., Gerald, W., Egan, J. E., Pandolfi, P. P., Rafii, S., Manova, K., Mittal, V., Benezra, R. (2003) Effect of angiogenesis inhibition by Id loss and the contribution of bone-marrow-derived endothelial cells in spontaneous murine tumors. Cancer Cell, 4 (4). pp. 277-289. ISSN 1535-6108

Rye, I. H., Lundin, P., Maner, S., Fjelldal, R., Naume, B., Wigler, M., Hicks, J., Borresen-Dale, A. L., Zetterberg, A., Russnes, H. G. (2015) Quantitative multigene FISH on breast carcinomas identifies der(1;16)(q10;p10) as an early event in luminal A tumors. Genes, Chromosomes & Cancer, 54 (4). pp. 235-48. ISSN 1045-2257

Ryu, S., Joshi, N., McDonnell, K., Woo, J., Choi, H., Gao, D., McCombie, W. R., Mittal, V. (2011) Discovery of novel human breast cancer micrornas from deep sequencing data by analysis of pri-microrna secondary structures. PLoS ONE, 6 (2).

S

Saavedra, C. A., Hammell, C. M., Heath, C. V., Cole, C. N. (1997) Yeast heat shock mRNAs are exported through a distinct pathway defined by Rip1p. Genes and Development, 11 (21). pp. 2845-2856. ISSN 08909369 (ISSN)

Sabin, L. R., Cherry, S. (2013) Small creatures use small RNAs to direct antiviral defenses. European Journal of Immunology, 43 (1). pp. 27-33. ISSN 1521-4141 (Electronic)0014-2980 (Linking)

Sabin, L. R., Delas, M. J., Hannon, G. J. (2013) Dogma derailed: the many influences of RNA on the genome. Molecular Cell, 49 (5). pp. 783-94. ISSN 1097-2765

Sabin, L. R., Zheng, Q., Thekkat, P., Yang, J., Hannon, G. J., Gregory, B. D., Tudor, M., Cherry, S. (2013) Dicer-2 Processes Diverse Viral RNA Species. PLoS ONE, 8 (2). ISSN 19326203 (ISSN)

Sabot, F., Picault, N., Elbaidouri, M., Llauro, C., Chaparro, C., Piegu, B., Roulin, A., Guiderdoni, E., Delabastide, M., McCombie, W. R., Panaud, O. (2011) Transpositional landscape of rice genome revealed by Paired-End Mapping of high-throughput resequencing data. Plant Journal, 66 (2). pp. 241-246. ISSN 0960-7412

Sachidanandam, R., Weissman, D., Schmidt, S. C., Kakol, J. M., Stein, L. D., Marth, G., Sherry, S., Mullikin, J. C., Mortimore, B. J., Willey, D. L., Hunt, S. E., Cole, C. G., Coggill, P. C., Rice, C. M., Ning, Z., Rogers, J., Bentley, D. R., Kwok, P. Y., Mardis, E. R., Yeh, R. T., Schultz, B., Cook, L., Davenport, R., Dante, M., Fulton, L., Hillier, L., Waterston, R. H., McPherson, J. D., Gilman, B., Schaffner, S., Van Etten, W. J., Reich, D., Higgins, J., Daly, M. J., Blumenstiel, B., Baldwin, J., Stange-Thomann, N., Zody, M. C., Linton, L., Lander, E. S., Altshuler, D. (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature, 409 (6822). pp. 928-33.

Sahashi, K., Hua, Y., Ling, K. K., Hung, G., Rigo, F., Horev, G., Katsuno, M., Sobue, G., Ko, C. P., Bennett, C. F., Krainer, A. R. (2012) TSUNAMI: an antisense method to phenocopy splicing-associated diseases in animals. Genes Dev, 26 (16). pp. 1874-84. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Salzberg, S. L., Sommer, D. D., Schatz, M. C., Phillippy, A. M., Rabinowicz, P. D., Tsuge, S., Furutani, A., Ochiai, H., Delcher, A. L., Kelley, D., Madupu, R., Puiu, D., Radune, D., Shumway, M., Trapnell, C., Aparna, G., Jha, G., Pandey, A., Patil, P. B., Ishihara, H., Meyer, D. F., Szurek, B., Verdier, V., Koebnik, R., Maxwell, J. M., Ryan, R. P., Hirata, H., Tsuyumu, S., Won Lee, S., Ronald, P. C., Sonti, R. V., Van Sluys, M. A., Leach, J. E., White, F. F., Bogdanove, A. J. (2008) Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics, 9. ISSN 1471-2164

Sangha, N., Wu, R., Kuick, R., Powers, S., Mu, D., Fiander, D., Yuen, K., Katabuchi, H., Tashiro, H., Fearon, E. R., Cho, K. R. (2008) Neurofibromin 1 (NF1) defects are common in human ovarian serous carcinomas and co-occur with TP53 mutations. Neoplasia, 10 (12). pp. 1362-72.

Sanyal, M. K., Sachidanadam, R., Pant, D., Rao, A. R., Wang, S., Santella, R. M. (2008) Mutation sensitive nucleic acid sequence motifs to polynuclear aromatic hydrocarbon (PAH) in insulin like growth factor (IGF1) gene of human placenta. Placenta, 29 (8). A36-A36. ISSN 0143-4004

Saw, J. H. W., Schatz, M., Brown, M. V., Kunkel, D. D., Foster, J. S., Shick, H., Christensen, S., Hou, S., Wan, X., Donachie, S. P. (2013) Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kīlauea Caldera, Hawai'i. PLoS ONE, 8 (10). ISSN 19326203 (ISSN)

Sawey, E. T., Chanrion, M., Cai, C., Wu, G., Zhang, J., Zender, L., Zhao, A., Busuttil, R. W., Yee, H., Stein, L. D., French, D. M., Finn, Richard S, Lowe, S. W., Powers, S. (2011) Identification of a Therapeutic Strategy Targeting Amplified FGF19 in Liver Cancer by Oncogenomic Screening. Cancer Cell, 19 (3). pp. 347-358. ISSN 1535-6108

Scanlon, M. J., Ohtsu, K., Timmermans, M. C. P., Schnable, P. S. (2009) Laser microdissection-mediated isolation and in vitro transcriptional amplification of plant RNA. Current Protocols in Molecular Biology (SUPPL.). 25A.3.1-25A.3.15.

Scanlon, M. J., Timmermans, M. (2013) Growth and development: from genes to networks and a mechanistic understanding of plant development. Current Opinion in Plant Biology, 16 (1). pp. 1-4. ISSN 1369-5266

Schaniel, C., Ang, Y. S., Ratnakumar, K., Cormier, C., James, T., Bernstein, E., Lemischka, I. R., Paddison, P. J. (2009) Smarcc1/Baf155 couples self-renewal gene repression with changes in chromatin structure in mouse embryonic stem cells. Stem Cells, 27 (12). pp. 2979-2991.

Schatz, M. C. (2009) CloudBurst: Highly sensitive read mapping with MapReduce. Bioinformatics, 25 (11). pp. 1363-1369. ISSN 13674803 (ISSN)

Schatz, M. C. (2012) Talk from Mike Schatz at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Schatz, M. C., Langmead, B. (2013) THE DNA DATA DELUGE FAST, EFFICIENT GENOME-SEQUENCING MACHINES ARE SPEWING OUT MORE DATA THAN GENETICISTS CAN ANALYZE. IEEE Spectrum, 50 (7). pp. 28-33. ISSN 0018-9235

Schatz, M. C., Phillippy, A. M., Shneiderman, B., Salzberg, S. L. (2007) Hawkeye: An interactive visual analytics tool for genome assemblies. Genome Biology, 8 (3). ISSN 14747596 (ISSN)

Schatz, M. C., Phillippy, A. M., Sommer, D. D., Delcher, A. L., Puiu, D., Narzisi, G., Salzberg, S. L., Pop, M. (2013) Hawkeye and AMOS: Visualizing and assessing the quality of genome assemblies. Briefings in Bioinformatics, 14 (2). pp. 213-224. ISSN 14675463

Schatz, M. C., Trapnell, C., Delcher, A. L., Varshney, A. (2007) High-throughput sequence alignment using Graphics Processing Units. Bmc Bioinformatics, 8. ISSN 14712105 (ISSN)

Scheinfeldt, L. B., Soi, S., Thompson, S., Ranciaro, A., Woldemeskel, D., Beggs, W., Lambert, C., Jarvis, J. P., Abate, D., Belay, G., Tishkoff, S. A. (2012) Genetic adaptation to high altitude in the Ethiopian highlands. Genome Biology, 13 (1). R1. ISSN 1474-7596

Schlabach, M. R., Luo, J., Solimini, N. L., Hu, G., Xu, Q. K., Li, M. Z., Zhao, Z. M., Smogorzewska, A., Sowa, M. E., Ang, X. L. L., Westbrook, T. F., Liang, A. C., Chang, K., Hackett, J. A., Harper, J. W., Hannon, G. J., Elledge, S. J. (2008) Cancer proliferation gene discovery through functional Genomics. Science, 319 (5863). pp. 620-624. ISSN 0036-8075

Schlesinger, F., Smith, A. D., Gingeras, T. R., Hannon, G. J., Hodges, E. (2013) De novo DNA demethylation and non-coding transcription define active intergenic regulatory elements. Genome Research, 23 (10). pp. 1601-1614. ISSN 10889051 (ISSN)

Schmidt, C. J., Romanov, M., Ryder, O., Magrini, V., Hickenbotham, M., Glasscock, J., McGrath, S., Mardis, E., Stein, L. D. (2008) Gallus GBrowse: a unified genomic database for the chicken. Nucleic Acids Res, 36 (Databa). D719-23.

Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T. A., Minx, P., Reily, A. D., Courtney, L., Kruchowski, S. S., Tomlinson, C., Strong, C., Delehaunty, K., Fronick, C., Courtney, B., Rock, S. M., Belter, E., Du, F., Kim, K., Abbott, R. M., Cotton, M., Levy, A., Marchetto, P., Ochoa, K., Jackson, S. M., Gillam, B., Chen, W., Yan, L., Higginbotham, J., Cardenas, M., Waligorski, J., Applebaum, E., Phelps, L., Falcone, J., Kanchi, K., Thane, T., Scimone, A., Thane, N., Henke, J., Wang, T., Ruppert, J., Shah, N., Rotter, K., Hodges, J., Ingenthron, E., Cordes, M., Kohlberg, S., Sgro, J., Delgado, B., Mead, K., Chinwalla, A., Leonard, S., Crouse, K., Collura, K., Kudrna, D., Currie, J., He, R., Angelova, A., Rajasekar, S., Mueller, T., Lomeli, R., Scara, G., Ko, A., Delaney, K., Wissotski, M., Lopez, G., Campos, D., Braidotti, M., Ashley, E., Golser, W., Kim, H., Lee, S., Lin, J., Dujmic, Z., Kim, W., Talag, J., Zuccolo, A., Fan, C., Sebastian, A., Kramer, M., Spiegel, L., Nascimento, L., Zutavern, T., Miller, B., Ambroise, C., Muller, S., Spooner, W., Narechania, A., Ren, L., Wei, S., Kumari, S., Faga, B., Levy, M. J., McMahan, L., Van Buren, P., Vaughn, M. W. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science, 326 (5956). pp. 1112-5. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Scholl, R., Sachs, M. M., Ware, D. (2003) Maintaining collections of mutants for plant functional genomics. Methods in Molecular Biology, 236. pp. 311-26. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Schumann, G., Rujescu, D., Kissling, C., Soyka, M., Dahmen, N., Preuss, U. W., Wieman, S., Depner, M., Wellek, S., Lascorz, J., Bondy, B., Giegling, I., Anghelescu, I., Cowen, M. S., Poustka, A., Spanagel, R., Mann, K., Henn, F. A., Szegedi, A. (2003) Analysis of genetic variations of protein tyrosine kinase fyn and their association with alcohol dependence in two independent cohorts. Biol Psychiatry, 54 (12). pp. 1422-6. ISSN 0006-3223 (Print)0006-3223 (Linking)

Schwab, R., Maizel, A., Ruiz-Ferrer, V., Garcia, D., Bayer, M., Crespi, M., Voinnet, O., Martienssen, R. A. (2009) Endogenous TasiRNAs mediate non-cell autonomous effects on gene regulation in Arabidopsis thaliana. PloS one, 4 (6). e5980. ISSN 1932-6203 (Electronic)1932-6203 (Linking)

Scorer, C. A., Clare, J. J., McCombie, W. R., Romanos, M. A., Sreekrishna, K. (1994) Rapid selection using G418 of high copy number transformants of Pichia pastoris for high-level foreign gene expression. Nature Biotechnology, 12 (2). pp. 181-184. ISSN 10870156 (ISSN)

Scott, C. L., Gil, J., Hernando, E., Teruya-Feldstein, J., Narita, M., Martinez, D., Visakorpi, T., Mu, D., Cordon-Cardo, C., Peters, G., Beach, D., Lowe, S. W. (2007) Role of the chromobox protein CBX7 in lymphomagenesis. Proc Natl Acad Sci U S A, 104 (13). pp. 5389-94. ISSN 0027-8424 (Print)

Screaton, G. R., Caceres, J. F., Mayeda, A., Bell, M. V., Plebanski, M., Jackson, D. G., Bell, J. I., Krainer, A. R. (1995) Identification and characterization of three members of the human SR family of pre-mRNA splicing factors. EMBO Journal, 14 (17). pp. 4336-4349. ISSN 0261-4189

Scuoppo, C., Miething, C., Lindqvist, L., Reyes, J., Ruse, C., Appelmann, I., Yoon, S., Krasnitz, A., Teruya-Feldstein, J., Pappin, D., Pelletier, J., Lowe, S. W. (2012) A tumour suppressor network relying on the polyamine-hypusine axis. Nature, 487 (7406). pp. 244-8. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Seaver, S. M., Gerdes, S., Frelin, O., Lerma-Ortiz, C., Bradbury, L. M., Zallot, R., Hasnain, G., Niehaus, T. D., El Yacoubi, B., Pasternak, S., Olson, R., Pusch, G., Overbeek, R., Stevens, R., de Crecy-Lagard, V., Ware, D., Hanson, A. D., Henry, C. S. (2014) High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. Proceedings of the National Academy of Sciences of the United States of America, 111 (26). pp. 9645-9650. ISSN 0027-8424

Sebat, J., Lakshmi, B., Troge, J. E., Alexander, J., Young, J., Lundin, P., Maner, S., Massa, H., Walker, M., Chi, M., Navin, N. E., Lucito, R., Healy, J., Hicks, J. B., Ye, K., Reiner, A., Gilliam, T. C., Trask, B., Patterson, N., Zetterberg, A., Wigler, M. H. (2004) Large-scale copy number polymorphism in the human genome. Science, 305 (5683). pp. 525-8. ISSN 1095-9203 (Electronic)

Sebat, J., Levy, D. L., McCarthy, S. E. (2009) Rare structural variants in schizophrenia: one disorder, multiple mutations; one mutation, multiple disorders. Trends Genet.

Sebat, J. L., Colwell, F. S., Crawford, R. L. (2003) Metagenomic profiling: microarray analysis of an environmental genomic library. Applied and Environmental Microbiology, 69 (8). pp. 4927-34. ISSN 00992240 (ISSN)

Seeger, G., Schloss, P., Schmidt, M. H., Ruter-Jungfleisch, A., Henn, F. A. (2004) Gene-environment interaction in hyperkinetic conduct disorder (HD + CD) as indicated by season of birth variations in dopamine receptor (DRD4) gene polymorphism. Neurosci Lett, 366 (3). pp. 282-6. ISSN 0304-3940 (Print)0304-3940 (Linking)

Segal, N. H., Pavlidis, P., Antonescu, C. R., Maki, R. G., Noble, W. S., DeSantis, D., Woodruff, J. M., Lewis, J. J., Brennan, M. F., Houghton, A. N., Cordon-Cardo, C. (2003) Classification and subtype prediction of adult soft tissue sarcoma by functional genomics. Am J Pathol, 163 (2). pp. 691-700. ISSN 0002-9440 (Print)0002-9440 (Linking)

Senturk, S., Shirole, N. H., Nowak, D. G., Corbo, V., Pal, D., Vaughan, A., Tuveson, D. A., Trotman, L. C., Kinney, J. B., Sordella, R. (2017) Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization. Nat Commun, 8. p. 14370. ISSN 2041-1723

Sever, R., Glass, C. K. (2013) Signaling by nuclear receptors. Cold Spring Harbor Perspectives in Biology, 5 (3). ISSN 1943-0264 (Electronic)

Shanmugam, M., Hernandez, N. (2008) Mitotic Functions for SNAP45, a Subunit of the Small Nuclear RNA-activating Protein Complex SNAPc. J Biol Chem, 283 (21). pp. 14845-56.

Shen, M. L., Eyras, E., Wu, J., Khanna, A., Josiah, S., Rederstorff, M., Zhang, M. Q., Stamm, S. (2011) Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression. Nucleic Acids Research, 39 (22). pp. 9720-9730. ISSN 0305-1048

Shi, L., Guo, Y., Dong, C., Huddleston, J., Yang, H., Han, X., Fu, A., Li, Q., Li, N., Gong, S., Lintner, K. E., Ding, Q., Wang, Z., Hu, J., Wang, D., Wang, F., Wang, L., Lyon, G. J., Guan, Y., Shen, Y., Evgrafov, O. V., Knowles, J. A., Thibaud-Nissen, F., Schneider, V., Yu, C. Y., Zhou, L., Eichler, E. E., So, K. F., Wang, K. (2016) Long-read sequencing and de novo assembly of a Chinese genome. Nat Commun, 7. p. 12065. ISSN 2041-1723 (Electronic)2041-1723 (Linking)

Shi, L., Zhang, X., Golhar, R., Otieno, F. G., He, M., Hou, C., Kim, C., Keating, B., Lyon, G. J., Wang, K., Hakonarson, H. (2013) Whole-genome sequencing in an autism multiplex family. Molecular Autism, 4 (1). p. 8. ISSN 2040-2392 (Electronic)

Shi, Y., Alpatov, R., Wagner, U., Nakamoto-Kinoshita, M., Ye, Z., Luu, Y., Armache, K. J., Simon, M. D., Stuetzer, A., Greer, E. L., Wang, Z. B., Hu, G. Q., Wu, F. Z., Xu, C., Beavers, W. N., Guo, Y. H., Bian, C. B., Morrison, P. T., Vakoc, C. R., Min, J. R., Fischle, W., Kingston, R. E., Zhao, K. J., Ren, B., Warren, S. T. (2012) The fragile X mental retardation protein FMRP plays a role in the DNA damage response. Faseb Journal, 26. ISSN 0892-6638

Shi, J., Whyte, W. A., Zepeda-Mendoza, C. J., Milazzo, J. P., Shen, C., Roe, J. S., Minder, J. L., Mercan, F., Wang, E., Eckersley-Maslin, M. A., Campbell, A. E., Kawaoka, S., Shareef, S., Zhu, Z., Kendall, J., Muhar, M., Haslinger, C., Yu, M., Roeder, R. G., Wigler, M. A., Blobel, G. A., Zuber, J., Spector, D. L., Young, R. A., Vakoc, C. R. (2013) Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation. Genes and Development, 27 (24). pp. 264-273. ISSN 08909369 (ISSN)

Shi, L, Li, Bingbin, Huang, Y., Liu, T, Lyon, Gholson J., Xu, A, Wang, Kai (2014) "Genotype-first" approaches on a curious case of idiopathic progressive cognitive decline. BMC Med Genomics, 7 (1). p. 66.

Shi, L., Wang, J., Hong, F., Spector, D. L., Fang, Y. (2011) Four amino acids guide the assembly or disassembly of Arabidopsis histone H3.3-containing nucleosomes. Proceedings of the National Academy of Sciences of the United States of America, 108 (26). pp. 10574-10578. ISSN 0027-8424

Shimabukuro, K., Yasuda, R., Muneyuki, E., Hara, K. Y., Kinosita, K., Yoshida, M. (2003) Catalysis and rotation of F-1 motor: Cleavage of ATP at the catalytic site occurs in 1 ms before 40 degrees substep rotation. Proceedings of the National Academy of Sciences of the United States of America, 100 (25). pp. 14731-14736. ISSN 0027-8424

Shimokawa, T., Mohammed Ferdous-Ur, Rahman, Tostar, U., Sonkoly, E., Ståhle, M., Pivarcsi, A., Palaniswamy, R., Zaphiropoulos, P. G. (2013) RNA editing of the GLI1 transcription factor modulates the output of Hedgehog signaling. Rna Biology, 10 (2). pp. 321-333. ISSN 15476286 (ISSN)

Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., Weinstock, G. M., Wilson, R. K., Gibbs, R. A., Kent, W. J., Miller, W., Haussler, D. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res, 15 (8). pp. 1034-50. ISSN 1088-9051 (Print)1088-9051

Silva, J. M., Marran, K., Parker, J. S., Silva, J., Golding, M., Schlabach, M. R., Elledge, S. J., Hannon, G. J., Chang, K. (2008) Profiling essential genes in human mammary cells by multiplex RNAi screening. Science, 319 (5863). pp. 617-20.

Sinclair, A. M., Rogers, N., Busse, L., Archibeque, I., Brown, W., Kassner, P. D., Watson, J. E. V., Arnold, G. E., Nguyen, K. C. Q., Powers, S., Elliott, S. (2008) Erythropoietin receptor transcription is neither elevated nor predictive of surface expression in human tumour cells. British Journal of Cancer, 98 (6). pp. 1059-1067. ISSN 0007-0920

Singh, N. K., Raghuvanshi, S., Srivastava, S. K., Gaur, A., Pal, A. K., Dalal, V., Singh, A., Ghazi, I. A., Bhargav, A., Yadav, M., Dixit, A., Batra, K., Gaikwad, K., Sharma, T. R., Mohanty, A., Bharti, A. K., Kapur, A., Gupta, V., Kumar, D., Vij, S., Vydianathan, R., Khurana, P., Sharma, S., McCombie, W. R., Messing, J., Wing, R., Sasaki, T., Mohapatra, T., Khurana, J. P., Tyagi, A. K. (2004) Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny. Functional and Integrative Genomics, 4 (2). pp. 102-117. ISSN 1438793X (ISSN)

Singh, R., Ong-Abdullah, M., Low, E. T. L., Manaf, M. A. A., Rosli, R., Nookiah, R., Ooi, L. C. L., Ooi, S. E., Chan, K. L., Halim, M. A., Azizi, N., Nagappan, J., Bacher, B., Lakey, N., Smith, S. W., He, D., Hogan, M., Budiman, M. A., Lee, E. K., Desalle, R., Kudrna, D., Goicoechea, J. L., Wing, R. A., Wilson, R. K., Fulton, R. S., Ordway, J. M., Martienssen, R. A., Sambanthamurthi, R. (2013) Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature, 500 (7462). pp. 335-339. ISSN 00280836

Slotkin, R. K., Vaughn, M., Borges, F., Tanurdzic, M., Becker, J. D., Feijo, J. A., Martienssen, R. A. (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell, 136 (3). pp. 461-72. ISSN 1097-4172 (Electronic)0092-8674 (Linking)

Smith, A. D., Chung, W. Y., Hodges, E., Kendall, Jude T., Hannon, G. J., Hicks, J. B., Xuan, Z., Zhang, M. Q. (2009) Updates to the RMAP short-read mapping software. Bioinformatics, 25 (21). pp. 2841-2842.

Smith, A. D., Xuan, Z. Y., Zhang, M. Q. (2008) Using quality scores and longer reads improves accuracy of Solexa read mapping. Bmc Bioinformatics, 9 (128). ISSN 1471-2105

Smith, P. J., Spurrell, E. L., Coakley, J., Hinds, C. J., Ross, R. J. M., Krainer, A. R., Chew, S. L. (2002) An exonic splicing enhancer in human IGF-I pre-mRNA mediates recognition of alternative exon 5 by the serine-arginine protein splicing factor-2/alternative splicing factor. Endocrinology, 143 (1). pp. 146-154. ISSN 0013-7227

Smith, H. C., Ochs, R. L., Fernandez, E. A., Spector, D. L. (1986) Macromolecular domains containing nuclear protein p107 and U-snRNP protein p28: further evidence for an in situ nuclear matrix. Molecular and Cellular Biology, 70 (2). pp. 151-168. ISSN 0270-7306

Smolka, M., Rescheneder, P., Schatz, M. C., von Haeseler, A., Sedlazeck, F. J. (2015) Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol, 16 (1). p. 235. ISSN 1474-760X (Electronic)1474-7596 (Linking)

Sordella, R. (2012) Talk from Raffaella Sordella at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Sordella, R., Classon, M., Hu, K. Q., Matheson, S., Brouns, M., Fine, B., Yamada, Y., Settleman, J. (2001) Modulation of CREB activity by the Rho GTPase determines cell size during embryonic development. Molecular Biology of the Cell, 12 (Supple). 401A-402A. ISSN 1059-1524

Sordella, R., Jiang, W., Ligeti, E., Settleman, J. (2005) Regulation of p190 RhoGAP function. Febs Journal, 272. p. 324. ISSN 1742-464X

Sounni, N. E., Dehne, K., Van Kempen, L., Egeblad, M., Affara, N. I., Cuevas, I., Wiesen, J., Junankar, S., Korets, L., Lee, J., Shen, J., Morrison, C. J., Overall, C. M., Krane, S. M., Werb, Z., Boudreau, N., Coussens, L. M. (2010) Stromal regulation of vessel stability by MMP14 and TGFbeta. Disease Models and Mechanisms, 3 (5-6). pp. 317-332. ISSN 17548403 (ISSN)

Spector, D. L. (1990) Higher order nuclear organization: three-dimensional distribution of small nuclear ribonucleoprotein particles. Proceedings of the National Academy of Sciences of the United States of America, 87 (1). pp. 147-151. ISSN 0027-8424

Spector, D. L. (1996) Nuclear organization and gene expression. Experimental Cell Research, 229 (2). pp. 189-197. ISSN 0014-4827

Spector, D. L. (2004) Visualizing the central dogma in living cells: DNA -> RNA -> protein. Faseb Journal, 18 (8). C312-C312. ISSN 0892-6638

Spector, D. L., Fu, X. D., Maniatis, T. (1991) Associations between distinct pre-mRNA splicing components and the cell nucleus. Embo Journal, 10 (11). pp. 3467-3481. ISSN 0261-4189

Spector, D. L., Landon, S., O'Keefe, R. T. (1993) Organization of RNA polymerase II transcription and pre-mRNA splicing within the mammalian cell nucleus. Biochemical Society Transactions, 21 (4). pp. 918-920. ISSN 03005127 (ISSN)

Spector, D. L., Lark, G., Huang, S. (1992) Differences in snRNP localization between transformed and nontransformed cells. Molecular Biology of the Cell, 3 (5). pp. 555-569. ISSN 1059-1524

Spector, D. L., O'Keefe, R. T., Jimenez-Garcia, L. F. (1993) Dynamics of transcription and pre-mRNA splicing within the mammalian cell nucleus. Cold Spring Harbor Symposia on Quantitative Biology, 58. pp. 799-805. ISSN 00917451 (ISSN)

Spooner, W., Youens-Clark, K., Staines, D., Ware, D. (2012) GrameneMart: the BioMart data portal for the Gramene project. Database (Oxford), 2012. ISSN 1758-0463 (Electronic)

Spruck, C. H., Smith, A. P. L., Reed, S. E., Sangfelt, O., Keck, J., Strohmaier, H., Mendez, J., Widschwendter, M., Stillman, B., Zetterberg, A., Reed, S. I. (2005) Deregulation of cyclin E and genomic instability. In: International Symposium on Hormonal Carcinogenesis IV, Valencia, Spain.

Sreekrishna, K., Potenz, R. H. B., Cruze, J. A., McCombie, W. R., Parker, K. A., Nelles, L., Mazzaferro, P. K., Holden, K. A., Harrison, R. G., Wood, P. J., Phelps, D. A., Hubbard, C. E., Fuke, M. (1988) High level expression of heterologous proteins in methylotrophic yeast Pichia pastoris. Journal of Basic Microbiology, 28 (4). pp. 265-278. ISSN 0233111X (ISSN)

Srivastava, S., Swanson, S. K., Manel, N., Florens, L., Washburn, M. P., Skowronski, J. (2008) Lentiviral Vpx accessory factor targets VprBP/DCAF1 substrate adaptor for cullin 4 E3 ubiquitin ligase to enable macrophage infection. PLoS Pathog, 4 (5). e1000059.

Stadler, Z. K., Esposito, D., Shah, S., Vijai, J., Yamrom, B., Levy, D., Lee, Y. H., Kendall, J., Leotta, A., Ronemus, M., Hansen, N. , Sarrel, K., Rau-Murthy, R., Schrader, K., Kauff, N., Klein, R., Lipkin, S., Murali, R., Robson, M., Sheinfeld, J., Feldman, D., Bosl, G., Norton, L., Wigler, M., Offit, K. (2012) Rare De Novo Germline Copy-Number Variation in Testicular Cancer. The American Journal of Human Genetics, 91 (2). pp. 379-383. ISSN 0002-9297

Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., Fuellen, G., Gilbert, J. G., Korf, I., Lapp, H., Lehvaslaiho, H., Matsalla, C., Mungall, C. J., Osborne, B. I., Pocock, M. R., Schattner, P., Senger, M., Stein, L. D., Stupka, E., Wilkinson, M. D., Birney, E. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Research, 12 (10). pp. 1611-8. ISSN 10889051 (ISSN)

Stamatoyannopoulos, J. A., Snyder, M., Hardison, R., Ren, B., Gingeras, T., Gilbert, D. M., Groudine, M., Bender, M., Kaul, R., Canfield, T., Giste, E., Johnson, A., Zhang, M., Balasundaram, G., Byron, R., Roach, V., Sabo, P. J., Sandstrom, R., Stehling, A. S., Thurman, R. E., Weissman, S. M., Cayting, P., Hariharan, M., Lian, J., Cheng, Y., Landt, S. G., Ma, Z., Wold, B. J., Dekker, J., Crawford, G. E., Keller, C. A., Wu, W., Morrissey, C., Kumar, S. A., Mishra, T., Jain, D., Byrska-Bishop, M., Blankenberg, D., Lajoiel, B. R., Jain, G., Sanyal, A., Chen, K. B., Denas, O., Taylor, J., Blobel, G. A., Weiss, M. J., Pimkin, M., Deng, W., Marinov, G. K., Williams, B. A., Fisher-Aylor, K. I., Desalvo, G., Kiralusha, A., Trout, D., Amrhein, H., Mortazavi, A., Edsall, L., McCleary, D., Kuan, S., Shen, Y., Yue, F., Ye, Z., Davis, C. A., Zaleski, C., Jha, S., Xue, C., Dobin, A., Lin, W., Fastuca, M., Wang, H., Guigo, R., Djebali, S., Lagarde, J., Ryba, T., Sasaki, T., Malladi, V. S., Cline, M. S., Kirkup, V. M., Learned, K., Rosenbloom, K. R., Kent, W. J., Feingold, E. A., Good, P. J., Pazin, M., Lowdon, R. F., Adams, L. B. (2012) An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology, 13 (8).

Stamm, S., Zhu, J., Nakai, K., Stoilov, P., Stoss, O., Zhang, M. Q. (2000) An alternative-exon database and its statistical analysis. DNA and Cell Biology, 19 (12). pp. 739-756. ISSN 1044-5498

Stanbridge, E., Farmer, A., Mills, A., Loftus, T., Kongkasuriyachai, D., Dowdy, S., Weissman, B. (1994) Molecular characterization of QM, a novel gene with properties consistent with tumor suppressor function. Cold Spring Harbor Symposia on Quantitative Biology, 59. pp. 573-576. ISSN 00917451 (ISSN)

Stark, A., Bushati, N., Jan, C. H., Kheradpour, P., Hodges, E., Brennecke, J., Bartel, D. P., Cohen, S. M., Kellis, M. (2008) A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev, 22 (1). pp. 8-13.

Stark, K. L., Xu, B., Bagchi, A., Lai, W. S., Liu, H., Hsu, R., Wan, X., Pavlidis, P., Mills, A. A., Karayiorgou, M., Gogos, J. A. (2008) Altered brain microRNA biogenesis contributes to phenotypic deficits in a 22q11-deletion mouse model. Nat Genet, 40 (6). pp. 751-760.

Starr, T. K., Allaei, R., Silverstein, K. A. T., Staggs, R. A., Sarver, A. L., Bergemann, T. L., Gupta, M., O'Sullivan, M. G., Matise, I., Dupuy, A. J., Collier, L. S., Powers, S., Oberg, A. L., Asmann, Y. W., Thibodeau, S. N., Tessarollo, L., Copeland, N. G., Jenkins, N. A., Cormier, R. T., Largaespada, D. A. (2009) A Transposon-Based Genetic Screen in Mice Identifies Genes Altered in Colorectal Cancer. Science, 323 (5922). pp. 1747-1750. ISSN 0036-8075

Steger, D. J., Lefterova, M. I., Ying, L., Stonestrom, A. J., Schupp, M., Zhuo, D., Vakoc, A. L., Kim, J. E., Chen, J., Lazar, M. A., Blobel, G. A., Vakoc, C. R. (2008) DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells. Molecular and Cellular Biology, 28 (8). pp. 2825-2839. ISSN 02707306 (ISSN)

Stein, L. (2002) Creating databases for biological information: an introduction. Current protocols in bioinformatics, Chapte. Unit 9.1.

Stein, L. (2003) Large scale sequencing. Current Protocols in Bioinformatics. Unit 11.01. ISSN 1934-340X (Electronic)1934-3396 (Linking)

Stein, L., Sternberg, P., Durbin, R., Thierry-Mieg, J., Spieth, J. (2001) WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Research, 29 (1). pp. 82-86. ISSN 0305-1048

Stein, L. D. (2004) Human genome: end of the beginning. Nature, 431 (7011). pp. 915-6. ISSN 1476-4687 (Electronic)

Stein, L. D. (2003) Integrating biological databases. Nature Reviews Genetics, 4 (5). pp. 337-345. ISSN 1471-0056

Stein, L. D. (2008) Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges. Nat Rev Genet, 9 (9). pp. 678-688.

Stein, L. D. (2001) Using Perl to facilitate biological analysis. In: Bioinformatics: a practical guide to the analysis of genes and proteins. Methods of Biochemical Analysis, 43 . Wiley, New York, pp. 413-49. ISBN 0076-6941 (Print)

Stein, L. D., Bao, Z., Blasiar, D., Blumenthal, T., Brent, M. R., Chen, N., Chinwalla, A., Clarke, L., Clee, C., Coghlan, A., Coulson, A., D'Eustachio, P., Fitch, D. H., Fulton, L. A., Fulton, R. E., Griffiths-Jones, S., Harris, T. W., Hillier, L. W., Kamath, R., Kuwabara, P. E., Mardis, E. R., Marra, M. A., Miner, T. L., Minx, P., Mullikin, J. C., Plumb, R. W., Rogers, J., Schein, J. E., Sohrmann, M., Spieth, J., Stajich, J. E., Wei, C., Willey, D., Wilson, R. K., Durbin, R., Waterston, R. H. (2003) The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biology, 1 (2). E45. ISSN 1544-9173

Stein, L. D., Mungall, C., Shu, S. Q., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J. E., Harris, T. W., Arva, A., Lewis, S. (2002) The Generic Genome Browser: A building block for a model organism system database. Genome Research, 12 (10). pp. 1599-1610. ISSN 1088-9051

Steitz, J. A., Dreyfuss, G., Krainer, A. R., Lamond, A. I., Matera, A. G., Padgett, R. A. (2008) Where in the cell is the minor spliceosome? Proc Natl Acad Sci U S A, 105 (25). pp. 8485-6.

Stenlund, A., Bream, G. L., Botchan, M. R. (1987) A promoter with an internal regulatory domain is part of the origin of replication in BPV-1. Science, 236 (4809). pp. 1666-71. ISSN 0036-8075 (Print)0036-8075 (Linking)

Stenlund, A., Lamy, D., Moreno-Lopez, J., Ahola, H., Pettersson, U., Tiollais, P. (1983) Secretion of the hepatitis B virus surface antigen from mouse cells using an extra-chromosomal eucaryotic vector. EMBO J, 2 (5). pp. 669-73. ISSN 0261-4189 (Print)0261-4189 (Linking)

Stenlund, A., Moreno-Lopez, J., Ahola, H., Pettersson, U. (1983) European elk papillomavirus: characterization of the genome, induction of tumors in animals, and transformation in vitro. J Virol, 48 (2). pp. 370-6. ISSN 0022-538X (Print)0022-538X (Linking)

Stenlund, A., Perricaudet, M., Tiollais, P., Pettersson, U. (1980) Construction of restriction enzyme fragment libraries containing DNA from human adenovirus types 2 and 5. Gene, 10 (1). pp. 47-52. ISSN 0378-1119 (Print)0378-1119 (Linking)

Stenlund, A., Zabielski, J., Ahola, H., Moreno-Lopez, J., Pettersson, U. (1985) Messenger RNAs from the transforming region of bovine papilloma virus type I. J Mol Biol, 182 (4). pp. 541-54. ISSN 0022-2836 (Print)0022-2836 (Linking)

Stillman, B. (2001) DNA replication - Genomic views of genome duplication. Science, 294 (5550). pp. 2301-2304. ISSN 0036-8075

Stillman, B. (2013) Deoxynucleoside triphosphate (dNTP) synthesis and destruction regulate the replication of both cell and virus genomes. Proceedings of the National Academy of Sciences of the United States of America, 110 (35). pp. 14120-14121. ISSN 0027-8424

Stillman, B. (2011) Talk from Bruce Stillman at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Stillman, B., Bell, S. P., Dutta, A., Marahrens, Y. (1992) DNA replication and the cell cycle. Regulation of the eukaryotic cell cycle. Ciba Foundation symposium, 170. 147-156; discussion 156. ISSN 03005208 (ISSN)

Stillman, B., Gerard, R. D., Guggenheimer, R. A., Gluzman, Y. (1985) T antigen and template requirements for SV40 DNA replication in vitro. EMBO Journal, 4 (11). pp. 2933-2939. ISSN 0261-4189

Stillman, B., Grodzicker, T., Martienssen, R., Stewart, D. (2012) The Biology of Plants. Cold Spring Harbor Symposia on Quantitative Biology, 77. ISSN 00917451 (ISSN)

Stillman, B. W., Bellett, A. J. D. (1979) Replication of DNA in adenovirus-infected cells. Cold Spring Harbor Symposia on Quantitative Biology, 43 (2). pp. 729-739. ISSN 00917451 (ISSN)

Strathern, J., Klar, A., Hicks, J., Abraham, J., Ivy, J., Kelly, M., Weisbrod, S., Stephens, C. (1983) Mechanism of Mating Type Cassette Switching. Journal of Cellular Biochemistry , 21 (S7B). pp. 89-90. ISSN 1097-4644

Strathern, J. N., Newlon, C. S., Herskowitz, I., Hicks, J. B. (1979) Isolation of a circular derivative of yeast chromosome III: Implications for the mechanism of mating type interconversion. Cell, 18 (2). pp. 309-319.

Strick, T. R. (2005) Course 6 Single-molecule studies of DNA mechanics and DNA/Protein interactions. Les Houches, 82. pp. 161-209.

Strick, T. R., Sachidanandam, R., Revyakin, A., Ebright, R. H. (2003) Single-molecule observations of DNA denaturation: mechanical and enzymatic effects. Biophysical Journal, 84 (2). 309A-309A. ISSN 0006-3495

Su, H., Mills, A. A., Wang, X. Z., Bradley, A. (2002) A targeted X-linked CMV-Cre line. Genesis, 32 (2). pp. 187-188. ISSN 1526-954X

Sun, S. Y., Zhang, Z., Fregoso, O., Krainer, A. R. (2012) Mechanisms of activation and repression by the alternative splicing factors RBFOX1/2. RNA, 18 (2). pp. 274-283. ISSN 1355-8382

Sun, J., Evrin, C., Samel, S. A., Fernandez-Cid, A., Riera, A., Kawakami, H., Stillman, B., Speck, C., Li, H. (2013) Cryo-EM structure of a helicase loading intermediate containing ORC-Cdc6-Cdt1-MCM2-7 bound to DNA. Nature Structural and Molecular Biology, 20 (8). pp. 944-951. ISSN 15459993

Sun, J., Kawakami, H., Zech, J., Speck, C., Stillman, B., Li, H. (2012) Cdc6-Induced Conformational Changes in ORC Bound to Origin DNA Revealed by Cryo-Electron Microscopy. Structure, 20 (3). pp. 534-544. ISSN 0969-2126

Sundvall, M., Maatta, J. A., Peri, L., Junttila, T. T., Egeblad, M., Elenius, K. (2004) Ligand-independent signaling by a tumor-associated isoform of ErbB4. Cancer Research, 64 (7 Supp). p. 23. ISSN 1078-0432

Swanson-Wagner, R. A., Eichten, S. R., Kumari, S., Tiffin, P., Stein, J. C., Ware, D. H., Springer, N. M. (2010) Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Research, 20 (12). pp. 1689-1699.

T

Tabata, S., Kaneko, T., Nakamura, Y., Kotani, H., Kato, T., Asamizu, E., Miyajima, N., Sasamoto, S., Kimura, T., Hosouchi, T., Kawashima, K., Kohara, M., Matsumoto, M., Matsuno, A., Muraki, A., Nakayama, S., Nakazaki, N., Naruo, K., Okumura, S., Shinpo, S., Takeuchi, C., Wada, T., Watanabe, A., Yamada, M., Yasuda, M., Sato, S., de la Bastide, M., Huang, E., Spiegel, L., Gnoj, L., O'Shaughnessy, A., Preston, R., Habermann, K., Murray, J., Johnson, D., Rohlfing, T., Nelson, J., Stoneking, T., Pepin, K., Spieth, J., Sekhon, M., Armstrong, J., Becker, M., Belter, E., Cordum, H., Cordes, M., Courtney, L., Courtney, W., Dante, M., Du, H., Edwards, J., Fryman, J., Haakensen, B., Lamar, E., Latreille, P., Leonard, S., Meyer, R., Mulvaney, E., Ozersky, P., Riley, A., Strowmatt, C., Wagner-McPherson, C., Wollam, A., Yoakum, M., Bell, M., Dedhia, N., Parnell, L., Shah, R., Rodriguez, M., See, L. H., Vil, D., Baker, J., Kirchoff, K., Toth, K., King, L., Bahret, A., Miller, B., Marra, M., Martienssen, R., McCombie, W. R., Wilson, R. K., Murphy, G., Bancroft, I., Volckaert, G., Wambutt, R., Düsterhöft, A., Stiekema, W., Pohl, T., Entian, K. D., Terryn, N., Hartley, N., Bent, E., Johnson, S., Langham, S. A., McCullagh, B., Robben, J., Grymonprez, B., Zimmermann, W., Ramsperger, U., Wedler, H. (2000) Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature, 408 (6814). pp. 823-826. ISSN 00280836 (ISSN)

Tabet, F., Schiffrin, E. L., Callera, G., He, Y., Yao, G., Ostman, A., Kappert, K., Tonks, N. K., Touyz, R. M. (2008) Redox-Sensitive Signaling by Angiotensin II Involves Oxidative Inactivation and Blunted Phosphorylation of Protein Tyrosine Phosphatase SHP-2 in Vascular Smooth Muscle Cells From SHR. Circ Res, 103 (2). pp. 149-158.

Tamanoi, F., Stillman, B. W. (1984) The origin of adenovirus DNA replication. Current Topics in Microbiology and Immunology, 109. pp. 75-87. ISSN 0070217X (ISSN)

Tan, X., Lu, Z. J., Gao, G., Xu, Q., Hu, L., Fellmann, C., Li, M. Z., Qu, H., Lowe, S. W., Hannon, G. J., Elledge, S. J. (2012) Tiling genomes of pathogenic viruses identifies potent antiviral shRNAs and reveals a role for secondary structure in shRNA efficacy. Proceedings of the National Academy of Sciences of the United States of America, 109 (3). pp. 869-874. ISSN 00278424 (ISSN)

Tanaka, T., Antonio, B. A., Kikuchi, S., Matsumoto, T., Nagamura, Y., Numa, H., Sakai, H., Wu, J., Itoh, T., Sasaki, T., Aono, R., Fujii, Y., Habara, T., Harada, E., Kanno, M., Kawahara, Y., Kawashima, H., Kubooka, H., Matsuya, A., Nakaoka, H., Saichi, N., Sanbonmatsu, R., Sato, Y., Shinso, Y., Suzuki, M., Takeda, J. I., Tanino, M., Todokoro, F., Yamaguchi, K., Yamamoto, N., Yamasaki, C., Imanishi, T., Okido, T., Tada, M., Ikeo, K., Tateno, Y., Gojobori, T., Lin, Y. C., Wei, F. J., Hsing, Y. I., Zhao, Q., Han, B., Kramer, M. R., McCombie, R. W., Lonsdale, D., O'Donovan, C. C., Whitfield, E. J., Apweiler, R., Koyanagi, K. O., Khurana, J. P., Raghuvanshi, S., Singh, N. K., Tyagi, A. K., Haberer, G., Fujisawa, M., Hosokawa, S., Ito, Y., Ikawa, H., Shibata, M., Yamamoto, M., Bruskiewich, R. M., Hoen, D. R., Bureau, T. E., Namiki, N., Ohyanagi, H., Sakai, Y., Nobushima, S., Sakata, K., Barrero, R. A., Sato, Y., Souvorov, A., Smith-White, B., Tatusova, T., An, S., An, G., Oota, S., Fuks, G., Messing, J., Christie, K. R., Lieberherr, D., Kim, H., Zuccolo, A., Wing, R. A., Nobuta, K., Green, P. J., Lu, C., Meyers, B. C., Chaparro, C., Piegu, B., Panaud, O., Echeverria, M. (2008) The rice annotation project database (RAP-DB): 2008 update. Nucleic Acids Research, 36 (Databa). D1028-D1033. ISSN 0305-1048

Tanurdzic, M., Vaughn, M. W., Jiang, H., Lee, T. J., Slotkin, R. K., Sosinski, B., Thompson, W. F., Doerge, R. W., Martienssen, R. A. (2008) Epigenomic consequences of immortalized plant cell suspension culture. PLoS biology, 6 (12). pp. 2880-95. ISSN 1545-7885 (Electronic)1544-9173 (Linking)

Tanurdžić, M., Doerge, R., Martienssen, R. (2005) Microarrays: Design, analysis, and applications in functional genomics. Archive of Oncology, 13 (3-4). pp. 124-125. ISSN 03547310 (ISSN)

Tegay, D. H., Chan, K. K., Leung, L., Wang, C., Burkett, S., Stone, G., Stanyon, R., Toriello, H. V., Hatchwell, E. (2009) Toriello-Carey syndrome in a patient with a de novo balanced translocation [46,XY,t(2;14)(q33;q22)] interrupting SATB2. Clinical Genetics, 75 (3). pp. 259-264. ISSN 0009-9163

Temple, G., Gerhard, D. S., Rasooly, R., Feingold, E. A., Good, P. J., Robinson, C., Mandich, A., Derge, J. G., Lewis, J., Shoaf, D., Collins, F. S., Jang, W., Wagner, L., Shenmen, C. M., Misquitta, L., Schaefer, C. F., Buetow, K. H., Bonner, T. I., Yankie, L., Ward, M., Phan, L., Astashyn, A., Brown, G., Farrell, C., Hart, J., Landrum, M., Maidak, B. L., Murphy, M., Murphy, T., Rajput, B., Riddick, L., Webb, D., Weber, J., Wu, W., Pruitt, K. D., Maglott, D., Siepel, A., Brejova, B., Diekhans, M., Harte, R., Baertsch, R., Kent, J., Haussler, D., Brent, M., Langton, L., Comstock, C. L., Stevens, M., Wei, C., van Baren, M. J., Salehi-Ashtiani, K., Murray, R. R., Ghamsari, L., Mello, E., Lin, C., Pennacchio, C., Schreiber, K., Shapiro, N., Marsh, A., Pardes, E., Moore, T., Lebeau, A., Muratet, M., Simmons, B., Kloske, D., Sieja, S., Hudson, J., Sethupathy, P., Brownstein, M., Bhat, N., Lazar, J., Jacob, H., Gruber, C. E., Smith, M. R., McPherson, J., Garcia, A. M., Gunaratne, P. H., Wu, J., Muzny, D., Gibbs, R. A., Young, A. C., Bouffard, G. G., Blakesley, R. W., Mullikin, J., Green, E. D., Dickson, M. C., Rodriguez, A. C., Grimwood, J., Schmutz, J., Myers, R. M., Hirst, M., Zeng, T., Tse, K., Moksa, M., Deng, M., Ma, K., Mah, D., Pang, J., Taylor, G., Chuah, E., Deng, A. (2009) The completion of the Mammalian Gene Collection (MGC). Genome Research, 19 (12). pp. 2324-33. ISSN 1088-9051

Tessanne, K., Golding, M. C., Long, C. R., Peoples, M. D., Hannon, G., Westhusin, M. E. (2012) Production of transgenic calves expressing an shRNA targeting myostatin. Molecular Reproduction and Development, 79 (3). pp. 176-185. ISSN 1040452X (ISSN)

Tessanne, K., Stroud, T., Long, C., Hannon, G. J., Sadeghieh, S., Hwang, E., Chen, S., Polejaeva, I., Westhusin, M. (2009) Development of Transgenic Livestock with Reduced Myostatin Expression Using Rna Interference. Reproduction Fertility and Development, 21 (1). p. 251. ISSN 1031-3613

Teta, M., Andl, T., Okegbe, T., Murchison, E. P., Nagy, A., Hannon, G. J., Millar, S. E. (2008) Global changes in mRNA levels and failure of hair follicle stem cell maintenance in adult Dicer-deleted skin. Journal of Investigative Dermatology, 128 (Suppl.). S154-S154. ISSN 0022-202X

Teta, M., Choi, Y. S., Okegbe, T., Wong, G., Tam, O. H., Chong, M. M. W., Seykora, J. T., Nagy, A., Littman, D. R., Andl, T., Millar, S. E. (2012) Inducible deletion of epidermal Dicer and Drosha reveals multiple functions for miRNAs in postnatal skin. Development, 139 (8). pp. 1405-1416. ISSN 09501991 (ISSN)

Teta, M., Thomas, A., Okegbe, T., Murchison, E. P., Nagy, A., Hannon, G. J., Millar, S. E. (2008) Dicer is required for maintenance of hair follicle stem cells in adult skin. Developmental Biology, 319 (2). p. 556. ISSN 0012-1606

The Tomato Genome Consortium, (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485 (7400). pp. 635-41. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Thiebaut, F., Grativol, C., Carnavale-Bottino, M., Rojas, C. A., Tanurdzic, M., Farinelli, L., Martienssen, R. A., Hemerly, A. S., Ferreira, P. C. (2012) Computational identification and analysis of novel sugarcane microRNAs. BMC genomics, 13. p. 290. ISSN 1471-2164 (Electronic)1471-2164 (Linking)

Thomas, E. E. (2004) Exploring Repetitive Sequences in the Human Genome. PhD thesis, Cold Spring Harbor Laboratory.

Thomas, R., Rebbeck, C. A., Leroi, A. M., Burt, A., Breen, M. (2009) Extensive conservation of genomic imbalances in canine transmissible venereal tumors (CTVT) detected by microarray-based CGH analysis. Chromosome Research, 17 (7). pp. 927-934. ISSN 0967-3849

Thomas, S. R., Vollbrecht, E. W., Meglen, R. (2001) Functional genomics approach to maize cell wall biochemistry. Abstracts of Papers of the American Chemical Society, 221. U193-U193. ISSN 0065-7727

Thorisson, G. A., Stein, L. D. (2003) The SNP Consortium website: past, present and future. Nucleic Acids Research, 31 (1). pp. 124-127. ISSN 0305-1048

Thorsen, K., Mansilla, F., Schepeler, T., Oster, B., Rasmussen, M. H., Dyrskjot, L., Karni, R., Akerman, M., Krainer, A. R., Laurberg, S., Andersen, C. L., Orntoft, T. F. (2011) Alternative splicing of SLC39A14 in colorectal cancer is regulated by the Wnt pathway. Molecular and Cellular Proteomics, 10 (1).

Thorsen, K., Sorensen, K. D., Brems-Eskildsen, A. S., Modin, C., Gaustadnes, M., Hein, A. M. K., Kruhoffer, M., Laurberg, S., Borre, M., Wang, K., Brunak, S., Krainer, A. R., Torring, N., Dyrskjot, L., Andersen, C. L., Orntoft, T. F. (2008) Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis. Molecular & Cellular Proteomics, 7 (7). pp. 1214-1224. ISSN 1535-9476

Tian, D., Stoppel, L. J., Heynen, A. J., Lindemann, L., Jaeschke, G., Mills, A. A., Bear, M. F. (2015) Contribution of mGluR5 to pathophysiology in a mouse model of human chromosome 16p11.2 microdeletion. Nature Neuroscience, 18. pp. 182-184. ISSN 1097-6256

Tilgner, H., Knowles, D. G., Johnson, R., Davis, C. A., Chakrabortty, S., Djebali, S., Curado, J., Snyder, M., Gingeras, T. R., Guigo, R. (2012) Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for IncRNAs. Genome Research, 22 (9). pp. 1616-1625. ISSN 1088-9051

Timmermans, M. C. P., Chitwood, D., Nogueira, F., Madi, S. (2008) Pattern formation by small RNA signals. Developmental Biology, 319 (2). pp. 463-464. ISSN 0012-1606

Titmus, M. A., Gurtowski, J., Schatz, M. C. (2014) Answering the demands of digital genomics. Concurrency Computation Practice and Experience, 26 (4). pp. 917-928. ISSN 15320626

Tomov, B. W., Bernal, J. S. (2003) Effects of GNA transgenic sugarcane on life history parameters of Parallorhogas pyralophagus (Marsh) (Hymenoptera : Braconidae), a parasitoid of Mexican rice borer. Journal of Economic Entomology, 96 (3). pp. 570-576. ISSN 0022-0493

Tonks, N. (2012) HARNESSING REDOX REGULATION OF PROTEIN TYROSINE PHOSPHATASES. Free Radical Biology and Medicine, 53 (Supple). S3-S3. ISSN 0891-5849

Tonks, N., Krishnan, N. (2008) Regulation of Protein Tyrsoine Phosphatase by Hydrogen Sulphide. Free Radical Biology and Medicine, 45 (Suppl.). S18-S19. ISSN 0891-5849

Tonks, N., Krishnan, N. (2008) Unraveling the Mechanism of Redox Regulation in Protein Tyrosine Phosphatases. Free Radical Biology and Medicine, 45 (Suppl.). S62-S62. ISSN 0891-5849

Tonks, N. K. (2013) Protein tyrosine phosphatases - from housekeeping enzymes to master regulators of signal transduction. Febs Journal, 280 (2). pp. 346-378. ISSN 1742464X

Tonks, N. K. (2009) Pseudophosphatases: grab and hold on. Cell, 139 (3). pp. 464-5.

Tripathi, V., Song, D. Y., Zong, X., Shevtsov, S. P., Hearn, S., Fu, X. D., Dundr, M., Prasanth, K. V. (2012) SRSF1 modulates the organization of splicing factors in nuclear speckles and regulates transcription. Mol Biol Cell, 23 (18). pp. 3694-3706. ISSN 1939-4586 (Electronic)1059-1524 (Linking)

Tripic, T., Deng, W., Cheng, Y., Zhang, Y., Vakoc, C. R., Gregory, G. D., Hardison, R. C., Blobel, G. A. (2009) SCL and associated proteins distinguish active from repressive GATA transcription factor complexes. Blood, 113 (10). pp. 2191-2201. ISSN 00064971 (ISSN)

Trotman, L. C., Powers, S. (2010) New views into the prostate cancer genome. Cancer Cell, 18 (1). pp. 1-2. ISSN 1878-3686 (Electronic) 1535-6108 (Linking)

Tschudi, C., Krainer, A. R., Ullu, E. (1988) The U6 small nuclear RNA from Trypanosoma brucei. Nucleic Acids Research, 16 (23). p. 11375. ISSN 0305-1048

Tsesmetzis, N., Couchman, M., Higgins, J., Smith, A., Doonan, J. H., Seifert, G. J., Schmidt, E. E., Vastrik, I., Birney, E., Wu, G., D'Eustachio, P., Stein, L. D., Morris, R. J., Bevan, M. W., Walsh, S. V. (2008) Arabidopsis Reactome: A Foundation Knowledgebase for Plant Systems Biology. Plant Cell, 20 (6). pp. 1426-36.

Tummala, M., Ryzhov, V., Ravi, K., Black, S. M., Ravi, K. (2008) Identification of the cysteine nitrosylation sites in human endothelial nitric oxide synthase. DNA and Cell Biology, 27 (1). pp. 25-33. ISSN 1044-5498

Tworkowski, K. A., Chakraborty, A. A., Samuelson, A. V., Seger, Y. R., Narita, M., Hannon, G. J., Lowe, S. W., Tansey, W. P. (2008) Adenovirus E1A targets p400 to induce the cellular oncoprotein Myc. Proc Natl Acad Sci U S A, 105 (16). pp. 6103-6108.

Tyekucheva, S., Yolken, R. H., McCombie, W. R., Parla, J., Kramer, M., Wheelan, S. J., Sabunciyan, S. (2011) Establishing the baseline level of repetitive element expression in the human cortex. BMC Genomics, 12. article number 495. ISSN 1471-2164

U

Uchiyama, K., Jokitalo, E., Kano, F., Murata, M., Zhang, X., Canas, B., Newman, R., Rabouille, C., Pappin, D., Freemont, P., Kondo, H. (2002) VCIP135, a novel essential factor for p97/p47-mediated membrane fusion, is required for Golgi and ER assembly in vivo. J Cell Biol, 159 (5). pp. 855-66. ISSN 0021-9525 (Print)0021-9525 (Linking)

Uziel, T., Karginov, F. V., Xie, S. Q., Parker, J. S., Wang, Y. D., Gajjar, A., He, L., Ellison, D., Gilbertson, R. J., Hannon, G. J., Roussel, M. F. (2009) The miR-17 similar to 92 cluster collaborates with the Sonic Hedgehog pathway in medulloblastoma. Proceedings of the National Academy of Sciences of the United States of America, 106 (8). pp. 2812-2817. ISSN 0027-8424

V

Vacic, V., Markwick, P. R. L., Oldfield, C. J., Zhao, X., Haynes, C., Uversky, V. N., Iakoucheva, L. M. (2012) Disease-Associated Mutations Disrupt Functionally Important Regions of Intrinsic Protein Disorder. PLoS Computational Biology, 8 (10). ISSN 1553734X

Vacic, V., McCarthy, S. E., Malhotra, D., Murray, F., Chou, H. H., Peoples, A., Makarov, V., Yoon, S., Bhandari, A., Corominas, R., Iakoucheva, L. M., Krastoshevsky, O., Krause, V., Larach-Walters, V., Welsh, D. K., Craig, D., Kelsoe, J. R., Gershon, E. S., Leal, S. M., Aquila, M. D., Morris, D. W., Gill, M., Corvin, A., Insel, P. A., McClellan, J., King, M. C., Karayiorgou, M., Levy, D. L., Delisi, L. E., Sebat, J. (2011) Duplications of the neuropeptide receptor gene VIPR2 confer significant risk for schizophrenia. Nature, 471 (7339). pp. 499-503. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Vagin, V. V., Wohlschlegel, J., Qu, J., Jonsson, Z., Huang, X., Chuma, S., Girard, A., Sachidanandam, R., Hannon, G. J., Aravin, A. A. (2009) Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members. Genes and Development, 23 (15). pp. 1749-1762. ISSN 08909369 (ISSN)

Vagin, V. V., Yu, Y., Jankowska, A., Luo, Y., Wasik, K. A., Malone, C. D., Harrison, E., Rosebrock, A., Wakimoto, B. T., Fagegaltier, D., Muerdter, F., Hannon, G. J. (2013) Minotaur is critical for primary piRNA biogenesis. RNA, 19 (8). pp. 1064-1077. ISSN 1469-9001 (Electronic)1355-8382 (Linking)

Vakoc, C. R. (2012) Talk from Chris Vakoc at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Vakoc, C. R., Blobel, G. A., Wen, Y.-Y., Gibbs, R. A., Johnstone, C. N., Rustgi, A. K. (2009) Low frequency of MLL3 mutations in colorectal carcinoma. Cancer Genetics and Cytogenetics, 189 (2). pp. 140-141. ISSN 0165-4608

Vakoc, C. R., Letting, D. L., Gheldof, N., Sawado, T., Bender, M. A., Groudine, M., Weiss, M. J., Dekker, J., Blobel, G. A. (2005) Proximity among distant regulatory elements at the β-globin locus requires GATA-1 and FOG-1. Molecular Cell, 17 (3). pp. 453-462. ISSN 10972765 (ISSN)

Vakoc, C. R., Mandat, S. A., Olenchock, B. A., Blobel, G. A. (2005) Histone H3 lysine 9 methylation and HP1γ are associated with transcription elongation through mammalian chromatin. Molecular Cell, 19 (3). pp. 381-391. ISSN 10972765 (ISSN)

Vakoc, C. R., Mandat, S. A., Olenschock, B. A., Blobel, G. A. (2005) Histone H3 lysine 9 methylation and HP1 gamma are associated with transcription elongation through mammalian chromatin. Blood, 106 (11). 493A-493A. ISSN 0006-4971

Vakoc, C. R., Sachdeva, M. M., Wang, H., Blobel, G. A. (2006) Profile of histone lysine methylation across transcribed mammalian chromatin. Molecular and Cellular Biology, 26 (24). pp. 9185-9195. ISSN 02707306 (ISSN)

Vakoc, C. R., Zuber, J., Lowe, S., Wang, E., Rappaport, A. R., Shi, J. W. (2010) An RNA1 Screen Reveals a Pattern of Addiction to Epigenetic Pathways That Distinguishes MLL AF9 Leukemia From Normal Hematopoietic Cells. Blood, 116 (21). p. 35. ISSN 0006-4971

Van Ex, F., Jacob, Y., Martienssen, R. A. (2011) Multiple roles for small RNAs during plant reproduction. Current opinion in plant biology, 14 (5). pp. 588-93. ISSN 1879-0356 (Electronic)1369-5266 (Linking)

Varmus, H., Stillman, B. (2005) Support for the Human Cancer Genome Project. Science, 310 (5754). p. 1615. ISSN 0036-8075

Varshavsky, A., Turner, G., Du, F., Xie, Y. (2000) The ubiquitin system and the N-end rule pathway. Biological Chemistry, 381 (9-10). pp. 779-789. ISSN 14316730 (ISSN)

Varshney, R. K., Chen, W. B., Li, Y. P., Bharti, A. K., Saxena, R. K., Schlueter, J. A., Donoghue, M. T. A., Azam, S., Fan, G. Y., Whaley, A. M., Farmer, A. D., Sheridan, J., Iwata, A., Tuteja, R., Penmetsa, R. V., Wu, W., Upadhyaya, H. D., Yang, S. P., Shah, T., Saxena, K. B., Michael, T., McCombie, W. R., Yang, B. C., Zhang, G. Y., Yang, H. M., Wang, J., Spillane, C., Cook, D. R., May, G. D., Xu, X., Jackson, S. A. (2012) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nature Biotechnology, 30 (1). 83-U128. ISSN 1087-0156

Venter, J. C., Adams, M. D., Martin-Gallardo, A., McCombie, W. R., Fields, C. (1992) Genome sequence analysis: Scientific objectives and practical strategies. Trends in Biotechnology, 10 (1-2). pp. 8-11. ISSN 01679430 (ISSN)

Venter, J. C., McCombie, W. R., McConnell, J. B. (1990) Genome sequencing conference I: Summary. Genomics, 8 (1). pp. 186-188. ISSN 08887543 (ISSN)

Verleyen, W., Ballouz, S., Gillis, J. (2016) Positive and negative forms of replicability in gene network analysis. Bioinformatics, 32 (7). pp. 1065-73. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

Vielle-Calzada, J. P., Baskar, R., Grossniklaus, U. (2000) Delayed activation of the paternal genome during seed development. Nature, 404 (6773). pp. 91-94. ISSN 0028-0836

Volpe, T., Martienssen, R. A. (2011) RNA interference and heterochromatin assembly. Cold Spring Harbor perspectives in biology, 3 (9). a003731. ISSN 1943-0264 (Electronic)

Volpe, T. A., Kidner, C., Hall, I. M., Teng, G., Grewal, S. I., Martienssen, R. A. (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science, 297 (5588). pp. 1833-7. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Vu, T. M., Nakamura, M., Calarco, J. P., Susaki, D., Lim, P. Q., Kinoshita, T., Higashiyama, T., Martienssen, R. A., Berger, F. (2013) RNA-directed DNA methylation regulates parental genomic imprinting at several loci in Arabidopsis. Development, 140 (14). pp. 2953-2960. ISSN 0950-1991

van Ham, M., van Lith, M., Lillemeier, B., Tjin, E., Gruneberg, U., Rahman, D., Pastoors, L., van Meijgaarden, K., Roucard, C., Trowsdale, J., Ottenhoff, T., Pappin, D., Neefjes, J. (2000) Modulation of the major histocompatibility complex class II-associated peptide repertoire by human histocompatibility leukocyte antigen (HLA)-DO. J Exp Med, 191 (7). pp. 1127-36. ISSN 0022-1007 (Print)0022-1007 (Linking)

van Schouwenburg, Pauline A., Davenport, Emma E., Kienzler, Anne-Kathrin, Marwah, Ishita, Wright, Benjamin, Lucas, Mary, Malinauskas, Tomas, Martin, Hilary C., Lockstone, Helen E., Cazier, Jean-Baptiste, Chapel, Helen M., Knight, Julian C., Patel, Smita Y. (2015) Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency. Clinical Immunology, 160 (2). pp. 301-314. ISSN 1521-6616

W

Wall, C. E., Cozza, S., Riquelme, C. A., McCombie, W. R., Heimiller, J. K., Marr, T. G., Leinwand, L. A. (2011) Whole transcriptome analysis of the fasting and fed Burmese python heart: insights into extreme physiological cardiac adaptation. Physiological Genomics, 43 (2). pp. 69-76. ISSN 1094-8341

Wall, M., Poortinga, G., Stanley, K. L., Lindemann, R. K., Bots, M., Chan, C. J., Bywater, M. J., Kinross, K. M., Astle, M. V., Waldeck, K., Hannan, K. M., Shortt, J., Smyth, M. J., Lowe, S. W., Hannan, R. D., Pearson, R. B., Johnstone, R. W., McArthur, G. A. (2013) The mTORC1 inhibitor everolimus prevents and treats Eμ-Myc lymphoma by restoring oncogene-induced senescence. Cancer Discovery, 3 (1). pp. 82-95. ISSN 21598274

Walsh, T., McClellan, J. M., McCarthy, S. E., Addington, A. M., Pierce, S. B., Cooper, G. M., Nord, A. S., Kusenda, M., Malhotra, D., Bhandari, A., Stray, S. M., Rippey, C. F., Roccanova, P., Makarov, V., Lakshmi, B., Findling, R. L., Sikich, L., Stromberg, T., Merriman, B., Gogtay, N., Butler, P., Eckstrand, K., Noory, L., Gochman, P., Long, R., Chen, Z., Davis, S., Baker, C., Eichler, E. E., Meltzer, P. S., Nelson, S. F., Singleton, A. B., Lee, M. K., Rapoport, J. L., King, M. C., Sebat, J. (2008) Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science, 320 (5875). pp. 539-43.

Wang, D., Pan, E., Fang, G., Kumari, S., He, F., Ware, D., Maslov, S., Gerstein, M. (2013) Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between arabidopsis and poplar. 2013 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013 . ACM, pp. 689-690. ISBN 9781450324342 (ISBN)

Wang, E., Kawaoka, S., Yu, M., Shi, J., Ni, T., Yang, W., Zhu, J., Roeder, R. G., Vakoc, C. R. (2013) Histone H2B ubiquitin ligase RNF20 is required for MLL-rearranged leukemia. Proceedings of the National Academy of Sciences of the United States of America, 110 (10). pp. 3901-6. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Wang, K., Kim, C., Bradfield, J., Guo, Y. F., Toskala, E., Otieno, F. G., Hou, C. P., Thomas, K., Cardinale, C., Lyon, G. J., Golhar, R., Hakonarson, H. (2013) Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement. Genome Medicine, 5. ISSN 1756-994X

Wang, X., Xuan, Z., Zhao, X., Li, Y., Zhang, M. Q. (2009) High-resolution human core-promoter prediction with CoreBoost_HM. Genome Res, 19 (2). pp. 266-75.

Wang, X. W., Gu, J., Zhang, M. Q., Li, Y. D. (2008) Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. Bioinformatics, 24 (2). pp. 165-171. ISSN 1367-4803

Wang, Z., Jeon, H. Y., Rigo, F., Bennett, C. F., Krainer, A. R. (2012) Manipulation of PK-M mutually exclusive alternative splicing by antisense oligonucleotides. Open Biol, 2 (10). p. 120133. ISSN 2046-2441 (Electronic)2046-2441 (Linking)

Wang, Z., Zang, C., Rosenfeld, J. A., Schones, D. E., Barski, A., Cuddapah, S., Cui, K., Roh, T. Y., Peng, W., Zhang, M. Q., Zhao, K. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet, 40 (7). pp. 897-903.

Wang, Z. X., Chatterjee, D., Jeon, H. Y., Akerman, M., Vander Heiden, M. G., Cantley, L. C., Krainer, A. R. (2012) Exon-centric regulation of pyruvate kinase M alternative splicing via mutually exclusive exons. Journal of Molecular Cell Biology, 4 (2). pp. 79-87.

Ware, D., Jaiswal, P., Ni, J. J., Pan, X. K., Chang, K., Clark, K., Teytelman, L., Schmidt, S., Zhao, W., Cartinhour, S., McCouch, S., Stein, L. (2002) Gramene: a resource for comparative grass genomics. Nucleic Acids Research, 30 (1). pp. 103-105. ISSN 0305-1048

Ware, D., Stein, L. (2003) Comparison of genes among cereals. Current Opinion in Plant Biology, 6 (2). pp. 121-7. ISSN 1369-5266

Ware, D. H. (2011) Talk from Doreen Ware at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Ware, D. H., Jaiswal, P. J., Ni, J. J., Yap, I., Pan, X. K., Clark, K. Y., Teytelman, L., Schmidt, S. C., Zhao, W., Chang, K., Cartinhour, S., Stein, L. D., McCouch, S. R. (2002) Gramene, a tool for grass Genomics. Plant Physiology, 130 (4). pp. 1606-1613. ISSN 0032-0889

Warren, W. C., Hillier, L. W., Marshall Graves, J. A., Birney, E., Ponting, C. P., Grützner, F., Belov, K., Miller, W., Clarke, L., Chinwalla, A. T., Yang, S. P., Heger, A., Locke, D. P., Miethke, P., Waters, P. D., Veyrunes, F., Fulton, L., Fulton, B., Graves, T., Wallis, J., Puente, X. S., López-Otín, C., Ordóñez, G. R., Eichler, E. E., Chen, L., Cheng, Z., Deakin, J. E., Alsop, A., Thompson, K., Kirby, P., Papenfuss, A. T., Wakefield, M. J., Olender, T., Lancet, D., Huttley, G. A., Smit, A. F. A., Pask, A., Temple-Smith, P., Batzer, M. A., Walker, J. A., Konkel, M. K., Harris, R. S., Whittington, C. M., Wong, E. S. W., Gemmell, N. J., Buschiazzo, E., Vargas Jentzsch, I. M., Merkel, A., Schmitz, J., Zemann, A., Churakov, G., Ole Kriegs, J., Brosius, J., Murchison, E. P., Sachidanandam, R., Smith, C., Hannon, G. J., Tsend-Ayush, E., McMillan, D., Attenborough, R., Rens, W., Ferguson-Smith, M., Lefèvre, C. M., Sharp, J. A., Nicholas, K. R., Ray, D. A., Kube, M., Reinhardt, R., Pringle, T. H., Taylor, J., Jones, R. C., Nixon, B., Dacheux, J. L., Niwa, H., Sekita, Y., Huang, X., Stark, A., Kheradpour, P., Kellis, M., Flicek, P., Chen, Y., Webber, C., Hardison, R., Nelson, J., Hallsworth-Pepin, K., Delehaunty, K., Markovic, C., Minx, P., Feng, Y., Kremitzki, C., Mitreva, M., Glasscock, J., Wylie, T., Wohldmann, P., Thiru, P., Nhan, M. N., Pohl, C. S., Smith, S. M., Hou, S., Renfree, M. B. (2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature, 453 (7192). pp. 175-183. ISSN 00280836 (ISSN)

Wasik, K. A., Rebbeck, C. A. (2011) Keystone Symposia 40th Season: MicroRNAs and Noncoding RNAs in Cancer. Cancer Res, 71 (19). ISSN 0008-5472

Waterston, R. H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J. F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., Antonarakis, S. E., Attwood, J., Baertsch, R., Bailey, J., Barlow, K., Beck, S., Berry, E., Birren, B., Bloom, T., Bork, P., Botcherby, M., Bray, N., Brent, M. R., Brown, D. G., Brown, S. D., Bult, C., Burton, J., Butler, J., Campbell, R. D., Carninci, P., Cawley, S., Chiaromonte, F., Chinwalla, A. T., Church, D. M., Clamp, M., Clee, C., Collins, F. S., Cook, L. L., Copley, R. R., Coulson, A., Couronne, O., Cuff, J., Curwen, V., Cutts, T., Daly, M., David, R., Davies, J., Delehaunty, K. D., Deri, J., Dermitzakis, E. T., Dewey, C., Dickens, N. J., Diekhans, M., Dodge, S., Dubchak, I., Dunn, D. M., Eddy, S. R., Elnitski, L., Emes, R. D., Eswara, P., Eyras, E., Felsenfeld, A., Fewell, G. A., Flicek, P., Foley, K., Frankel, W. N., Fulton, L. A., Fulton, R. S., Furey, T. S., Gage, D., Gibbs, R. A., Glusman, G., Gnerre, S., Goldman, N., Goodstadt, L., Grafham, D., Graves, T. A., Green, E. D., Gregory, S., Guigó, R., Guyer, M., Hardison, R. C., Haussler, D., Hayashizaki, Y., LaHillier, D. W., Hinrichs, A., Hlavina, W., Holzer, T., Hsu, F., Hua, A., Hubbard, T., Hunt, A., Jackson, I., Jaffe, D. B., Johnson, L. S., Jones, M., Jones, T. A., Joy, A., Kamal, M., Karlsson, E. K. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420 (6915). pp. 520-562. ISSN 00280836 (ISSN)

Watson, J. D. (2009) Living with my personal genome. Personalized Medicine, 6 (6). p. 607. ISSN 1741-0541

Watson, J. D., Caudy, A. A., Myers, R. M., Witkowski, J. (2006) Recombinant DNA: Genes and Genomes -- a short course. W. H. Freeman & Co., New York. ISBN 9780716728665

Watts, J. A., Zhang, C. L., Klein-Szanto, A. J., Kormish, J. D., Fu, J., Zhang, M. Q., Zaret, K. S. (2011) Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development. PLoS Genetics, 7 (9). ISSN 1553-7390

Wei, F., Stein, J. C., Liang, C., Zhang, J., Fulton, R. S., Baucom, R. S., De Paoli, E., Zhou, S., Yang, L., Han, Y., Pasternak, S., Narechania, A., Zhang, L., Yeh, C. T., Ying, K., Nagel, D. H., Collura, K., Kudrna, D., Currie, J., Lin, J., Kim, H., Angelova, A., Scara, G., Wissotski, M., Golser, W., Courtney, L., Kruchowski, S., Graves, T. A., Rock, S. M., Adams, S., Fulton, L. A., Fronick, C., Courtney, W., Kramer, M., Spiegel, L., Nascimento, L., Kalyanaraman, A., Chaparro, C., Deragon, J. M., Miguel, P. S., Jiang, N., Wessler, S. R., Green, P. J., Yu, Y., Schwartz, D. C., Meyers, B. C., Bennetzen, J. L., Martienssen, R. A., McCombie, W. R., Aluru, S., Clifton, S. W., Schnable, P. S., Ware, D., Wilson, R. K., Wing, R. A. (2009) Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS genetics, 5 (11). e1000728. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Wei, F., Zhang, J., Zhou, S., He, R., Schaeffer, M., Collura, K., Kudrna, D., Faga, B. P., Wissotski, M., Golser, W., Rock, S. M., Graves, T. A., Fulton, R. S., Coe, E., Schnable, P. S., Schwartz, D. C., Ware, D. H., Clifton, S. W., Wilson, R. K., Wing, R. A. (2009) The physical and genetic framework of the maize b73 genome. PLoS Genet, 5 (11). e1000715. ISSN 1553-7404 (Electronic)

Wei, Y., Koulakov, A. A. (2012) An Exactly Solvable Model of Random Site-Specific Recombinations. Bulletin of Mathematical Biology, 74 (12). pp. 2897-20. ISSN 00928240

Weil, C., Martienssen, R. (2008) Epigenetic interactions between transposons and genes: lessons from plants. Current opinion in genetics & development, 18 (2). pp. 188-92. ISSN 0959-437X (Print)0959-437X (Linking)

Weirauch, M. T., Cote, A., Norel, R., Annala, M., Zhao, Y., Riley, T. R., Saez-Rodriguez, J., Cokelaer, T., Vedenko, A., Talukder, S., Bussemaker, H. J., Quaid, M. D., Bulyk, M. L., Stolovitzky, G., Hughes, T. R., Agius, P., Arvey, A., Bucher, P., Callan Jr, C. G., Chang, C. W., Chen, C. Y., Chen, Y. S., Chu, Y. W., Grau, J., Grosse, I., Jagannathan, V., Keilwagen, J., Kiebasa, S. M., Kinney, J. B., Klein, H., Kursa, M. B., Lähdesmäki, H., Laurila, K., Lei, C., Leslie, C., Linhart, C., Murugan, A., Myšičková, A., Noble, W. S., Nykter, M., Orenstein, Y., Posch, S., Ruan, J., Rudnicki, W. R., Schmid, C. D., Shamir, R., Sung, W. K., Vingron, M., Zhang, Z. (2013) Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology, 31 (2). pp. 126-134. ISSN 10870156 (ISSN)

Welch, J. J., Watts, J. A., Vakoc, C. R., Yao, Y., Wang, H., Hardison, R. C., Blobel, G. A., Chodosh, L. A., Weiss, M. J. (2004) Global regulation of erythroid gene expression by transcription factor GATA-1. Blood, 104 (10). pp. 3136-3147. ISSN 00064971 (ISSN)

Wences, A. H., Schatz, M. C. (2015) Metassembler: merging and optimizing de novo genome assemblies. Genome Biol, 16 (1). p. 207. ISSN 1474-760X (Electronic)1474-7596 (Linking)

West, J., Healy, J., Wigler, M. H., Casey, W., Mishra, B. (2006) Validation of S. Pombe sequence assembly by microarray hybridization. J Comput Biol, 13 (1). pp. 1-20. ISSN 1066-5277 (Print)

Wicker, T., Narechania, A., Sabot, F., Stein, J. C., Vu, G. T. H., Graner, A., Ware, D. H., Stein, N. (2008) Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics, 9. p. 518.

Wigler, M. (2012) Broad applications of single-cell nucleic acid analysis in biomedical research. Genome Med, 4 (10). p. 79. ISSN 1756-994X (Electronic)

Wigler, M. H. (2011) Talk from Mike Wigler at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Wilusz, J. E., Jnbaptiste, C. K., Lu, L. Y., Kuhn, C. D., Joshua-Tor, L., Sharp, P. A. (2012) A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails. Genes Dev, 26 (21). pp. 2392-407. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Wines, M. E., Lee, L., Katari, M. S., Zhang, L., DeRossi, C., Shi, Y., Perkins, S., Feldman, M., McCombie, W. Richard, Holdener, B. C. (2001) Identification of mesoderm development (mesd) candidate genes by comparative mapping and genome sequence analysis. Genomics, 72 (1). pp. 88-98. ISSN 08887543 (ISSN)

Wood, V., Gwilliam, R., Rajandream, M. A., Lyne, M., Lyne, R., Stewart, A., Sgouros, J., Peat, N., Hayles, J., Baker, S., Basham, D., Bowman, S., Brooks, K., Brown, D., Brown, S., Chillingworth, T., Churcher, C., Collins, M., Connor, R., Cronin, A., Davis, P., Feltwell, T., Fraser, A., Gentles, S., Goble, A., Hamlin, N., Harris, D., Hidalgo, J., Hodgson, G., Holroyd, S., Hornsby, T., Howarth, S., Huckle, E. J., Hunt, S., Jagels, K., James, K., Jones, L., Jones, M., Leather, S., McDonald, S., McLean, J., Mooney, P., Moule, S., Mungall, K., Murphy, L., Niblett, D., Odell, C., Oliver, K., O'Neil, S., Pearson, D., Quail, M. A., Rabbinowitsch, E., Rutherford, K., Rutter, S., Saunders, D., Seeger, K., Sharp, S., Skelton, J., Simmonds, M., Squares, R., Squares, S., Stevens, K., Taylor, K., Taylor, R. G., Tivey, A., Walsh, S., Warren, T., Whitehead, S., Woodward, J., Volckaert, G., Aert, R., Robben, J., Grymonprez, B., Weltjens, I., Vanstreels, E., Rieger, M., Schäfer, M., Müller-Auer, S., Gabel, C., Fuchs, M., Fritzc, C., Holzer, E., Moestl, D., Hilbert, H., Borzym, K., Langer, I., Beck, A., Lehrach, H., Reinhardt, R., Pohl, T. M., Eger, P., Zimmermann, W., Wedler, H., Wambutt, R., Purnelle, B., Goffeau, A., Cadieu, E., Dréano, S., Gloux, S., Lelaure, V. (2002) The genome sequence of Schizosaccharomyces pombe. Nature, 415 (6874). pp. 871-880. ISSN 00280836 (ISSN)

Wrzeszczynski, K. O., Fan, G. F., Fu, C. X., Pappin, D. J., Lucito, R., Tonks, N. K. (2013) Proteomic identification of carboplatin resistance in ovarian cancer cells. Cancer Research, 73 (8 Supp). p. 2502. ISSN 0008-5472

Wrzeszczynski, K. O., Varadan, V., Kamalakaran, S., Levine, D. A., Dimitrova, N., Lucito, R. (2013) Integrative prediction of gene function and platinum-free survival from genomic and epigenetic features in ovarian cancer. Methods Mol Biol, 1049. pp. 35-51. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Wu, J., Akerman, M., Sun, S., McCombie, W. R., Krainer, A. R., Zhang, M. Q. (2011) SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics, 27 (21). 3010-3016 . ISSN 1367-4803

Wu, J., Anczukow, O., Krainer, A. R., Zhang, M. Q., Zhang, C. (2013) OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucleic Acids Research, 41 (10). pp. 5149-5163. ISSN 03051048 (ISSN)

Wu, Q., Kim, Y. C., Lu, J., Xuan, Z. Y., Chen, J., Zheng, Y., Zhou, T., Zhang, M. Q., Wu, C. I., Wang, S. M. (2008) Poly A- transcripts expressed in HeLa cells. PLoS ONE, 3 (7). e2803.

Wu, Q., Krainer, A. R. (1996) U1-mediated exon definition interactions between AT-AC and GT-AG introns. Science, 274 (5289). pp. 1005-1008. ISSN 0036-8075

Wu, Q., Shigaki, T., Han, J. S., Kim, C. K., Hirschi, K. D., Park, S. (2012) Ectopic expression of a maize calreticulin mitigates calcium deficiency-like disorders in sCAX1-expressing tobacco and tomato. Plant Molecular Biology, 80 (6). pp. 609-619.

Wu, X., Jiang, R., Zhang, M. Q., Li, S. (2008) Network-based global inference of human disease genes. Mol Syst Biol, 4. p. 189.

Wu, Yiyang (2013) The evolution of MIP technology. Journal Club. (Unpublished)

Wu, Yiyang (2014) "A splice donor mutation in NAA10 results in the dysregulation of the retinoic acid signalling pathway and causes Lenz microphthalmia syndrome". Journal Club. (Unpublished)

Wu, Yiyang, Lyon, Gholson J. (2014) A splice donor mutation in NAA10 results in the dysregulation of the retinoic acid signalling pathway and causes Lenz microphthalmia syndrome. Journal Club. (Unpublished)

X

Xiang, B., Chatti, K., Qiu, H., Lakshmi, B., Krasnitz, A., Hicks, J. B., Yu, M., Miller, W. T., Muthuswamy, S. K. (2008) Brk is coamplified with ErbB2 to promote proliferation in breast cancer. Proc Natl Acad Sci U S A, 105 (34). pp. 12463-8.

Xie, W. W., Liang, C. Z., Birchler, J. A. (2011) Inhibition of RNA Interference and Modulation of Transposable Element Expression by Cell Death in Drosophila. Genetics, 188 (4). pp. 823-834. ISSN 0016-6731

Xing, H., Mo, Y., Liao, W., Zhang, M. Q. (2012) Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data. PLoS Comput Biol, 8 (7). e1002613. ISSN 1553-7358 (Electronic)1553-734X (Linking)

Xu, M.X., Jackson, D. (2012) Cell-to-cell Movement of Homeodomain Transcription Factors: Yesterday, Today and Tomorrow. In: Short and Long Distance Signaling. Advances in Plant Biology, 3 (3). Springer, pp. 87-98. ISBN 978-1-4419-1531-3

Xu, X., Zhang, Y., Williams, J., Antoniou, E., McCombie, W. R., Wu, S., Zhu, W., Davidson, N. O., Denoya, P., Li, E. (2013) Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets. BMC Bioinformatics, 14 Sup. S1. ISSN 1471-2105 (Electronic)1471-2105 (Linking)

Xu, X. M., Wang, J., Benitez-Alfonso, Y., Jackson, D. P. (2009) Regulation of KNOTTED1 cell-to-cell trafficking by a chaperonin protein. Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology, 153 (2, Sup). S211.

Xu, X. M., Zhao, Q., Rodrigo-Peiris, T., Brkljacic, J., He, C. S., Muller, S., Meier, I. (2008) RanGAP1 is a continuous marker of the Arabidopsis cell division plane. Proc Natl Acad Sci U S A, 105 (47). pp. 18637-18642.

Xuan, Z., McCombie, W. R., Zhang, M. Q. (2002) GFScan: A gene family search tool at genomic DNA level. Genome Research, 12 (7). pp. 1142-1149. ISSN 10889051 (ISSN)

Xuan, Z., Wang, J., Zhang, M. Q. (2003) Computational comparison of two mouse draft genomes and the human golden path. Genome Biology, 4 (1). R1. ISSN 1474-7596

Xue, W., Kitzing, T., Roessler, S., Zuber, J., Krasnitz, A., Schultz, N., Revill, K., Weissmueller, S., Rappaport, A. R., Simon, J., Zhang, J., Luo, W. J., Hicks, J., Zender, L., Wang, X. W., Powers, S., Wigler, M., Lowe, S. W. (2012) A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. Proceedings of the National Academy of Sciences of the United States of America, 109 (21). pp. 8212-8217. ISSN 0027-8424

Xue, W., Krasnitz, A., Lucito, R., Sordella, R., Van Aelst, L., Cordon-Cardo, C., Singer, S., Kuehnel, F., Wigler, M. H., Powers, S., Zender, L., Lowe, S. W. (2008) DLC1 is a chromosome 8p tumor suppressor whose loss promotes hepatocellular carcinoma. Genes & Development, 22 (11). pp. 1439-44. ISSN 0890-9369

Y

Yajnik, V., Paulding, C., Sordella, R., McClatchey, A. I., Saito, M., Wahrer, D. C., Reynolds, P., Bell, D. W., Lake, R., van den Heuvel, S., Settleman, J., Haber, D. A. (2003) DOCK4, a GTPase activator, is disrupted during tumorigenesis. Cell, 112 (5). pp. 673-84. ISSN 0092-8674 (Print)

Yang, M., Hu, Y., Lodhi, M., McCombie, W. R., Ma, H. (1999) The Arabidopsis SKP1-LIKE1 gene is essential for male meiosis and may control homologue separation. Proceedings of the National Academy of Sciences of the United States of America, 96 (20). pp. 11416-11421. ISSN 00278424 (ISSN)

Yang, Y., Tashman, A. P., Lee, J. Y., Yoon, S., Mao, W., Ahn, K., Kim, W., Mendell, N. R., Gordon, D., Finch, S. J. (2007) Mixture modeling of microarray gene expression data. BMC Proc, 1 (Suppl ). S50.

Yao, J., Zhang, K. X., Kramer, M., Pellegrini, M., McCombie, W. R. (2014) FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies. Bioinformatics. ISSN 1367-4803

Yoon, S., Xuan, Z., Makarov, V., Ye, K., Sebat, J. (2009) Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res, 19. p. 9.

Youens-Clark, K., Buckler, E., Casstevens, T., Chen, C., DeClerck, G., Derwent, P., Dharmawardhana, P., Jaiswal, P., Kersey, P., Karthikeyan, A. S., Lu, J., McCouch, S. R., Ren, L., Spooner, W., Stein, J. C., Thomason, J., Wei, S., Ware, D. H. (2011) Gramene database in 2010: Updates and extensions. Nucleic Acids Research, 39 (SUPPL.).

Youens-Clark, K., Faga, B. P., Yap, I. V., Stein, L. D., Ware, D. H. (2009) CMap 1.01: A comparative mapping application for the Internet. Bioinformatics, 25 (22). pp. 3040-3042.

Yu, Y., Rambo, T., Currie, J., Saski, C., Kim, H. R., Collura, K., Thompson, S., Simmons, J., Yang, T. J., Nah, G., Patel, A. J., Thurmond, S., Henry, D., Oates, R., Palmer, M., Pries, G., Gibson, J., Anderson, H., Paradkar, M., Crane, L., Dale, J., Carver, M. B., Wood, T., Frisch, D., Engler, F., Soderlund, C., Palmer, L. E., Tetylman, L., Nascimento, L., de la Bastide, M., Spiegel, L., Ware, D., O'Shaughnessy, A., Dike, S., Dedhia, N., Preston, R., Huang, E., Ferraro, K., Kuit, K., Miller, B., Zutavern, T., Katzenberger, F., Muller, S., Balija, V., Martienssen, R. A., Stein, L., Minx, P., Johnson, D., Cordum, H., Mardis, E., Cheng, Z., Jiang, J., Wilson, R., McCombie, W. R., Wing, R. A., Yuan, Q., Ouyang, S., Liu, J., Jones, K. M., Gansberger, K., Moffat, K., Hill, J., Tsitrin, T., Overton, L., Bera, J., Kim, M., Jin, S., Tallon, L., Ciecko, A., Pai, G., van Aken, S., Utterback, T., Reidmuller, S., Bormann, J., Feldblyum, T., Hsiao, J., Zismann, V., Blunt, S., de Vazeilles, A., Shaffer, T., Koo, H., Suh, B., Yang, Q., Haas, B., Peterson, J., Pertea, M., Volfovsky, N., Wortman, J., White, O., Salzberg, S. L., Fraser, C. M., Robin Buell, C., Messing, J., Song, R., Fuks, G., Llaca, V., Kovchak, S., Young, S., Bowers, J. E., Paterson, A. H. (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science, 300 (5625). pp. 1566-1569. ISSN 00368075 (ISSN)

Z

Zain, S., Sambrook, J., Roberts, R. J., Keller, W., Fried, M., Dunn, A. R. (1979) Nucleotide sequence analysis of the leader segments in a cloned copy of adenovirus 2 fiber mRNA. Cell, 16 (4). pp. 851-61. ISSN 0092-8674 (Print)0092-8674 (Linking)

Zaratiegui, B. M., Vaughn, M. W., Irvine, D. V., Goto, D. , Watt, S., Bahler, J., Arcangioli, B., Martienssen, R. A. (2011) CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR. Nature, 469 (7328). pp. 112-5. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Zaratiegui, M., Castel, S. E., Irvine, D. V., Kloc, A., Ren, J., Li, F., de Castro, E., Marin, L., Chang, A. Y., Goto, D., Cande, W. Z., Antequera, F., Arcangioli, B., Martienssen, R. A. (2011) RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II. Nature, 479 (7371). pp. 135-8. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Zaratiegui, M., Martienssen, R. (2012) The persistence of a silent memory. Nature genetics, 44 (2). pp. 118-9. ISSN 1546-1718 (Electronic)1061-4036 (Linking)

Zaratiegui, M., Martienssen, R. A. (2012) SnapShot: Small RNA-Mediated Epigenetic Modifications. Cell, 151 (2). 456-456 e1. ISSN 1097-4172 (Electronic)0092-8674 (Linking)

Zender, L., Lowe, S. W. (2008) Integrative oncogenomic approaches for accelerated cancer-gene discovery. Curr Opin Oncol, 20 (1). pp. 72-6.

Zeng, P. Y., Vakoc, C. R., Chen, Z. C., Blobel, G. A., Berger, S. L. (2006) In vivo dual cross-linking for identification of indirect DNA-associated proteins by chromatin immunoprecipitation. Biotechniques, 41 (6). pp. 694-698. ISSN 07366205 (ISSN)

Zhang, C., Krainer, A. R., Zhang, M. Q. (2007) Evolutionary impact of limited splicing fidelity in mammalian genes. Trends Genet, 23 (10). pp. 484-488. ISSN 0168-9525 (Print)

Zhang, C., Li, W. H., Krainer, A. R., Zhang, M. Q. (2008) RNA landscape of evolution for optimal exon and intron discrimination. Proc Natl Acad Sci U S A, 105 (15). 5797-5802 .

Zhang, C., Zhang, Z., Castle, J., Sun, S., Johnson, J., Krainer, A. R., Zhang, M. Q. (2008) Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev, 22 (18). pp. 2550-63.

Zhang, L., Chia, J. M., Kumari, S., Stein, J. C., Liu, Z., Narechania, A., Maher, C. A., Guill, K., McMullen, M. D., Ware, D. H. (2009) A Genome-Wide Characterization of MicroRNA Genes in Maize. PLoS Genet, 5 (11). e1000716. ISSN 1553-7404 (Electronic)

Zhang, M. Q. (2002) Computational prediction of eukaryotic protein-coding genes. Nature Reviews Genetics, 3 (9). pp. 698-709. ISSN 1471-0056

Zhang, M. Q. (2000) Discriminant analysis and its application in DNA sequence motif recognition. Brief Bioinform, 1 (4). pp. 331-42. ISSN 1467-5463 (Print)

Zhang, M. Q. (2002) Extracting functional information from microarrays: A challenge for functional genomics. Proceedings of the National Academy of Sciences of the United States of America, 99 (20). pp. 12509-12511. ISSN 0027-8424

Zhang, M. Q. (1998) Identification of human gene core promoters in silico. Genome Research, 8 (3). pp. 319-26. ISSN 1088-9051 (Print)

Zhang, M. Q. (2003) Prediction, annotation, and analysis of human promoters. Cold Spring Harbor Symposia on Quantitative Biology, 68. pp. 217-25. ISSN 0091-7451 (Print)

Zhang, M. Q. (2002) Using MZEF to find internal coding exons. Current Protocols in Bioinformatics , 4. Unit 4.2 .

Zhang, M. Q., Marr, T. G. (1993) Genome Mapping by Random Anchoring - a Discrete Theoretical-Analysis. Journal of Statistical Physics, 73 (3-4). pp. 611-623. ISSN 0022-4715

Zhang, M. Q., Smith, A. D. (2010) Challenges in understanding genome-wide DNA methylation. Journal of Computer Science and Technology, 25 (1). pp. 26-34.

Zhang, X., Douglas, R. N., Strable, J., Lee, M., Buckner, B., Janick-Buckner, D., Schnable, P. S., Timmermans, M. C. P., Scanlon, M. J. (2012) Punctate vascular expression1 is a novel maize gene required for leaf pattern formation that functions downstream of the trans-acting small interfering RNA pathway. Plant Physiology, 159 (4). pp. 1453-1462. ISSN 0032-0889

Zhang, Y., Mei, P. C., Lou, R., Zhang, M. Q., Wu, G. Y., Qiang, B. Q., Zhang, Z. G., Shen, Y. (2002) Gene expression profiling in developing human hippocampus. Journal of Neuroscience Research, 70 (2). pp. 200-208. ISSN 0360-4012

Zhang, Y., Shin, S. J., Liu, D., Ivanova, E., Foerster, F., Ying, H., Zheng, H., Xiao, Y., Chen, Z., Protopopov, A., Depinho, R. A., Paik, J. H. (2013) ZNF365 Promotes Stability of Fragile Sites and Telomeres. Cancer Discovery, 3 (7). pp. 798-811. ISSN 21598274

Zhao, W., Canaran, P., Jurkuta, R., Fulton, T., Glaubitz, J., Buckler, E., Doebley, J., Gaut, B., Goodman, M., Holland, J., Kresovich, S., McMullen, M., Stein, L. D., Ware, D. (2006) Panzea: a database and resource for molecular and functional diversity in the maize genome. Nucleic Acids Res, 34 (Databa). D752-7. ISSN 1362-4962 (Electronic)

Zhao, X., Herr, W. (2003) Role of the inhibitory DNA-binding surface of human TATA-binding protein in recruitment of human TFIIB family members. Molecular and Cellular Biology, 23 (22). pp. 8152-60. ISSN 0270-7306 (Print)

Zhao, X. M., Herr, W. (2002) A regulated two-step mechanism of TBP binding to DNA: A solvent-exposed surface of TBP inhibits TATA box recognition. Cell, 108 (5). pp. 615-627. ISSN 0092-8674

Zheng, B., Mills, A. A., Bradley, A. (2001) Introducing defined chromosomal rearrangements into the mouse genome. Methods, 24 (1). pp. 81-94. ISSN 10462023 (ISSN)

Zheng, B., Mills, A. A., Bradley, A. (1999) A system for rapid generation of coat color-tagged knockouts and defined chromosomal rearrangements in mice. Nucleic Acids Research, 27 (11). pp. 2354-2360. ISSN 03051048 (ISSN)

Zheng, J. Y., Sachidanandam, R., Bennett, K., Bonkovsky, H. L. (2008) Microrna 16 Regulates Expression of the Human 5-Aminolevulinic Acid Synthase-1 (Alas 1) Gene through Targeting the Coding Region of the Gene. Hepatology, 48 (4 Supp). 1117A. ISSN 0270-9139

Zheng, J. Y., Yang, X. M., Harrell, J. M., Ryzhikov, S., Shim, E. H., Lykke-Andersen, K., Wei, N., Sun, H., Kobayashi, R., Zhang, H. (2002) CAND1 binds to unneddylated CUL1 and regulates the formation of SCF ubiquitin E3 ligase complex. Molecular Cell, 10 (6). pp. 1519-1526. ISSN 1097-2765

Zheng, S. Y., Tansey, W. P., Hiebert, S. W., Zhao, Z. M. (2011) Integrative network analysis identified key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma. BMC Medical Genomics, 4 (62). ISSN 1755-8794

Zhou, S., Wei, F., Nguyen, J., Bechner, M., Potamousis, K., Goldstein, S., Pape, L., Mehan, M. R., Churas, C., Pasternak, S., Forrest, D. K., Wise, R., Ware, D. H., Wing, R. A., Waterman, M. S., Livny, M., Schwartz, D. C. (2009) A single molecule scaffold for the maize genome. PLoS Genet, 5 (11). e1000711. ISSN 1553-7404 (Electronic)

Zhu, H., Kim, D. J., Baek, J. M., Choi, H. K., Ellis, L. C., Küester, H., McCombie, W. R., Peng, H. M., Cook, D. R. (2003) Syntenic relationships between Medicago truncatula and Arabidopsis reveal extensive divergence of genome organization. Plant Physiology, 131 (3). pp. 1018-1026. ISSN 00320889 (ISSN)

Zimin, A. V., Delcher, A. L., Florea, L., Kelley, D. R., Schatz, M. C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C. P., Sonstegard, T. S., Marçais, G., Roberts, M., Subramanian, P., Yorke, J. A., Salzberg, S. L. (2009) A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology, 10 (4). ISSN 14747596 (ISSN)

Zink, M., Rapp, S., Gebicke-Haerter, P. J., Henn, F. A., Thome, J. (2005) Antidepressants differentially affect expression of complexin I and II RNA in rat hippocampus. Psychopharmacology (Berl), 181 (3). pp. 560-5. ISSN 0033-3158 (Print)0033-3158 (Linking)

Zink, M., Schmitt, A., May, B., Muller, B., Braus, D. F., Henn, F. A. (2004) Differential effects of long-term treatment with clozapine or haloperidol on GABA transporter expression. Pharmacopsychiatry, 37 (4). pp. 171-4. ISSN 0176-3679 (Print)0176-3679 (Linking)

Zorner, B., Wolfer, D. P., Brandis, D., Kretz, O., Zacher, C., Madani, R., Grunwald, I., Lipp, H. P., Klein, R., Henn, F. A., Gass, P. (2003) Forebrain-specific trkB-receptor knockout mice: behaviorally more hyperactive than "depressive". Biol Psychiatry, 54 (10). pp. 972-82. ISSN 0006-3223 (Print)0006-3223 (Linking)

Zoubarev, A., Hamer, K. M., Keshav, K. D., McCarthy, E. L., Santos, J. R. C., Van Rossum, T., McDonald, C., Hall, A., Wan, X., Lim, R., Gillis, J., Pavlidis, P. (2012) Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data. Bioinformatics, 28 (17). pp. 2272-2273. ISSN 1367-4803

Zuber, J., Rappaport, A. R., Luo, W., Wang, E., Chen, C., Vaseva, A. V., Shi, J., Weissmueller, S., Fellman, C., Taylor, M. J., Weissenboeck, M., Graeber, T. G., Kogan, S. C., Vakoc, C. R., Lowe, S. W. (2011) An integrated approach to dissecting oncogene addiction implicates a Myb-coordinated self-renewal program as essential for leukemia maintenance. Genes & Development, 25 (15). pp. 1628-1640. ISSN 0890-9369

Zylstra, G. J., McCombie, W. R., Gibson, D. T., Finette, B. A. (1988) Toluene Degradation by Pseudomonas putida Fl:Genetic Organization of the tod Operon. Applied and Environmental Microbiology, 54 (6). pp. 1498-1503. ISSN 0099-2240

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