Items where Community is "CSHL labs > Siepel lab"

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Paper

Huang, Yi-Fei, Siepel, Adam (October 2018) Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease. bioRxiv.

Fang, Han, Huang, Yi-Fei, Radhakrishnan, Aditya, Siepel, Adam, Lyon, Gholson J., Schatz, Michael C. (February 2018) Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution. Cell Systems, 6 (2). pp. 180-191. ISSN 2405-4712

Danko, C. G., Choate, L. A., Marks, B. A., Rice, E. J., Wang, Z., Chu, T., Martins, A. L., Dukler, N., Coonrod, S. A., Tait Wojno, E. D., Lis, J. T., Kraus, W. L., Siepel, A. (January 2018) Dynamic evolution of regulatory element ensembles in primate CD4(+) T cells. Nat Ecol Evol. ISSN 2397-334x

Mohammed, J., Flynt, A. S., Panzarino, A. M., Mondal, M. M. H., DeCruz, M., Siepel, A., Lai, E. C. (January 2018) Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus. Genome Res, 28 (1). pp. 52-65. ISSN 1088-9051

Dukler, N., Booth, G. T., Huang, Y. F., Tippens, N., Waters, C. T., Danko, C. G., Lis, J. T., Siepel, A. (November 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. (September 2017) New genes often acquire male-specific functions but rarely become essential in Drosophila. Genes Dev, 31 (18). pp. 1841-1846. ISSN 0890-9369

Ramani, R., Megason, G., Schallheim, J., Karlson, C., Vijayakumar, V., Vijayakumar, S., Hicks, C. (April 2017) Integrative Analysis of MicroRNA-Mediated Gene Signatures and Pathways Modulating White Blood Cell Count in Childhood Acute Lymphoblastic Leukemia. Biomarker Insights, 12. p. 1177271917702895. ISSN 1177-2719

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

Hicks, C., Ramani, R., Sartor, O., Bhalla, R., Miele, L., Dlamini, Z., Gumede, N. (March 2017) An integrative genomics approach for associating genome-wide association studies information with localized and metastatic prostate cancer phenotypes. Biomarker Insights, 12.

Dukler, N., Gulko, B., Huang, Y. F., Siepel, A. (December 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. (March 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. (February 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. (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)

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. (May 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. (March 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. (March 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. (December 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. (December 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. (December 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. (December 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. (September 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. (August 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. (July 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. (June 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. (January 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. (September 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. (July 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. (May 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. (April 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. (April 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. (November 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. (March 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. (October 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. (October 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. (August 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. (August 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. (May 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. (February 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. (January 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. (January 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. (September 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. (February 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. (January 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. (December 2009) The completion of the Mammalian Gene Collection (MGC). Genome Research, 19 (12). pp. 2324-33. ISSN 1088-9051

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

Siepel, A. (October 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. (August 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. (October 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. (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

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. (December 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. (December 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. (July 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. (June 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. (April 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. (January 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. (October 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. (September 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. (May 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. (April 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. (January 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. (August 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. (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

International Chicken Genome SequencingConsortium, (December 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, (October 2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306 (5696). pp. 636-40. ISSN 0036-8075

International Human Genome Sequencing Consortium, (October 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. (August 2004) Efficient approximations for learning phylogenetic HMM models from data. Bioinformatics, 20 Sup. i161-8. ISSN 1367-4803

Siepel, A., Haussler, D. (March 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. (August 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. (January 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. (January 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. (January 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. (January 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. (November 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 Sat Dec 15 21:04:18 2018 EST.
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