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

A

Abdelhamid, R. F., Plessy, C., Yamauchi, Y., Taoka, M., de Hoon, M., Gingeras, T. R., Isobe, T., Carninci, P. (2014) Multiplicity of 5' Cap Structures Present on Short RNAs. PLoS One, 9 (7). e102895. ISSN 1932-6203

Abraham, J., Nasmyth, K. A., Strathern, J. N., Klar, A. J. S., Hicks, J. B. (1984) Regulation of mating-type information in yeast. Negative control requiring sequences both 5′ and 3′ to the regulated region. Journal of Molecular Biology, 176 (3). pp. 307-331. ISSN 00222836 (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)

Alcorta, D. A., Xiong, Y., Phelps, D., Hannon, G., Beach, D., Barrett, J. C. (1996) Involvement of the cyclin-dependent kinase inhibitor p16 (INK4a) in replicative senescence of normal human fibroblasts. Proceedings of the National Academy of Sciences of the United States of America, 93 (24). pp. 13742-13747. ISSN 00278424 (ISSN)

Almagro, S., Dimitrov, S., Hirano, T., Vallade, M., Riveline, D. (2003) Individual chromosomes as viscoelastic copolymers. Europhysics Letters, 63 (6). pp. 908-914. ISSN 0295-5075

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

Alpatov, R., Lesch, B. J., Nakamoto-Kinoshita, M., Blanco, A., Chen, S., Stutzer, A., Armache, K. J., Simon, M. D., Xu, C., Ali, M., Murn, J., Prisic, S., Kutateladze, T. G., Vakoc, C. R., Min, J., Kingston, R. E., Fischle, W., Warren, S. T., Page, D. C., Shi, Y. (2014) A Chromatin-Dependent Role of the Fragile X Mental Retardation Protein FMRP in the DNA Damage Response. Cell, 157 (4). pp. 869-81. ISSN 0092-8674

Amero, S. A., Raychaudhuri, G., Cass, C. L., Vanvenrooij, W. J., Habets, W. J., Krainer, A. R., Beyer, A. L. (1992) Independent deposition of heterogeneous nuclear ribonucleoproteins and small nuclear ribonucleoprotein particles at sites of transcription. Proceedings of the National Academy of Sciences of the United States of America, 89 (18). pp. 8409-8413. ISSN 0027-8424

Ando, S., Sarlis, N. J., Krishnan, J., Feng, X., Refetoff, S., Zhang, M. Q., Oldfield, E. H., Yen, P. M. (2001) Aberrant alternative splicing of thyroid hormone receptor in a TSH-secreting pituitary tumor is a mechanism for hormone resistance. Molecular Endocrinology, 15 (9). pp. 1529-1538. ISSN 0888-8809

Andresen, B. S., Krainer, A. R. (2009) When the genetic code is not enough: How sequence variations can affect pre-mRNA splicing and cause (complex) disease. In: Genetics of Complex Human Diseases: A Laboratory Manual. Cold Spring Harbor Laboratory Press, pp. 165-182. ISBN 9780879698836

Andresen, B. S., Nielsen, K. B., Madsen, P. P., Corydon, T. J., Kjems, J., Krainer, A. R., Elpeleg, O. N., Schroeder, L. D., Gregersen, N. (2002) Simple mutations in the coding region of three acyl-CoA dehydrogenase genes may lead to skipping of the constitutive exon due to disruption of potential splice enhancer sequences or mRNA secondary structures. American Journal of Human Genetics, 71 (4). p. 196. ISSN 0002-9297

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

Aras, R. A., Small, A. J., Ando, T., Blaser, M. J. (2002) Helicobacter pylori interstrain restriction-modification diversity prevents genome subversion by chromosomal DNA from competing strains. Nucleic Acids Research, 30 (24). pp. 5391-5397. ISSN 0305-1048

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., Hannon, G. J. (2008) Small RNA silencing pathways in germ and stem cells. Cold Spring Harb Symp Quant Biol, 73. pp. 283-90. ISSN 1943-4456 (Electronic)0091-7451 (Linking)

Aravin, A. A., Sachidanandam, R., Bourc'his, D., Schaefer, C., Pezic, D., Toth, K. F., Bestor, T., Hannon, G. J. (2008) A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice. Molecular Cell, 31 (6). pp. 785-799. ISSN 10972765 (ISSN)

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

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

Atkins, J. F., Steitz, J. A., Anderson, C. W., Model, P. (1979) Binding of mammalian ribosomes to MS2 phage RNA reveals an overlapping gene encoding a lysis function. Cell, 18 (2). pp. 247-56. ISSN 0092-8674 (Print)0092-8674 (Linking)

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

Michael Wigler (1987) Processes for inserting DNA into eucaryotic cells and for producing proteinaceous materials. United States Patent 4634665. .

Ayoub, N., Noma, K., Isaac, S., Kahan, T., Grewal, S. I. S., Cohen, A. (2003) A novel jmjC domain protein modulates heterochromatization in fission yeast. Molecular and Cellular Biology, 23 (12). pp. 4356-4370. ISSN 0270-7306

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

Ballantyne, J., Sensabaugh, G., Witkowski, J.A. (1989) DNA technology and forensic science. Cold Spring Harbor Laboratory. ISBN 9780879692322

Ballesteros, M. L., Bolle, C., Lois, L. M., Moore, J. M., Vielle-Calzada, J. P., Grossniklaus, U., Chua, N. H. (2001) LAF1, a MYB transcription activator for phytochrome A signaling. Genes & Development, 15 (19). pp. 2613-2625. ISSN 0890-9369

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

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

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

Bardot, E. S., Valdes, V. J., Zhang, J., Perdigoto, C. N., Nicolis, S., Hearn, S. A., Silva, J. M., Ezhkova, E. (2013) Polycomb subunits Ezh1 and Ezh2 regulate the Merkel cell differentiation program in skin stem cells. Embo Journal, 32 (14). pp. 1990-2000. ISSN 02614189

Barkan, A., Martienssen, R. A. (1991) Inactivation of maize transposon Mu suppresses a mutant phenotype by activating an outward-reading promoter near the end of Mu1. Proceedings of the National Academy of Sciences of the United States of America, 88 (8). pp. 3502-3506. ISSN 0027-8424

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., Gingeras, T. R. (2013) RAMPAGE: Promoter activity profiling by paired-end sequencing of 5'-complete cDNAs. Current Protocols in Molecular Biology (SUPPL). Unit25B. ISSN 19343639 (ISSN)

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)

Baulcombe, D., Huttly, A., Martienssen, R. (1987) Hormonal and development control of gene expression in wheat. Biochem Soc Trans, 15 (1). pp. 9-11. ISSN 0300-5127

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Bazarov, A. V., van Sluis, M., Hines, W. C., Bassett, E., Beliveau, A., Campeau, E., Mukhopadhyay, R., Lee, W. J., Melodyev, S., Zaslavsky, Y., Lee, L., Rodier, F., Chicas, A., Lowe, S. W., Benhattar, J., Ren, B., Campisi, J., Yaswen, P. (2010) p16(INK4a)-mediated suppression of telomerase in normal and malignant human breast cells. Aging Cell, 9 (5). pp. 736-746. ISSN 1474-9718

Bazett-Jones, D. P., Kimura, K., Hirano, T. (2002) Efficient supercoiling of DNA by a single condensin complex as revealed by electron spectroscopic imaging. Molecular Cell, 9 (6). pp. 1183-1190. ISSN 1097-2765

Beausejour, C. M., Krtolica, A., Galimi, F., Narita, M., Lowe, S. W., Yaswen, P., Campisi, J. (2003) Reversal of human cellular senescence: roles of the p53 and p16 pathways. Embo Journal, 22 (16). pp. 4212-4222. ISSN 0261-4189

Bejerano, G., Lowe, C. B., Ahituv, N., King, B., Siepel, A., Salama, S. R., Rubin, E. M., Kent, W. J., Haussler, D. (2006) A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature, 441 (7089). pp. 87-90. ISSN 0028-0836

Bell, R. D., Long, X., Lin, M., Bergmann, J. H., Nanda, V., Cowan, S. L., Zhou, Q., Han, Y., Spector, D. L., Zheng, D., Miano, J. M. (2014) Identification and Initial Functional Characterization of a Human Vascular Cell-Enriched Long Noncoding RNA. Arteriosclerosis, thrombosis, and vascular biology, 34 (6). pp. 1249-1259. ISSN 1079-5642

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)

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

Bender, H. S., Murchison, E. P., Pickett, H. A., Deakin, J. E., Strong, M. A., Conlan, C., McMillan, D. A., Neumann, A. A., Greider, C. W., Hannon, G. J., Reddel, R. R., Graves, J. A. M. (2012) Extreme Telomere Length Dimorphism in the Tasmanian Devil and Related Marsupials Suggests Parental Control of Telomere Length. PLoS One, 7 (9). ISSN 19326203 (ISSN)

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.

Benitah, S. A., Valeron, P. F., Van Aelst, L., Marshall, C. J., Lacal, J. C. (2004) Rho GTPases in human cancer: an unresolved link to upstream and downstream transcriptional regulation. Biochimica Et Biophysica Acta-Reviews on Cancer, 1705 (2). pp. 121-132. ISSN 0304-419X

Berenstein, D., Olesen, K., Speck, C., Skovgaard, O. (2002) Genetic organization of the Vibrio harveyi dnaA gene region and analysis of the function of the V-harveyi DnaA protein in Escherichia coli. Journal of Bacteriology, 184 (9). 2533-+. ISSN 0021-9193

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

Bernstein, E., Caudy, A. A., Hammond, S. M., Hannon, G. J. (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409 (6818). pp. 363-366. ISSN 00280836 (ISSN)

Bernstein, E., Denli, A. M., Hannon, G. J. (2001) The rest is silence. RNA, 7 (11). pp. 1509-1521. ISSN 13558382 (ISSN)

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 .

Bhattacharjee, S., Osman, F., Feeney, L., Lorenz, A., Bryer, C., Whitby, M. C. (2013) MHF1-2/CENP-S-X performs distinct roles in centromere metabolism and genetic recombination. Open Biology, 3 (SEP). ISSN 20462441 (ISSN)

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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

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Blank, H. M., Sheltzer, J. M., Meehl, C. M., Amon, A. (2015) Mitotic entry in the presence of DNA damage is a widespread property of aneuploidy in yeast. Mol Biol Cell, 26 (8). pp. 1440-51. ISSN 1939-4586 (Electronic)1059-1524 (Linking)

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Bodnar, M. S., Spector, D. L. (2013) Chromatin Meets Its Organizers. Cell, 153 (6). pp. 1187-1189. ISSN 0092-8674

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Bolduc, N., Hake, S., Jackson, D. (2008) Dual functions of the KNOTTED1 homeodomain: sequence-specific DNA binding and regulation of cell-to-cell transport. Science Signaling, 1 (23). pe28.

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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

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., Calarco, J. P., Martienssen, R. A. (2013) Reprogramming the Epigenome in Arabidopsis Pollen. Cold Spring Harbor Symposia on Quantitative Biology, 77. pp. 1-5. ISSN 00917451 (ISSN)

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

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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

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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)

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