Adam C. Siepel, Ph.D. - Publications

University of California, Santa Cruz, Santa Cruz, CA, United States 

95 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Blumberg A, Zhao Y, Huang YF, Dukler N, Rice EJ, Chivu AG, Krumholz K, Danko CG, Siepel A. Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. Bmc Biology. 19: 30. PMID 33588838 DOI: 10.1186/s12915-021-00949-x  0.44
2020 Hejase HA, Salman-Minkov A, Campagna L, Hubisz MJ, Lovette IJ, Gronau I, Siepel A. Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. Proceedings of the National Academy of Sciences of the United States of America. 117: 30554-30565. PMID 33199636 DOI: 10.1073/pnas.2015987117  0.6
2020 Hubisz MJ, Williams AL, Siepel A. Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. Plos Genetics. 16. PMID 32760067 DOI: 10.1371/Journal.Pgen.1008895  0.6
2020 Adrion JR, Cole CB, Dukler N, Galloway JG, Gladstein AL, Gower G, Kyriazis CC, Ragsdale AP, Tsambos G, Baumdicker F, Carlson J, Cartwright RA, Durvasula A, Gronau I, Kim BY, ... ... Siepel A, et al. A community-maintained standard library of population genetic models. Elife. 9. PMID 32573438 DOI: 10.7554/Elife.54967  0.4
2020 Dukler N, Huang YF, Siepel A. Phylogenetic modeling of regulatory element turnover based on epigenomic data. Molecular Biology and Evolution. PMID 32176292 DOI: 10.1093/Molbev/Msaa073  0.44
2020 Joly-Lopez Z, Platts AE, Gulko B, Choi JY, Groen SC, Zhong X, Siepel A, Purugganan MD. An inferred fitness consequence map of the rice genome. Nature Plants. PMID 32042156 DOI: 10.1038/S41477-019-0589-3  0.68
2020 Hejase HA, Dukler N, Siepel A. From Summary Statistics to Gene Trees: Methods for Inferring Positive Selection. Trends in Genetics. 36: 243-258. PMID 31954511 DOI: 10.1016/J.Tig.2019.12.008  0.4
2020 Adrion JR, Cole CB, Dukler N, Galloway JG, Gladstein AL, Gower G, Kyriazis CC, Ragsdale AP, Tsambos G, Baumdicker F, Carlson J, Cartwright RA, Durvasula A, Gronau I, Kim BY, ... ... Siepel A, et al. Author response: A community-maintained standard library of population genetic models Elife. DOI: 10.7554/Elife.54967.Sa2  0.52
2019 Gulko B, Siepel A. Publisher Correction: An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences. Nature Genetics. 51: 577-577. PMID 30787474 DOI: 10.1038/S41588-019-0369-Z  0.68
2019 Gulko B, Siepel A. An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences. Nature Genetics. 51: 335-342. PMID 30559490 DOI: 10.1038/S41588-018-0300-Z  0.68
2018 Ramani R, Krumholz K, Huang YF, Siepel A. PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP. Bioinformatics (Oxford, England). PMID 30481262 DOI: 10.1093/Bioinformatics/Bty966  0.44
2018 Danko CG, Choate LA, Marks BA, Rice EJ, Wang Z, Chu T, Martins AL, Dukler N, Coonrod SA, Tait Wojno ED, Lis JT, Kraus WL, Siepel A. Dynamic evolution of regulatory element ensembles in primate CD4+ T cells. Nature Ecology & Evolution. PMID 29379187 DOI: 10.1038/S41559-017-0447-5  0.4
2018 Fang H, Huang YF, Radhakrishnan A, Siepel A, Lyon GJ, Schatz MC. Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution. Cell Systems. PMID 29361467 DOI: 10.1016/J.Cels.2017.12.007  0.44
2017 Dukler N, Booth GT, Huang YF, Tippens N, Waters CT, Danko CG, Lis JT, Siepel A. Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol. Genome Research. PMID 29025894 DOI: 10.1101/Gr.222935.117  0.44
2017 Huang YF, Gulko B, Siepel A. Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. Nature Genetics. PMID 28288115 DOI: 10.1038/Ng.3810  0.68
2016 Dukler N, Gulko B, Huang YF, Siepel A. Is a super-enhancer greater than the sum of its parts? Nature Genetics. 49: 2-3. PMID 28029159 DOI: 10.1038/Ng.3759  0.68
2016 Freedman AH, Schweizer RM, Ortega-Del Vecchyo D, Han E, Davis BW, Gronau I, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Ramirez O, Hormozdiari F, Alkan C, Vilà C, ... ... Siepel A, et al. Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs. Plos Genetics. 12: e1005851. PMID 26943675 DOI: 10.1371/Journal.Pgen.1005851  0.52
2016 Kuhlwilm M, Gronau I, Hubisz MJ, de Filippo C, Prado-Martinez J, Kircher M, Fu Q, Burbano HA, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajkovic D, Kucan Ž, Gušic I, ... ... Siepel A, et al. Ancient gene flow from early modern humans into Eastern Neanderthals. Nature. PMID 26886800 DOI: 10.1038/Nature16544  0.52
2015 Campagna L, Gronau I, Silveira LF, Siepel A, Lovette IJ. Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation. Molecular Ecology. 24: 4238-51. PMID 26175196 DOI: 10.1111/Mec.13314  0.52
2015 Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT. GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters. Plos Genetics. 11: e1005108. PMID 25815464 DOI: 10.1371/Journal.Pgen.1005108  0.52
2015 Danko CG, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, Siepel A. Identification of active transcriptional regulatory elements from GRO-seq data. Nature Methods. 12: 433-8. PMID 25799441 DOI: 10.1038/Nmeth.3329  0.52
2015 Gulko B, Hubisz MJ, Gronau I, Siepel A. A method for calculating probabilities of fitness consequences for point mutations across the human genome Nature Genetics. 47: 276-283. PMID 25599402 DOI: 10.1038/Ng.3196  0.68
2014 Peng X, Alföldi J, Gori K, Eisfeld AJ, Tyler SR, Tisoncik-Go J, Brawand D, Law GL, Skunca N, Hatta M, Gasper DJ, Kelly SM, Chang J, Thomas MJ, Johnson J, ... ... Siepel A, et al. The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease. Nature Biotechnology. 32: 1250-5. PMID 25402615 DOI: 10.1038/Nbt.3079  0.52
2014 Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT. Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nature Genetics. 46: 1311-20. PMID 25383968 DOI: 10.1038/Ng.3142  0.52
2014 Mohammed J, Siepel A, Lai EC. Diverse modes of evolutionary emergence and flux of conserved microRNA clusters. Rna (New York, N.Y.). 20: 1850-63. PMID 25332374 DOI: 10.1261/Rna.046805.114  0.52
2014 Siepel A, Arbiza L. Cis-regulatory elements and human evolution Current Opinion in Genetics & Development. 29: 81-89. PMID 25218861 DOI: 10.1016/J.Gde.2014.08.011  0.32
2014 Wen J, Mohammed J, Bortolamiol-Becet D, Tsai H, Robine N, Westholm JO, Ladewig E, Dai Q, Okamura K, Flynt AS, Zhang D, Andrews J, Cherbas L, Kaufman TC, Cherbas P, ... Siepel A, et al. Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines. Genome Research. 24: 1236-50. PMID 24985917 DOI: 10.1101/Gr.161554.113  0.52
2014 Mohammed J, Bortolamiol-Becet D, Flynt AS, Gronau I, Siepel A, Lai EC. Adaptive evolution of testis-specific, recently evolved, clustered miRNAs in Drosophila. Rna (New York, N.Y.). 20: 1195-209. PMID 24942624 DOI: 10.1261/Rna.044644.114  0.52
2014 Arbiza L, Gottipati S, Siepel A, Keinan A. Contrasting X-linked and autosomal diversity across 14 human populations. American Journal of Human Genetics. 94: 827-44. PMID 24836452 DOI: 10.1016/J.Ajhg.2014.04.011  0.52
2014 Rasmussen MD, Hubisz MJ, Gronau I, Siepel A. Genome-wide inference of ancestral recombination graphs. Plos Genetics. 10: e1004342. PMID 24831947 DOI: 10.1371/Journal.Pgen.1004342  0.6
2014 Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Beale H, Ramirez O, Hormozdiari F, Alkan C, Vilà C, ... ... Siepel A, et al. Genome sequencing highlights the dynamic early history of dogs. Plos Genetics. 10: e1004016. PMID 24453982 DOI: 10.1371/Journal.Pgen.1004016  0.52
2014 Brian Couger M, Pipes L, Squina F, Prade R, Siepel A, Palermo R, Katze MG, Mason CE, Blood PD. Enabling large-scale next-generation sequence assembly with Blacklight Concurrency Computation Practice and Experience. 26: 2157-2166. DOI: 10.1002/cpe.3231  0.52
2013 Ma X, Kelley JL, Eilertson K, Musharoff S, Degenhardt JD, Martins AL, Vinar T, Kosiol C, Siepel A, Gutenkunst RN, Bustamante CD. Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii). Plos One. 8: e77175. PMID 24194868 DOI: 10.1371/Journal.Pone.0077175  0.52
2013 Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A. A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes Plos Genetics. 9. PMID 23966869 DOI: 10.1371/Journal.Pgen.1003684  0.52
2013 Mohammed J, Flynt AS, Siepel A, Lai EC. The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution. Rna (New York, N.Y.). 19: 1295-308. PMID 23882112 DOI: 10.1261/Rna.039248.113  0.52
2013 Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B, Keinan A, Siepel A. Genome-wide inference of natural selection on human transcription factor binding sites Nature Genetics. 45: 723-729. PMID 23749186 DOI: 10.1038/Ng.2658  0.52
2013 Zeng L, Choi SC, Danko CG, Siepel A, Stanhope MJ, Burne RA. Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans. Plos One. 8: e60465. PMID 23555977 DOI: 10.1371/Journal.Pone.0060465  0.52
2013 Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Molecular Cell. 50: 212-22. PMID 23523369 DOI: 10.1016/J.Molcel.2013.05.025  0.52
2013 Gronau I, Arbiza L, Mohammed J, Siepel A. Inference of natural selection from interspersed genomic elements based on polymorphism and divergence. Molecular Biology and Evolution. 30: 1159-71. PMID 23386628 DOI: 10.1093/Molbev/Mst019  0.4
2013 Cornejo OE, Lefébure T, Bitar PD, Lang P, Richards VP, Eilertson K, Do T, Beighton D, Zeng L, Ahn SJ, Burne RA, Siepel A, Bustamante CD, Stanhope MJ. Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Molecular Biology and Evolution. 30: 881-93. PMID 23228887 DOI: 10.1093/Molbev/Mss278  0.52
2012 Choi SC, Rasmussen MD, Hubisz MJ, Gronau I, Stanhope MJ, Siepel A. Replacing and additive horizontal gene transfer in Streptococcus. Molecular Biology and Evolution. 29: 3309-20. PMID 22617954 DOI: 10.1093/Molbev/Mss138  0.52
2012 Guertin MJ, Martins AL, Siepel A, Lis JT. Accurate prediction of inducible transcription factor binding intensities in vivo. Plos Genetics. 8: e1002610. PMID 22479205 DOI: 10.1371/Journal.Pgen.1002610  0.52
2012 Kostka D, Hubisz MJ, Siepel A, Pollard KS. The role of GC-Biased gene conversion in shaping the fastest evolving regions of the human genome Molecular Biology and Evolution. 29: 1047-1057. PMID 22075116 DOI: 10.1093/Molbev/Msr279  0.52
2011 Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, ... ... Siepel A, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/Nature10530  0.52
2011 Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. Bayesian inference of ancient human demography from individual genome sequences Nature Genetics. 43: 1031-1034. PMID 21926973 DOI: 10.1038/Ng.937  0.68
2011 Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D. Three periods of regulatory innovation during vertebrate evolution. Science (New York, N.Y.). 333: 1019-24. PMID 21852499 DOI: 10.1126/Science.1202702  0.52
2011 Gottipati S, Arbiza L, Siepel A, Clark AG, Keinan A. Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing. Nature Genetics. 43: 741-3. PMID 21775991 DOI: 10.1038/Ng.877  0.52
2011 Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell. 145: 622-34. PMID 21549415 DOI: 10.1016/J.Cell.2011.03.042  0.52
2011 Hubisz MJ, Lin MF, Kellis M, Siepel A. Error and error mitigation in low-coverage genome assemblies. Plos One. 6: e17034. PMID 21340033 DOI: 10.1371/Journal.Pone.0017034  0.6
2011 Hubisz MJ, Pollard KS, Siepel A. PHAST and RPHAST: phylogenetic analysis with space/time models. Briefings in Bioinformatics. 12: 41-51. PMID 21278375 DOI: 10.1093/Bib/Bbq072  0.6
2011 Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, ... ... Siepel A, et al. Comparative and demographic analysis of orang-utan genomes. Nature. 469: 529-33. PMID 21270892 DOI: 10.1038/Nature09687  0.52
2011 Yang JS, Phillips MD, Betel D, Mu P, Ventura A, Siepel AC, Chen KC, Lai EC. Widespread regulatory activity of vertebrate microRNA* species. Rna (New York, N.Y.). 17: 312-26. PMID 21177881 DOI: 10.1261/Rna.2537911  0.52
2011 Hubisz MJ, Pollard KS, Siepel A. Phastand Rphast: Phylogenetic analysis with space/time models Briefings in Bioinformatics. 12: 41-51. DOI: 10.1093/bib/bbq072  0.52
2011 Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL. Erratum: A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells (Cell (2011) 145 (622-634)) Cell. 145. DOI: 10.1016/J.Cell.2011.06.003  0.52
2010 Vinar T, Brejová B, Song G, Siepel A. Reconstructing histories of complex gene clusters on a phylogeny. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 1267-79. PMID 20874408 DOI: 10.1089/Cmb.2010.0090  0.52
2010 Boyko AR, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, Lohmueller KE, Zhao K, Brisbin A, Parker HG, vonHoldt BM, Cargill M, Auton A, Reynolds A, Elkahloun AG, Castelhano M, ... ... Siepel A, et al. A simple genetic architecture underlies morphological variation in dogs. Plos Biology. 8: e1000451. PMID 20711490 DOI: 10.1371/Journal.Pbio.1000451  0.52
2010 da Fonseca RR, Kosiol C, Vinar T, Siepel A, Nielsen R. Positive selection on apoptosis related genes. Febs Letters. 584: 469-76. PMID 20026333 DOI: 10.1016/J.Febslet.2009.12.022  0.52
2010 Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies Genome Research. 20: 110-121. PMID 19858363 DOI: 10.1101/Gr.097857.109  0.52
2010 Ostrander EA, Boyko A, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, Lohmueller KE, Zhao K, Brisbin A, Parker HG, Holdt BMV, Cargill M, Auton A, Reynolds A, Elkahloun AG, ... ... Siepel A, et al. Tracking genes and finding mutations: finding genes for complex traits in the domestic dog (Canis familiaris) Genome Biology. 11: 1-1. DOI: 10.1186/Gb-2010-11-S1-I23  0.6
2009 Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, Robinson C, Mandich A, Derge JG, Lewis J, Shoaf D, Collins FS, Jang W, Wagner L, Shenmen CM, ... ... Siepel A, et al. The completion of the Mammalian Gene Collection (MGC). Genome Research. 19: 2324-33. PMID 19767417 DOI: 10.1101/Gr.095976.109  0.52
2009 Zhang Y, Song G, Vinar T, Green ED, Siepel A, Miller W. Evolutionary history reconstruction for Mammalian complex gene clusters. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 1051-70. PMID 19645598 DOI: 10.1089/Cmb.2009.0040  0.52
2009 Vinař T, Brejová B, Song G, Siepel A. Reconstructing Histories of Complex Gene Clusters on a Phylogeny Lecture Notes in Computer Science. 5817: 150. DOI: 10.1007/978-3-642-04744-2_13  0.52
2008 Wang Y, Diehl A, Wu F, Vrebalov J, Giovannoni J, Siepel A, Tanksley SD. Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics. 180: 391-408. PMID 18723883 DOI: 10.1534/Genetics.108.087981  0.52
2008 Kosiol C, Vinař T, Da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, Siepel A. Patterns of positive selection in six mammalian genomes Plos Genetics. 4. PMID 18670650 DOI: 10.1371/Journal.Pgen.1000144  0.52
2008 Holloway AK, Begun DJ, Siepel A, Pollard KS. Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Research. 18: 1592-601. PMID 18583644 DOI: 10.1101/Gr.077131.108  0.48
2008 Zhang Y, Song G, Vinař T, Green ED, Siepel A, Miller W. Reconstructing the evolutionary history of complex human gene clusters Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4955: 29-49. DOI: 10.1007/978-3-540-78839-3_4  0.52
2007 Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CLG, Davis C, Ewing B, Oommen S, Lau C, Yu HC, Li J, Roe BA, Green P, Gerhard DS, et al. Targeted discovery of novel human exons by comparative genomics Genome Research. 17: 1763-1773. PMID 17989246 DOI: 10.1101/Gr.7128207  0.52
2007 Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, ... ... Siepel A, et al. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research. 17: 1797-808. PMID 17984227 DOI: 10.1101/Gr.6761107  0.52
2007 Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/Gr.6034307  0.52
2007 Kininis M, Chen BS, Diehl AG, Isaacs GD, Zhang T, Siepel AC, Clark AG, Kraus WL. Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Molecular and Cellular Biology. 27: 5090-104. PMID 17515612 DOI: 10.1128/Mcb.00083-07  0.52
2007 Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, ... ... Siepel A, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science (New York, N.Y.). 316: 222-34. PMID 17431167 DOI: 10.1126/Science.1139247  0.52
2007 Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, et al. The UCSC genome browser database: update 2007. Nucleic Acids Research. 35: D668-73. PMID 17142222 DOI: 10.1093/Nar/Gkl928  0.52
2006 Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, Rosenbloom KR, Kent J, Haussler D. Forces shaping the fastest evolving regions in the human genome. Plos Genetics. 2: e168. PMID 17040131 DOI: 10.1371/Journal.Pgen.0020168  0.52
2006 Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M, Vanderhaeghen P, et al. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 443: 167-72. PMID 16915236 DOI: 10.1038/Nature05113  0.52
2006 Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. Identification and classification of conserved RNA secondary structures in the human genome. Plos Computational Biology. 2: e33. PMID 16628248 DOI: 10.1371/Journal.Pcbi.0020033  0.52
2006 Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 441: 87-90. PMID 16625209 DOI: 10.1038/Nature04696  0.52
2006 Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, ... ... Siepel A, et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Research. 34: D590-8. PMID 16381938 DOI: 10.1093/Nar/Gkj144  0.52
2006 Siepel A, Pollard KS, Haussler D. New methods for detecting lineage-specific selection Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 190-205. DOI: 10.1007/11732990_17  0.52
2005 Bejerano G, Siepel AC, Kent WJ, Haussler D. Computational screening of conserved genomic DNA in search of functional noncoding elements. Nature Methods. 2: 535-45. PMID 16170870 DOI: 10.1038/Nmeth0705-535  0.52
2005 Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Research. 15: 1034-50. PMID 16024819 DOI: 10.1101/Gr.3715005  0.52
2004 Siepel AC, Haussler D. Combining phylogenetic and hidden Markov models in biosequence analysis. Journal of Computational Biology. 11: 413-428. PMID 15285899 DOI: 10.1089/1066527041410472  0.52
2004 Jojic V, Jojic N, Meek C, Geiger D, Siepel A, Haussler D, Heckerman D. Efficient approximations for learning phylogenetic HMM models from data. Bioinformatics (Oxford, England). 20: i161-8. PMID 15262795 DOI: 10.1093/bioinformatics/bth917  0.52
2003 Siepel A, Haussler D. Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood Molecular Biology and Evolution. 21: 468-488. PMID 14660683 DOI: 10.1093/Molbev/Msh039  0.52
2003 Siepel AC. An algorithm to enumerate sorting reversals for signed permutations. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 575-97. PMID 12935346 DOI: 10.1089/10665270360688200  0.52
2003 Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, et al. Comparative analyses of multi-species sequences from targeted genomic regions. Nature. 424: 788-93. PMID 12917688 DOI: 10.1038/Nature01858  0.52
2002 Siepel AC, Steenhuis TS, Rose CW, Parlange JY, McIsaac GF. A simplified hillslope erosion model with vegetation elements for practical applications Journal of Hydrology. 258: 111-121. DOI: 10.1016/S0022-1694(01)00569-8  0.52
2002 Moret BME, Siepel AC, Tang J, Liu T. Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2452: 521-536.  0.52
2002 Siepel AC. An algorithm to find all sorting reversals Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 281-290.  0.52
2001 Sobral BW, Mangalam H, Siepel A, Mendes P, Pecherer R, McLaren G. Bioinformatics for rice resources. Novartis Foundation Symposium. 236: 59-81; discussion 81. PMID 11387987 DOI: 10.1002/9780470515778.Ch6  0.52
2001 Siepel AC, Tolopko AN, Farmer AD, Steadman PA, Schilkey FD, Perry BD, Beavis WD. An integration platform for heterogeneous bioinformatics software components Ibm Systems Journal. 40: 570-591. DOI: 10.1147/Sj.402.0570  0.52
2001 Siepel AC, Moret BME. Finding an optimal inversion median: Experimental results Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2149: 189-203. DOI: 10.1007/3-540-44696-6_15  0.52
1999 Skupski MP, 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, et al. The Genome Sequence DataBase: towards an integrated functional genomics resource. Nucleic Acids Research. 27: 35-8. PMID 9847136 DOI: 10.1093/Nar/27.1.35  0.52
1998 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, et al. The Genome Sequence DataBase (GSDB): improving data quality and data access. Nucleic Acids Research. 26: 21-6. PMID 9399793 DOI: 10.1093/Nar/26.1.21  0.52
1997 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, ... ... Siepel A, et al. The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes. Nucleic Acids Research. 25: 18-23. PMID 9016496 DOI: 10.1093/Nar/25.1.18  0.52
1995 Siepel AC, Halpern AL, Macken C, Korber BT. A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences. Aids Research and Human Retroviruses. 11: 1413-6. PMID 8573400 DOI: 10.1089/Aid.1995.11.1413  0.52
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