Siepel, Adam Publications

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Siepel, Adam

http://siepellab.labsites.cshl.edu/
Number of items at this level: 91.

Paper

Dukler, N., Booth, G. T., Huang, Y. F., Tippens, N., Waters, C. T., Danko, C. G., Lis, J. T., Siepel, A. (2017) Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol. Genome Res, 27 (11). pp. 1816-1829. ISSN 1088-9051

Kondo, S., Vedanayagam, J., Mohammed, J., Eizadshenass, S., Kan, L., Pang, N., Aradhya, R., Siepel, A., Steinhauer, J., Lai, E. C. (2017) New genes often acquire male-specific functions but rarely become essential in Drosophila. Genes Dev, 31 (18). pp. 1841-1846. ISSN 0890-9369

Huang, Y. F., Gulko, B., Siepel, A. (2017) Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. Nat Genet, 49 (4). pp. 618-624. ISSN 1061-4036

Dukler, N., Gulko, B., Huang, Y. F., Siepel, A. (2016) Is a super-enhancer greater than the sum of its parts? Nat Genet, 49 (1). pp. 2-3. ISSN 1546-1718 (Electronic)1061-4036 (Linking)

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

Kuhlwilm, M., Gronau, I., Hubisz, M. J., de Filippo, C., Prado-Martinez, J., Kircher, M., Fu, Q., Burbano, H. A., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Marques-Bonet, T., Andres, A. M., Viola, B., Paabo, S., Meyer, M., Siepel, A., Castellano, S. (2016) Ancient gene flow from early modern humans into Eastern Neanderthals. Nature, 530 (7591). pp. 429-433. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

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)

Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., Cheung, V. G., Kraus, W. L., Lis, J. T., Siepel, A. (2015) Identification of active transcriptional regulatory elements from GRO-seq data. Nat Methods, 12 (5). pp. 433-8. ISSN 1548-7105 (Electronic)1548-7091 (Linking)

Fuda, N. J., Guertin, M. J., Sharma, S., Danko, C. G., Martins, A. L., Siepel, A., Lis, J. T. (2015) GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters. Plos Genetics, 11 (3). e1005108. ISSN 1553-7390

Gulko, B., Hubisz, M. J., Gronau, I., Siepel, A. (2015) A method for calculating probabilities of fitness consequences for point mutations across the human genome. Nature Genetics, 47 (3). pp. 276-283. ISSN 1061-4036

Mohammed, J., Siepel, A., Lai, E. C. (2014) Diverse modes of evolutionary emergence and flux of conserved microRNA clusters. RNA, 20 (12). pp. 1850-1863. ISSN 13558382

Core, L. J., Martins, A. L., Danko, C. G., Waters, C. T., Siepel, A., Lis, J. T. (2014) Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet, 46 (12). pp. 1311-20. ISSN 1061-4036

Siepel, A., Arbiza, L. (2014) Cis-regulatory elements and human evolution. Curr Opin Genet Dev, 29c. pp. 81-89. ISSN 0959-437x

Peng, X., Alfoldi, J., Gori, K., Eisfeld, A. J., Tyler, S. R., Tisoncik-Go, J., Brawand, D., Law, G. L., Skunca, N., Hatta, M., Gasper, D. J., Kelly, S. M., Chang, J., Thomas, M. J., Johnson, J., Berlin, A. M., Lara, M., Russell, P., Swofford, R., Turner-Maier, J., Young, S., Hourlier, T., Aken, B., Searle, S., Sun, X., Yi, Y., Suresh, M., Tumpey, T. M., Siepel, A., Wisely, S. M., Dessimoz, C., Kawaoka, Y., Birren, B. W., Lindblad-Toh, K., Di Palma, F., Engelhardt, J. F., Palermo, R. E., Katze, M. G. (2014) The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease. Nat Biotechnol, 32 (12). pp. 1250-5. ISSN 1087-0156

Couger, M. B., Pipes, L., Squina, F., Prade, R., Siepel, A., Palermo, R., Katze, M. G., Mason, C. E., Blood, P. D. (2014) Enabling large-scale next-generation sequence assembly with Blacklight. Concurrency and computation : practice & experience, 26 (13). pp. 2157-2166. ISSN 1532-0626 (Print)1532-0626

Mohammed, J., Bortolamiol-Becet, D., Flynt, A. S., Gronau, I., Siepel, A., Lai, E. C. (2014) Adaptive evolution of testis-specific, recently evolved, clustered miRNAs in Drosophila. RNA, 20 (8). pp. 1195-209. ISSN 1355-8382

Wen, J., Mohammed, J., Bortolamiol-Becet, D., Tsai, H., Robine, N., Westholm, J. O., Ladewig, E., Dai, Q., Okamura, K., Flynt, A. S., Zhang, D., Andrews, J., Cherbas, L., Kaufman, T. C., Cherbas, P., Siepel, A., Lai, E. C. (2014) Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines. Genome Research, 24 (7). pp. 1236-50. ISSN 1088-9051

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

Freedman, A. H., Gronau, I., Schweizer, R. M., Ortega-Del Vecchyo, D., Han, E., Silva, P. M., Galaverni, M., Fan, Z., Marx, P., Lorente-Galdos, B., Beale, H., Ramirez, O., Hormozdiari, F., Alkan, C., Vila, C., Squire, K., Geffen, E., Kusak, J., Boyko, A. R., Parker, H. G., Lee, C., Tadigotla, V., Siepel, A., Bustamante, C. D., Harkins, T. T., Nelson, S. F., Ostrander, E. A., Marques-Bonet, T., Wayne, R. K., Novembre, J. (2014) Genome sequencing highlights the dynamic early history of dogs. PLoS Genetics, 10 (1). e1004016. ISSN 15537390 (ISSN)

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

Mohammed, J., Flynt, A. S., Siepel, A., Lai, E. C. (2013) The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution. RNA, 19 (9). pp. 1295-308. ISSN 1355-8382

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

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

Danko, C. G., Hah, N., Luo, X., Martins, A. L., Core, L., Lis, J. T., Siepel, A., Kraus, W. L. (2013) Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol Cell, 50 (2). pp. 212-22. ISSN 1097-2765

Cornejo, O. E., Lefebure, T., Bitar, P. D., Lang, P., Richards, V. P., Eilertson, K., Do, T., Beighton, D., Zeng, L., Ahn, S. J., Burne, R. A., Siepel, A., Bustamante, C. D., Stanhope, M. J. (2013) Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Mol Biol Evol, 30 (4). pp. 881-93. ISSN 0737-4038

Zeng, L., Choi, S. C., Danko, C. G., Siepel, A., Stanhope, M. J., Burne, R. A. (2013) Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans. PLoS One, 8 (3). e60465. ISSN 1932-6203

Ma, X., Kelley, J. L., Eilertson, K., Musharoff, S., Degenhardt, J. D., Martins, A. L., Vinar, T., Kosiol, C., Siepel, A., Gutenkunst, R. N., Bustamante, C. D. (2013) Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii). PLoS One, 8 (10). e77175. ISSN 1932-6203

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)

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

Kostka, D., Hubisz, M. J., Siepel, A., Pollard, K. S. (2012) The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome. Mol Biol Evol, 29 (3). pp. 1047-57. ISSN 0737-4038

Guertin, M. J., Martins, A. L., Siepel, A., Lis, J. T. (2012) Accurate prediction of inducible transcription factor binding intensities in vivo. PLoS Genet, 8 (3). e1002610. ISSN 1553-7390

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

Gronau, I., Hubisz, M. J., Gulko, B., Danko, C. G., Siepel, A. (2011) Bayesian inference of ancient human demography from individual genome sequences. Nat Genet, 43 (10). pp. 1031-4. ISSN 1061-4036

Lowe, C. B., Kellis, M., Siepel, A., Raney, B. J., Clamp, M., Salama, S. R., Kingsley, D. M., Lindblad-Toh, K., Haussler, D. (2011) Three periods of regulatory innovation during vertebrate evolution. Science, 333 (6045). pp. 1019-24. ISSN 0036-8075

Gottipati, S., Arbiza, L., Siepel, A., Clark, A. G., Keinan, A. (2011) Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing. Nat Genet, 43 (8). pp. 741-3. ISSN 1061-4036

Hah, N., Danko, C. G., Core, L., Waterfall, J. J., Siepel, A., Lis, J. T., Kraus, W. L. (2011) A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell, 145 (4). pp. 622-34. ISSN 0092-8674

Yang, J. S., Phillips, M. D., Betel, D., Mu, P., Ventura, A., Siepel, A. C., Chen, K. C., Lai, E. C. (2011) Widespread regulatory activity of vertebrate microRNA* species. Rna, 17 (2). pp. 312-26. ISSN 1355-8382

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. (2011) Comparative and demographic analysis of orang-utan genomes. Nature, 469 (7331). pp. 529-33. ISSN 0028-0836

Hubisz, M. J., Pollard, K. S., Siepel, A. (2011) PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform, 12 (1). pp. 41-51. ISSN 1467-5463

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

Hubisz, M. J., Lin, M. F., Kellis, M., Siepel, A. (2011) Error and error mitigation in low-coverage genome assemblies. PLoS One, 6 (2). e17034. ISSN 1932-6203

Vinar, T., Brejova, B., Song, G., Siepel, A. (2010) Reconstructing histories of complex gene clusters on a phylogeny. J Comput Biol, 17 (9). pp. 1267-79. ISSN 1066-5277

da Fonseca, R. R., Kosiol, C., Vinar, T., Siepel, A., Nielsen, R. (2010) Positive selection on apoptosis related genes. FEBS Lett, 584 (3). pp. 469-76. ISSN 0014-5793

Pollard, K. S., Hubisz, M. J., Rosenbloom, K. R., Siepel, A. (2010) Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res, 20 (1). pp. 110-21. ISSN 1088-9051

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

Temple, G., Gerhard, D. S., Rasooly, R., Feingold, E. A., Good, P. J., Robinson, C., Mandich, A., Derge, J. G., Lewis, J., Shoaf, D., Collins, F. S., Jang, W., Wagner, L., Shenmen, C. M., Misquitta, L., Schaefer, C. F., Buetow, K. H., Bonner, T. I., Yankie, L., Ward, M., Phan, L., Astashyn, A., Brown, G., Farrell, C., Hart, J., Landrum, M., Maidak, B. L., Murphy, M., Murphy, T., Rajput, B., Riddick, L., Webb, D., Weber, J., Wu, W., Pruitt, K. D., Maglott, D., Siepel, A., Brejova, B., Diekhans, M., Harte, R., Baertsch, R., Kent, J., Haussler, D., Brent, M., Langton, L., Comstock, C. L., Stevens, M., Wei, C., van Baren, M. J., Salehi-Ashtiani, K., Murray, R. R., Ghamsari, L., Mello, E., Lin, C., Pennacchio, C., Schreiber, K., Shapiro, N., Marsh, A., Pardes, E., Moore, T., Lebeau, A., Muratet, M., Simmons, B., Kloske, D., Sieja, S., Hudson, J., Sethupathy, P., Brownstein, M., Bhat, N., Lazar, J., Jacob, H., Gruber, C. E., Smith, M. R., McPherson, J., Garcia, A. M., Gunaratne, P. H., Wu, J., Muzny, D., Gibbs, R. A., Young, A. C., Bouffard, G. G., Blakesley, R. W., Mullikin, J., Green, E. D., Dickson, M. C., Rodriguez, A. C., Grimwood, J., Schmutz, J., Myers, R. M., Hirst, M., Zeng, T., Tse, K., Moksa, M., Deng, M., Ma, K., Mah, D., Pang, J., Taylor, G., Chuah, E., Deng, A. (2009) The completion of the Mammalian Gene Collection (MGC). Genome Research, 19 (12). pp. 2324-33. ISSN 1088-9051

Siepel, A. (2009) Phylogenomics of primates and their ancestral populations. Genome Res, 19 (11). pp. 1929-41. ISSN 1088-9051

Siepel, A. (2009) Darwinian alchemy: Human genes from noncoding DNA. Genome Res, 19 (10). pp. 1693-5. ISSN 1088-9051

Zhang, Y., Song, G., Vinar, T., Green, E. D., Siepel, A., Miller, W. (2009) Evolutionary history reconstruction for Mammalian complex gene clusters. J Comput Biol, 16 (8). pp. 1051-70. ISSN 1066-5277

Holloway, A. K., Begun, D. J., Siepel, A., Pollard, K. S. (2008) Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Research, 18 (10). pp. 1592-601. ISSN 1088-9051

Wang, Y., Diehl, A., Wu, F., Vrebalov, J., Giovannoni, J., Siepel, A., Tanksley, S. D. (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

Kosiol, C., Vinar, T., da Fonseca, R. R., Hubisz, M. J., Bustamante, C. D., Nielsen, R., Siepel, A. (2008) Patterns of positive selection in six Mammalian genomes. Plos Genetics, 4 (8). e1000144. ISSN 1553-7390

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

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. (2007) Targeted discovery of novel human exons by comparative genomics. Genome Res, 17 (12). pp. 1763-73. ISSN 1088-9051 (Print)1088-9051

Kininis, M., Chen, B. S., Diehl, A. G., Isaacs, G. D., Zhang, T., Siepel, A. C., Clark, A. G., Kraus, W. L. (2007) Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Mol Cell Biol, 27 (14). pp. 5090-104. ISSN 0270-7306 (Print)0270-7306

Margulies, E. H., Cooper, G. M., Asimenos, G., Thomas, D. J., Dewey, C. N., Siepel, A., Birney, E., Keefe, D., Schwartz, A. S., Hou, M., Taylor, J., Nikolaev, S., Montoya-Burgos, J. I., Loytynoja, A., Whelan, S., Pardi, F., Massingham, T., Brown, J. B., Bickel, P., Holmes, I., Mullikin, J. C., Ureta-Vidal, A., Paten, B., Stone, E. A., Rosenbloom, K. R., Kent, W. J., Bouffard, G. G., Guan, X., Hansen, N. F., Idol, J. R., Maduro, V. V., Maskeri, B., McDowell, J. C., Park, M., Thomas, P. J., Young, A. C., Blakesley, R. W., Muzny, D. M., Sodergren, E., Wheeler, D. A., Worley, K. C., Jiang, H., Weinstock, G. M., Gibbs, R. A., Graves, T., Fulton, R., Mardis, E. R., Wilson, R. K., Clamp, M., Cuff, J., Gnerre, S., Jaffe, D. B., Chang, J. L., Lindblad-Toh, K., Lander, E. S., Hinrichs, A., Trumbower, H., Clawson, H., Zweig, A., Kuhn, R. M., Barber, G., Harte, R., Karolchik, D., Field, M. A., Moore, R. A., Matthewson, C. A., Schein, J. E., Marra, M. A., Antonarakis, S. E., Batzoglou, S., Goldman, N., Hardison, R., Haussler, D., Miller, W., Pachter, L., Green, E. D., Sidow, A. (2007) Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research, 17 (6). pp. 760-74. ISSN 1088-9051

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

Kuhn, R. M., Karolchik, D., Zweig, A. S., Trumbower, H., Thomas, D. J., Thakkapallayil, A., Sugnet, C. W., Stanke, M., Smith, K. E., Siepel, A., Rosenbloom, K. R., Rhead, B., Raney, B. J., Pohl, A., Pedersen, J. S., Hsu, F., Hinrichs, A. S., Harte, R. A., Diekhans, M., Clawson, H., Bejerano, G., Barber, G. P., Baertsch, R., Haussler, D., Kent, W. J. (2007) The UCSC genome browser database: update 2007. Nucleic Acids Res, 35 (Databa). D668-73. ISSN 0305-1048

Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guig├│, R., Gingeras, T. R., Margulies, E. H., Weng, Z., Snyder, M., Dermitzakis, E. T., Thurman, R. E., Kuehn, M. S., Taylor, C. M., Neph, S., Koch, C. M., Asthana, S., Malhotra, A., Adzhubei, I., Greenbaum, J. A., Andrews, R. M., Flicek, P., Boyle, P. J., Cao, H., Carter, N. P., Clelland, G. K., Davis, S., Day, N., Dhami, P., Dillon, S. C., Dorschner, M. O., Fiegler, H., Giresi, P. G., Goldy, J., Hawrylycz, M., Haydock, A., Humbert, R., James, K. D., Johnson, B. E., Johnson, E. M., Frum, T. T., Rosenzweig, E. R., Karnani, N., Lee, K., Lefebvre, G. C., Navas, P. A., Neri, F., Parker, S. C. J., Sabo, P. J., Sandstrom, R., Shafer, A., Vetrie, D., Weaver, M., Wilcox, S., Yu, M., Collins, F. S., Dekker, J., Lieb, J. D., Tullius, T. D., Crawford, G. E., Sunyaev, S., Noble, W. S., Dunham, I., Denoeud, F., Reymond, A., Kapranov, P., Rozowsky, J., Zheng, D., Castelo, R., Frankish, A., Harrow, J., Ghosh, S., Sandelin, A., Hofacker, I. L., Baertsch, R., Keefe, D., Dike, S., Cheng, J., Hirsch, H. A., Sekinger, E. A., Lagarde, J., Abril, J. F., Shahab, A., Flamm, C., Fried, C., Hackerm├╝ller, J., Hertel, J., Lindemeyer, M., Missal, K., Tanzer, A., Washietl, S., Korbel, J., Emanuelsson, O., Pedersen, J. S., Holroyd, N., Taylor, R., Swarbreck, D., Matthews, N., Dickson, M. C., Thomas, D. J., Weirauch, M. T., Gilbert, J., Siepel, A. C. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447 (7146). pp. 799-816. ISSN 00280836 (ISSN)

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. (2006) Forces shaping the fastest evolving regions in the human genome. PLoS Genet, 2 (10). e168. ISSN 1553-7390

Pollard, K. S., Salama, S. R., Lambert, N., Lambot, M. A., Coppens, S., Pedersen, J. S., Katzman, S., King, B., Onodera, C., Siepel, A., Kern, A. D., Dehay, C., Igel, H., Ares, M., Vanderhaeghen, P., Haussler, D. (2006) An RNA gene expressed during cortical development evolved rapidly in humans. Nature, 443 (7108). pp. 167-72. ISSN 0028-0836

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

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

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

Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., Weinstock, G. M., Wilson, R. K., Gibbs, R. A., Kent, W. J., Miller, W., Haussler, D. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res, 15 (8). pp. 1034-50. ISSN 1088-9051 (Print)1088-9051

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

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

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

International Human Genome Sequencing Consortium, (2004) Finishing the euchromatic sequence of the human genome. Nature, 431 (7011). pp. 931-45. ISSN 0028-0836

Jojic, V., Jojic, N., Meek, C., Geiger, D., Siepel, A., Haussler, D., Heckerman, D. (2004) Efficient approximations for learning phylogenetic HMM models from data. Bioinformatics, 20 Sup. i161-8. ISSN 1367-4803

Siepel, A., Haussler, D. (2004) Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol, 21 (3). pp. 468-88. ISSN 0737-4038 (Print)0737-4038

Siepel, A., Haussler, D. (2004) Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol, 11 (2-3). pp. 413-28. ISSN 1066-5277 (Print)1066-5277

Siepel, A., Haussler, D. (2004) Computational identification of evolutionarily conserved exons. Proceedings of the eighth annual international conference on Resaerch in computational molecular biology. pp. 177-186.

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. (2003) Comparative analyses of multi-species sequences from targeted genomic regions. Nature, 424 (6950). pp. 788-93. ISSN 0028-0836

Siepel, A., Haussler, D. (2003) Combining phylogenetic and hidden Markov models in biosequence analysis. Proceedings of the seventh annual international conference on Research in computational molecular biology. pp. 277-286.

Siepel, A. C. (2003) An algorithm to enumerate sorting reversals for signed permutations. J Comput Biol, 10 (3-4). pp. 575-97. ISSN 1066-5277 (Print)1066-5277

Siepel, A. (2002) An algorithm to find all sorting reversals. Proceedings of the sixth annual international conference on Computational biology. pp. 281-290.

Siepel, A. C., Steenhuis, T. S., Rose, C. W., Parlange, J. Y., McIsaac, G. F. (2002) A simplified hillslope erosion model with vegetation elements for practical applications. Journal of Hydrology, 258 (1-4). pp. 111-121.

Siepel, A., Farmer, A., Tolopko, A., Zhuang, M., Mendes, P., Beavis, W., Sobral, B. (2001) ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinformatics, 17 (1). pp. 83-94. ISSN 1367-4803 (Print)1367-4803

Siepel, A. C., Tolopko, A. N., Farmer, A. D., Steadman, P. A., Schilkey, F. D., Perry, B. D., Beavis, W. D. (2001) An integration platform for heterogeneous bioinformatics software components. IBM Systems Journal, 40 (2). pp. 570-591.

Skupski, M. P., Booker, M., Farmer, A., Harpold, M., Huang, W., Inman, J., Kiphart, D., Kodira, C., Root, S., Schilkey, F., Schwertfeger, J., Siepel, A., Stamper, D., Thayer, N., Thompson, R., Wortman, J., Zhuang, J. J., Harger, C. (1999) The Genome Sequence DataBase: towards an integrated functional genomics resource. Nucleic Acids Research, 27 (1). pp. 35-8. ISSN 0305-1048

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

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

Siepel, A. C., Halpern, A. L., Macken, C., Korber, B. T. (1995) A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences. AIDS Res Hum Retroviruses, 11 (11). pp. 1413-6. ISSN 0889-2229 (Print)0889-2229

Book Section

Vinar, Tomas, Brejova, B., Song, Giltae, Siepel, Adam (2009) Reconstructing Histories of Complex Gene Clusters on a Phylogeny. In: Comparative Genomics. Lecture Notes in Computer Science, 5817 . Springer Berlin Heidelberg, pp. 150-163. ISBN 978-3-642-04743-5

Zhang, Yu, Song, Giltae, Vinar, Tomas, Green, EricD, Siepel, Adam, Miller, Webb (2008) Reconstructing the Evolutionary History of Complex Human Gene Clusters. In: Research in Computational Molecular Biology. Lecture Notes in Computer Science, 4955 . Springer Berlin Heidelberg, pp. 29-49. ISBN 978-3-540-78838-6

Sobral, Bruno W. S., Mangalam, Harry, Siepel, Adam, Mendes, Pedro, Pecherer, Rob, McLaren, Graham (2007) Bioinformatics for Rice Resources. In: Novartis Foundation Symposium 236 - Rice Biotechnology: Improving Yield, Stress Tolerance and Grain Quality. John Wiley & Sons, Ltd., pp. 59-84. ISBN 9780470515778

Siepel, Adam, Pollard, Katherine, Haussler, David (2006) New Methods for Detecting Lineage-Specific Selection. In: Research in Computational Molecular Biology. Lecture Notes in Computer Science, 3909 . Springer Berlin Heidelberg, pp. 190-205. ISBN 978-3-540-33295-4

Siepel, Adam, Haussler, David (2005) Phylogenetic Hidden Markov Models. In: Statistical Methods in Molecular Evolution. Statistics for Biology and Health . Springer New York, pp. 325-351. ISBN 978-0-387-22333-9

Moret, Bernard, Siepel, Adam, Tang, Jijun, Liu, Tao (2002) Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data. In: Algorithms in Bioinformatics. Lecture Notes in Computer Science, 2452 . Springer Berlin Heidelberg, pp. 521-536. ISBN 978-3-540-44211-0

Siepel, Adam, Moret, Bernard (2001) Finding an Optimal Inversion Median: Experimental Results. In: Algorithms in Bioinformatics. Lecture Notes in Computer Science, 2149 . Springer Berlin Heidelberg, pp. 189-203. ISBN 978-3-540-42516-8

This list was generated on Mon Dec 11 23:22:29 2017 EST.
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