Items where Subject is "comparative genomics"

Paper

Abeshouse, A., Adebamowo, C., Adebamowo, S. N., Akbani, R., Akeredolu, T., Ally, A., Anderson, M. L., Anur, P., Appelbaum, E. L., Armenia, J., Auman, J. T., Bailey, M. H., Baker, L., Balasundaram, M., Balu, S., Barthel, F. P., Bartlett, J., Baylin, S. B., Behera, M., Belyaev, D., Bennett, J., Benz, C., Beroukhim, R., Birrer, M., Bocklage, T., Bodenheimer, T., Boice, L., Bootwalla, M. S., Bowen, J., Bowlby, R., Boyd, J., Brohl, A. S., Brooks, D., Byers, L., Carlsen, R., Castro, P., Chen, H. W., Cherniack, A. D., Chibon, F., Chin, L., Cho, J., Chuah, E., Chudamani, S., Cibulskis, C., Cooper, L. A. D., Cope, L., Cordes, M. G., Crain, D., Curley, E., Danilova, L., Dao, F., Davis, I. J., Davis, L. E., Defreitas, T., Delman, K., Demchok, J. A., Demetri, G. D., Demicco, E. G., Dhalla, N., Diao, L., Ding, L., DiSaia, P., Dottino, P., Doyle, L. A., Drill, E., Dubina, M., Eschbacher, J., Fedosenko, K., Felau, I., Ferguson, M. L., Frazer, S., Fronick, C. C., Fulidou, V., Fulton, L. A., Fulton, R. S., Gabriel, S. B., Gao, J., Gao, Q., Gardner, J., Gastier-Foster, J. M., Gay, C. M., Gehlenborg, N., Gerken, M., Getz, G., Godwin, A. K., Godwin, E. M., Gordienko, E., Grilley-Olson, J. E., Gutman, D. A., Gutmann, D. H., Hayes, D. N., Hegde, A. M., Heiman, D. I., Heins, Z., Helsel, C., Hepperla, A. J., Higgins, K., Hoadley, K. A., Hobensack, S., Holt, R. A., Hoon, D. B., Hornick, J. L., Hoyle, A. P., Hu, X., Huang, M., Hutter, C. M., Iacocca, M., Ingram, D. R., Ittmann, M., Iype, L., Jefferys, S. R., Jones, K. B., Jones, C. D., Jones, S. J. M., Kalir, T., Karlan, B. Y., Karseladze, A., Kasaian, K., Kim, J., Kundra, R., Kuo, H., Ladanyi, M., Lai, P. H., Laird, P. W., Larsson, E., Lawrence, M. S., Lazar, A. J., Lee, S., Lee, D., Lehmann, K. V., Leraas, K. M., Lester, J., Levine, D. A., Li, I., Lichtenberg, T. M., Lin, P., Liu, J., Liu, W., Liu, E. M., Lolla, L., Lu, Y., Ma, Y., Madan, R., Maglinte, D. T., Magliocco, A., Maki, R. G., Mallery, D., Manikhas, G., Mardis, E. R., Mariamidze, A., Marra, M. A., Martignetti, J. A., Martinez, C., Mayo, M., McLellan, M. D., Meier, S., Meng, S., Meyerson, M., Mieczkowski, P. A., Miller, C. A., Mills, G. B., Moore, R. A., Morris, S., Mose, L. E., Mozgovoy, E., Mungall, A. J., Mungall, K., Nalisnik, M., Naresh, R., Newton, Y., Noble, M. S., Novak, J. E., Ochoa, A., Olvera, N., Owonikoko, T. K., Paklina, O., Parfitt, J., Parker, J. S., Pastore, A., Paulauskis, J., Penny, R., Pereira, E., Perou, C. M., Perou, A. H., Pihl, T., Pollock, R. E., Potapova, O., Radenbaugh, A. J., Ramalingam, S. S., Ramirez, N. C., Rathmell, W. K., Raut, C. P., Riedel, R. F., Reilly, C., Reynolds, S. M., Roach, J., Robertson, A. G., Roszik, J., Rubin, B. P., Sadeghi, S., Saksena, G., Salner, A., Sanchez-Vega, F., Sander, C., Schein, J. E., Schmidt, H. K., Schultz, N., Schumacher, S. E., Sekhon, H., Senbabaoglu, Y., Setdikova, G., Shelton, C., Shelton, T., Shen, R., Shi, Y., Shih, J., Shmulevich, I., Sica, G. L., Simons, J. V., Singer, S., Sipahimalani, P., Skelly, T., Socci, N., Sofia, H. J., Soloway, M. G., Spellman, P., Sun, Q., Swanson, P., Tam, A., Tan, D., Tarnuzzer, R., Thiessen, N., Thompson, E., Thorne, L. B., Tong, P., Torres, K. E., van de Rijn, M., Van Den Berg, D. J., Van Tine, B. A., Veluvolu, U., Verhaak, R., Voet, D., Voronina, O., Wan, Y., Wang, Z., Wang, J., Weinstein, J. N., Weisenberger, D. J., Wilkerson, M. D., Wilson, R. K., Wise, L., Wong, T., Wong, W., Wrangle, J., Wu, Y., Wyczalkowski, M., Yang, L., Yau, C., Yellapantula, V., Zenklusen, J. C., Zhang, J. J., Zhang, H., Zhang, H., Zmuda, E., The Cancer Genome Atlas Research, Network (2017) Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas. Cell, 171 (4). 950-965.e28. (Public Dataset)

Hejase, H. A., Dukler, N., Siepel, A. (January 2020) From Summary Statistics to Gene Trees: Methods for Inferring Positive Selection. Trends Genet. ISSN 0168-9525 (Print)0168-9525

Hufford, Matthew B, Seetharam, Arun S, Woodhouse, Margaret R, Chougule, Kapeel M, Ou, Shujun, Liu, Jianing, Ricci, William A, Guo, Tingting, Olson, Andrew, Qiu, Yinjie, Della Coletta, Rafael, Tittes, Silas, Hudson, Asher I, Marand, Alexandre P, Wei, Sharon, Lu, Zhenyuan, Wang, Bo, Tello-Ruiz, Marcela K, Piri, Rebecca D, Wang, Na, Kim, Dong Won, Zeng, Yibing, O'Connor, Christine H, Li, Xianran, Gilbert, Amanda M, Baggs, Erin, Krasileva, Ksenia V, Portwood, John L, Cannon, Ethalinda KS, Andorf, Carson M, Manchanda, Nancy, Snodgrass, Samantha J, Hufnagel, David E, Jiang, Qiuhan, Pedersen, Sarah, Syring, Michael L, Kudrna, David A, Llaca, Victor, Fengler, Kevin, Schmitz, Robert J, Ross-Ibarra, Jeffrey, Yu, Jianming, Gent, Jonathan I, Hirsch, Candice N, Ware, Doreen, Dawe, R Kelly (August 2021) De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science, 373 (6555). pp. 655-662. ISSN 0036-8075

Locke, D. P., Hillier, L. W., Warren, W. C., Worley, K. C., Nazareth, L. V., Muzny, D. M., Yang, S. P., Wang, Z., Chinwalla, A. T., Minx, P., Mitreva, M., Cook, L., Delehaunty, K. D., Fronick, C., Schmidt, H., Fulton, L. A., Fulton, R. S., Nelson, J. O., Magrini, V., Pohl, C., Graves, T. A., Markovic, C., Cree, A., Dinh, H. H., Hume, J., Kovar, C. L., Fowler, G. R., Lunter, G., Meader, S., Heger, A., Ponting, C. P., Marques-Bonet, T., Alkan, C., Chen, L., Cheng, Z., Kidd, J. M., Eichler, E. E., White, S., Searle, S., Vilella, A. J., Chen, Y., Flicek, P., Ma, J., Raney, B., Suh, B., Burhans, R., Herrero, J., Haussler, D., Faria, R., Fernando, O., Darre, F., Farre, D., Gazave, E., Oliva, M., Navarro, A., Roberto, R., Capozzi, O., Archidiacono, N., Della Valle, G., Purgato, S., Rocchi, M., Konkel, M. K., Walker, J. A., Ullmer, B., Batzer, M. A., Smit, A. F., Hubley, R., Casola, C., Schrider, D. R., Hahn, M. W., Quesada, V., Puente, X. S., Ordonez, G. R., Lopez-Otin, C., Vinar, T., Brejova, B., Ratan, A., Harris, R. S., Miller, W., Kosiol, C., Lawson, H. A., Taliwal, V., Martins, A. L., Siepel, A., Roychoudhury, A., Ma, X., Degenhardt, J., Bustamante, C. D., Gutenkunst, R. N., Mailund, T., Dutheil, J. Y., Hobolth, A., Schierup, M. H., Ryder, O. A., Yoshinaga, Y., de Jong, P. J., Weinstock, G. M., Rogers, J., Mardis, E. R., Gibbs, R. A. (January 2011) Comparative and demographic analysis of orang-utan genomes. Nature, 469 (7331). pp. 529-33. ISSN 0028-0836

Majdandzic, Antonio, Rajesh, Chandana, Tang, Amber, Toneyan, Shushan, Labelson, Ethan, Tripathy, Rohit, Koo, Peter K (November 2022) Selecting deep neural networks that yield consistent attribution-based interpretations for genomics. Proc Mach Learn Res, 200. pp. 131-149. ISSN 2640-3498

McCombie, W. R., McPherson, J. D., Mardis, E. R. (November 2018) Next-Generation Sequencing Technologies. Cold Spring Harb Perspect Med, 9 (11). ISSN 2157-1422

Parida, L., Atwal, G., Mishra, B. (October 2014) Proceedings of The Twelfth Annual RECOMB Comparative Genomics Conference. BMC Genomics, 15 (Suppl ). I1. ISSN 1471-2164

Pollard, K. S., Salama, S. R., King, B., Kern, A. D., Dreszer, T., Katzman, S., Siepel, A., Pedersen, J. S., Bejerano, G., Baertsch, R., Rosenbloom, K. R., Kent, J., Haussler, D. (October 2006) Forces shaping the fastest evolving regions in the human genome. PLoS Genet, 2 (10). e168. ISSN 1553-7390

Ramani, R., Krumholz, K., Huang, Y. F., Siepel, A. (November 2018) PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP. Bioinformatics, 35 (13). pp. 2320-2322. ISSN 1367-4803

Schmack, Katharina, Ott, Torben, Kepecs, Adam (November 2021) Computational Psychiatry Across Species to Study the Biology of Hallucinations. JAMA Psychiatry. ISSN 2168-622X

Siepel, A. (July 2019) Challenges in funding and developing genomic software: roots and remedies. Genome Biol, 20 (1). p. 147. ISSN 1474-7596

Siepel, A., Diekhans, M., Brejova, B., Langton, L., Stevens, M., Comstock, C. L., Davis, C., Ewing, B., Oommen, S., Lau, C., Yu, H. C., Li, J., Roe, B. A., Green, P., Gerhard, D. S., Temple, G., Haussler, D., Brent, M. R. (December 2007) Targeted discovery of novel human exons by comparative genomics. Genome Res, 17 (12). pp. 1763-73. ISSN 1088-9051 (Print)1088-9051

Sun, G., Krasnitz, A. (2019) CORE: A Software Tool for Delineating Regions of Recurrent DNA Copy Number Alteration in Cancer. Methods Mol Biol, 1878. pp. 85-93. ISSN 1064-3745

Suzuki, H., Lefebure, T., Hubisz, M. J., Pavinski Bitar, P., Lang, P., Siepel, A., Stanhope, M. J. (2011) Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution. Genome Biol Evol, 3. pp. 168-85. ISSN 1759-6653

Tello-Ruiz, M. K., Naithani, S., Stein, J. C., Gupta, P., Campbell, M., Olson, A., Wei, S., Preece, J., Geniza, M. J., Jiao, Y., Lee, Y. K., Wang, B., Mulvaney, J., Chougule, K., Elser, J., Al-Bader, N., Kumari, S., Thomason, J., Kumar, V., Bolser, D. M., Naamati, G., Tapanari, E., Fonseca, N., Huerta, L., Iqbal, H., Keays, M., Munoz-Pomer Fuentes, A., Tang, A., Fabregat, A., D'Eustachio, P., Weiser, J., Stein, L. D., Petryszak, R., Papatheodorou, I., Kersey, P. J., Lockhart, P., Taylor, C., Jaiswal, P., Ware, D. (January 2018) Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res, 46 (D1). D1181-D1189. ISSN 0305-1048

Tello-Ruiz, M. K., Stein, J., Wei, S., Preece, J., Olson, A., Naithani, S., Amarasinghe, V., Dharmawardhana, P., Jiao, Y., Mulvaney, J., Kumari, S., Chougule, K., Elser, J., Wang, B., Thomason, J., Bolser, D. M., Kerhornou, A., Walts, B., Fonseca, N. A., Huerta, L., Keays, M., Tang, Y. A., Parkinson, H., Fabregat, A., McKay, S., Weiser, J., D'Eustachio, P., Stein, L., Petryszak, R., Kersey, P. J., Jaiswal, P., Ware, D. (January 2016) Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res, 44 (D1). D1133-40. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Tello-Ruiz, M. K., Stein, J., Wei, S., Youens-Clark, K., Jaiswal, P., Ware, D. (January 2016) Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods Mol Biol, 1374. pp. 141-63. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Tello-Ruiz, Marcela Karey, Jaiswal, Pankaj, Ware, Doreen (January 2022) Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods in Molecular Biology, 2443. pp. 101-131. ISSN 1064-3745

Thomas, J. W., Touchman, J. W., Blakesley, R. W., Bouffard, G. G., Beckstrom-Sternberg, S. M., Margulies, E. H., Blanchette, M., Siepel, A. C., Thomas, P. J., McDowell, J. C., Maskeri, B., Hansen, N. F., Schwartz, M. S., Weber, R. J., Kent, W. J., Karolchik, D., Bruen, T. C., Bevan, R., Cutler, D. J., Schwartz, S., Elnitski, L., Idol, J. R., Prasad, A. B., Lee-Lin, S. Q., Maduro, V. V., Summers, T. J., Portnoy, M. E., Dietrich, N. L., Akhter, N., Ayele, K., Benjamin, B., Cariaga, K., Brinkley, C. P., Brooks, S. Y., Granite, S., Guan, X., Gupta, J., Haghighi, P., Ho, S. L., Huang, M. C., Karlins, E., Laric, P. L., Legaspi, R., Lim, M. J., Maduro, Q. L., Masiello, C. A., Mastrian, S. D., McCloskey, J. C., Pearson, R., Stantripop, S., Tiongson, E. E., Tran, J. T., Tsurgeon, C., Vogt, J. L., Walker, M. A., Wetherby, K. D., Wiggins, L. S., Young, A. C., Zhang, L. H., Osoegawa, K., Zhu, B., Zhao, B., Shu, C. L., De Jong, P. J., Lawrence, C. E., Smit, A. F., Chakravarti, A., Haussler, D., Green, P., Miller, W., Green, E. D. (August 2003) Comparative analyses of multi-species sequences from targeted genomic regions. Nature, 424 (6950). pp. 788-93. ISSN 0028-0836

Wang, Y., Diehl, A., Wu, F., Vrebalov, J., Giovannoni, J., Siepel, A., Tanksley, S. D. (September 2008) Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics, 180 (1). pp. 391-408. ISSN 0016-6731 (Print)0016-6731

Yang, N., Xu, X. W., Wang, R. R., Peng, W. L., Cai, L., Song, J. M., Li, W., Luo, X., Niu, L., Wang, Y., Jin, M., Chen, L., Luo, J., Deng, M., Wang, L., Pan, Q., Liu, F., Jackson, D., Yang, X., Chen, L. L., Yan, J. (November 2017) Contributions of Zea mays subspecies mexicana haplotypes to modern maize. Nat Commun, 8 (1). p. 1874. ISSN 2041-1723

Thesis

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