Items where Subject is "bioinformatics"

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Number of items at this level: 661.

ENCODE Project Consortium, (October 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. (January 2013) Kerfuffle: a web tool for multi-species gene colocalization analysis. BMC Bioinformatics, 14. ISSN 1471-2105

Aboukhalil, Robert (March 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. (November 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. (June 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. (October 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. (June 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. (July 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. (November 2012) Talk from Mickey Atwal at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Atwal, G. S., Bialek, W (December 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. (June 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. (April 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. (January 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. (April 2008) The quest for the 1p36 tumor suppressor. Cancer Res, 68 (8). pp. 2551-6.

Ballouz, S., Dobin, A., Gingeras, T. R., Gillis, J. (May 2018) The fractured landscape of RNA-seq alignment: the default in our STARs. Nucleic Acids Res. ISSN 0305-1048

Ballouz, S., Gillis, J. (April 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., Gillis, J. (October 2017) DISTINGUISHING BIOLOGICAL FROM TECHNOLOGICAL SIGNALS IN THE FUNCTIONAL INTERPRETATION OF NEUROPSYCHIATRIC DISEASE GENES. European Neuropsychopharmacology, 27 (Supple). Abstract 31; S223-S224. ISSN 0924-977X

Ballouz, S., Gillis, J. (July 2017) Strength of functional signature correlates with effect size in autism. Genome Med, 9 (1). p. 64. ISSN 1756-994x

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

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

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

Barone, L., Williams, J., Micklos, D. (October 2017) Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators. PLoS Comput Biol, 13 (10). e1005755. ISSN 1553-734x

Bejerano, G., Siepel, A. C., Kent, W. J., Haussler, D. (July 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. (August 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. (August 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.

Berstein, Y., McCarthy, S., Kramer, M., Zandi, P., Goes, F., Potash, J., McCombie, R. (October 2017) RARE VARIANT DETECTION IN COMPLEX DISORDERS USING THE BIRTHDAY MODEL. European Neuropsychopharmacology, 27 (Supple). S367-S368, Meeting Abstract 2. ISSN 0924-977X

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. (September 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. (January 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. (April 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. (November 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. (November 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. (May 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. (April 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. (August 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. (August 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 (June 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. (June 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. (February 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. (October 2004) WormBase as an integrated platform for the C. elegans ORFeome. Genome Res, 14 (10B). pp. 2155-61. ISSN 1088-9051 (Print)

Chen, W. C., Tareen, A., Kinney, J. B. (October 2018) Density Estimation on Small Data Sets. Physical Review Letters, 121 (16). ISSN 00319007 (ISSN)

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. (March 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 (November 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. (August 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. (February 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. (November 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. (September 2005) The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biology, 3. ISSN 1741-7007

Chougule, K. M., Wang, L., Stein, J. C., Wang, X., Devisetty, U. K., Klein, R. R., Ware, D. (August 2018) Improved RNA-seq Workflows Using CyVerse Cyberinfrastructure. Curr Protoc Bioinformatics. e53. ISSN 1934-3396

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. (January 2015) Extending reference assembly models. Genome Biology, 16. Article no. 13. ISSN 1465-6906

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

Lyon, G. J. (March 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. (February 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. (May 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. (April 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. (March 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. (June 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. (June 2014) "ARD1 and NAT1 proteins from a complex that has N-terminal acetyltransferase activity". Journal Club. (Unpublished)

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

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

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

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

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

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

Lyon, Gholson J. (December 2014) Crystal structure of a TAF1-TAF7 complex in human transcription factor IID reveals a promoter binding module. Journal Club. (Unpublished)

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

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

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

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

Lyon, Gholson J. (December 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. (June 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. (July 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. (April 2013) Genome Engineering Using CRISPR. Journal Club. (Unpublished)

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

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

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

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

Lyon, Gholson J. (July 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. (October 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. (December 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. (March 2014) "Inefficient SRP interaction with a nascent chain triggers a mRNA quality control pathway". Journal Club. (Unpublished)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Lyon, Gholson J. (September 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. (October 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)

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