Items where Subject is "bioinformatics"

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Number of items at this level: 626.

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

A

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.

Adam-Blondon, A. F., Alaux, M., Pommier, C., Cantu, D., Cheng, Z. M., Cramer, G. R., Davies, C., Delrot, S., Deluc, L., Di Gaspero, G., Grimplet, J., Fennell, A., Londo, J. P., Kersey, P., Mattivi, F., Naithani, S., Neveu, P., Nikolski, M., Pezzotti, M., Reisch, B. I., Topfer, R., Vivier, M. A., Ware, D., Quesneville, H. (2016) Towards an open grapevine information system. Horticulture Research, 3. p. 16056. ISSN 2052-7276 (Linking)

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)

Altpeter, F., Springer, N. M., Bartley, L. E., Blechl, A., Brutnell, T. P., Citovsky, V., Conrad, L., Gelvin, S. B., Jackson, D., Kausch, A. P., Lemaux, P. G., Medford, J. I., Orozo-Cardenas, M., Tricoli, D., VanEck, J., Voytas, D. F., Walbot, V., Wang, K., Zhang, Z. J., Stewart, C. N. (2016) Advancing Crop Transformation in the Era of Genome Editing. Plant Cell, 28 (7). pp. 1510-1520. ISSN 1532-298X (Electronic)1040-4651 (Linking)

Amin, M. R., Skiena, S., Schatz, M. C. (2016) NanoBLASTer: Fast alignment and characterization of Oxford Nanopore single molecule sequencing reads. 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).

Antoniotti, M., Policriti, A., Ugel, N., Mishra, B. (2003) Model building and model checking for biochemical processes. Cell Biochemistry and Biophysics, 38 (3). pp. 271-286. ISSN 1085-9195

Arbiza, L., Gottipati, S., Siepel, A., Keinan, A. (2014) Contrasting X-linked and autosomal diversity across 14 human populations. Am J Hum Genet, 94 (6). pp. 827-44. ISSN 0002-9297

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

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., Bialek, W (2004) Ambiguous model learning made unambiguous with 1/f priors. NIPS.

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)

Atwal, G. S., Rabadan, R., Lozano, G., Strong, L. C., Ruijs, M. W., Schmidt, M. K., van't Veer, L. J., Nevanlinna, H., Tommiska, J., Aittomaki, K., Bougeard, G., Frebourg, T., Levine, A. J., Bond, G. L. (2008) An information-theoretic analysis of genetics, gender and age in cancer patients. PLoS ONE, 3 (4). e1951. ISSN 1932-6203 (Electronic)

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

Badner, J. A., Koller, D., Foroud, T., Edenberg, H., Nurnberger, J. I., Zandi, P. P., Willour, V. L., McMahon, F. J., Potash, J. B., Hamshere, M., Grozeva, D., Green, E., Kirov, G., Jones, I., Jones, L., Craddock, N., Morris, D., Segurado, R., Gill, M., Sadovnick, D., Remick, R., Keck, P., Kelsoe, J., Ayub, M., MacLean, A., Blackwood, D., Liu, C. Y., Gershon, E. S., McMahon, W., Lyon, G. J., Robinson, R., Ross, J., Byerley, W. (2012) Genome-wide linkage analysis of 972 bipolar pedigrees using single-nucleotide polymorphisms. Molecular Psychiatry, 17 (8). pp. 818-826. ISSN 1476-5578

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

Ballouz, S., Gillis, J. (2016) AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression. PLoS Comput Biol, 12 (4). e1004868. ISSN 1553-7358 (Electronic)1553-734X (Linking)

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., Pavlidis, P., Gillis, J. (2016) Using predictive specificity to determine when gene set analysis is biologically meaningful. Nucleic Acids Res. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

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

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.

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.

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)

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.

Blakeslee, Albert Francis (1933) Book Reviews: Principles of Genetics; A test-book with problems. Science, 77 (1994). pp. 284-285.

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)

Boyko, A. R., Quignon, P., Li, L., Schoenebeck, J. J., Degenhardt, J. D., Lohmueller, K. E., Zhao, K., Brisbin, A., Parker, H. G., vonHoldt, B. M., Cargill, M., Auton, A., Reynolds, A., Elkahloun, A. G., Castelhano, M., Mosher, D. S., Sutter, N. B., Johnson, G. S., Novembre, J., Hubisz, M. J., Siepel, A., Wayne, R. K., Bustamante, C. D., Ostrander, E. A. (2010) A simple genetic architecture underlies morphological variation in dogs. PLoS Biology, 8 (8). e1000451. ISSN 1544-9173

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

Braasch, I., Gehrke, A. R., Smith, J. J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., Berlin, A. M., Campbell, M. S., Barrell, D., Martin, K. J., Mulley, J. F., Ravi, V., Lee, A. P., Nakamura, T., Chalopin, D., Fan, S., Wcisel, D., Canestro, C., Sydes, J., Beaudry, F. E., Sun, Y., Hertel, J., Beam, M. J., Fasold, M., Ishiyama, M., Johnson, J., Kehr, S., Lara, M., Letaw, J. H., Litman, G. W., Litman, R. T., Mikami, M., Ota, T., Saha, N. R., Williams, L., Stadler, P. F., Wang, H., Taylor, J. S., Fontenot, Q., Ferrara, A., Searle, S. M., Aken, B., Yandell, M., Schneider, I., Yoder, J. A., Volff, J. N., Meyer, A., Amemiya, C. T., Venkatesh, B., Holland, P. W., Guiguen, Y., Bobe, J., Shubin, N. H., Di Palma, F., Alfoldi, J., Lindblad-Toh, K., Postlethwait, J. H. (2016) The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet, 48 (4). pp. 427-37. ISSN 1546-1718 (Electronic)1061-4036 (Linking)

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

Brauch, H., Deloukas, P., Kroetz, D., Pirmohamed, M. (2010) PHARMACOGENOMICS & PERSONALIZED THERAPY. In: 2010 meeting of PHARMACOGENOMICS & PERSONALIZED THERAPY, November 17–November 21, 2010, Cold Spring Harbor Laboratory.

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

Brown, M. S., Collins, F. S., Goldstein, J. L., Watson, J. D., Wexler, N. S. (1993) Round-Table - the Human Genome Project. Issues in Science and Technology, 10 (1). pp. 43-48. ISSN 0748-5492

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)

C

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)

Campbell, Michael, Oakeson, Kelly F., Yandell, Mark, Halpert, James R., Dearing, Denise (2016) The draft genome sequence and annotation of the desert woodrat Neotoma lepida. Genomics Data, 9. pp. 58-59. ISSN 2213-5960

Canaran, P., Buckler, E. S., Glaubitz, J. C., Stein, L. D., Sun, Q., Zhao, W., Ware, D. H. (2008) Panzea: an update on new content and features. Nucleic Acids Res, 36 (Databa). D1041-3.

Capra, J. A., Hubisz, M. J., Kostka, D., Pollard, K. S., Siepel, A. (2013) A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PLoS Genetics, 9 (8). e1003684. ISSN 15537390 (ISSN)

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

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)

Chen, G., Li, W., Zhang, Q. S. , Regulski, M. R., Sinha, N., Barditch, J., Tully, T. , Krainer, A. R., Zhang, M. Q., Dubnau, J. T. (2008) Identification of Synaptic Targets of Drosophila Pumilio. PLoS Computational Biology, 4 (2). e1000026. ISSN 1553734X

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)

Cheng, R., Juo, S. H., Loth, J. E., Nee, J., Iossifov, I., Blumenthal, R., Sharpe, L., Kanyas, K., Lerer, B., Lilliston, B., Smith, M., Trautman, K., Gilliam, T. C., Endicott, J., Baron, M. (2006) Genome-wide linkage scan in a large bipolar disorder sample from the National Institute of Mental Health genetics initiative suggests putative loci for bipolar disorder, psychosis, suicide, and panic disorder. Mol Psychiatry, 11 (3). pp. 252-60. ISSN 1359-4184 (Print)1359-4184 (Linking)

Cheng, Y., Ma, Z., Kim, B. H., Wu, W., Cayting, P., Boyle, A. P., Sundaram, V., Xing, X., Dogan, N., Li, J., Euskirchen, G., Lin, S., Lin, Y., Visel, A., Kawli, T., Yang, X., Patacsil, D., Keller, C. A., Giardine, B., Kundaje, A., Wang, T., Pennacchio, L. A., Weng, Z., Hardison, R. C., Snyder, M. P., Consortium, Mouse ENCODE (2014) Principles of regulatory information conservation between mouse and human. Nature, 515 (7527). pp. 371-5. ISSN 0028-0836

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

Chien, Y., Lowe, S. W. (2008) Secreting tumor suppression. Cell, 132 (3). pp. 339-41. ISSN 0092-8674

Chklovskii, D. B., Halperin, B. I. (1998) Consequences of a possible adiabatic transition between nu=1/3 and nu=1 quantum Hall states in a narrow wire. Physical Review B, 57 (7). pp. 3781-3784. ISSN 0163-1829

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

Church, D. M., Schneider, V. A., Steinberg, K. M., Schatz, M. C., Quinlan, A. R., Chin, C. S., Kitts, P. A., Aken, B., Marth, G. T., Hoffman, M. M., Herrero, J., Mendoza, M. L. Z., Durbin, R., Flicek, P. (2015) Extending reference assembly models. Genome Biology, 16. Article no. 13. ISSN 1465-6906

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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. (2016) Speaker in Diagnostic Odyssey Session. In: Utah Rare Disease Symposium,, Salt Lake City, UT. (Unpublished)

Lyon, G. J. (2015) Speaker, Rare Human Diseases as a Window into New Biology. In: Rare Human Diseases as a Window into New Biology, Lawrence, KS. (Unpublished)

Lyon, G. J. (2015) Speaker, Utah’s Inaugural Rare Disease Day Symposium. In: Utah’s Inaugural Rare Disease Day Symposium, Salt Lake City, UT. (Unpublished)

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. (2013) Cambridge HealthTech Institute Clinical Genomics Podcast: Highlights from the Upcoming Clinical Exome Sequencing Conference. [Audio]

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) "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. (2014) Crystal structure of a TAF1-TAF7 complex in human transcription factor IID reveals a promoter binding module. Journal Club. (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) 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. (2014) Human Genetic Variation and the Genotype-Phenotype Problem. In: Lecture to GE510: Graduate Genetics Course, December 4, 2014, Stony Brook University, Stony Brook, NY . (Unpublished)

Lyon, Gholson J. (2014) Human Genetics and Orphan Diseases. In: Cold Spring Harbor Laboratory In-House Symposium XXVIII, November 24 - 25, 2014, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. (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. (2014) "Inefficient SRP interaction with a nascent chain triggers a mRNA quality control pathway". Journal Club. (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. (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. (2014) National Academy of Sciences Journal Summit - Invited Panelist. In: National Academy of Sciences Journal Summit, March 2014, National Academy of Sciences, Washington D.C.. (Unpublished)

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

Lyon, Gholson J. (2016) New human neurologic and intellectual disability syndromes involving transcription, translation, and protein degradation. In: Columbia Child Neurology and Institute of Genomic Medicine, Columbia University, New York, NY. (Unpublished)

Lyon, Gholson J. (2016) New human neurologic and intellectual disability syndromes involving transcription, translation, and protein degradation. In: Computational Genomics Seminar Series, Icahn School of Medicine at Mount Sinai, NY. (Unpublished)

Lyon, Gholson J. (2015) Ogden Syndrome and the role of Nα-acetylation in human health and disease. In: 2015 Symposium of National Creative Initiatives Center for Immune and Vascular Cell Network (NCIC-IVCN), Ewha Womans University, Seoul, Korea. (Unpublished)

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) 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. (2015) Variants in TAF1 are associated with a new syndrome with severe intellectual disability and characteristic dysmorphic features. In: 17th International Fragile X and Other Early-Onset Cognitive Disorders Workshop, Strasbourg, France. (Unpublished)

Lyon, Gholson J. (2015) Variants in TAF1 are associated with a new syndrome with severe intellectual disability and characteristic dysmorphic features. In: he American Society of Human Genetics (ASHG) 2015, Baltimore, MD. (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 sequencing, clinical interpretation, and deep brain stimulation in a severely mentally ill person". In: CSHL Neuronal Circuits Meeting, April 2nd-5th 2014, Cold Spring Harbor Laboratory. (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) A new intellectual disability syndrome. In: Seminar, Cold Spring Harbor Laboratory In-House Seminar Series, Cold Spring Harbor, NY. (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., 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., 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: New York Genome Center Lecture Series, May 22nd 2014, New York Genome Center - NYC . (Unpublished)

Lyon, Gholson J. (2015) Genetic Complexity and Neuropsychiatric Disorders. In: Institute of Medical Genetics and Functional Genomics, Hosted by Svetlana Gorokhova, Marseille, France. (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.

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