| Year |
Citation |
Score |
| 2023 |
Liu L, Zhao Y, Siepel A. DNA-sequence and epigenomic determinants of local rates of transcription elongation. Biorxiv : the Preprint Server For Biology. PMID 38187771 DOI: 10.1101/2023.12.21.572932 |
0.355 |
|
| 2023 |
Kuderna LFK, Ulirsch JC, Rashid S, Ameen M, Sundaram L, Hickey G, Cox AJ, Gao H, Kumar A, Aguet F, Christmas MJ, Clawson H, Haeussler M, Janiak MC, Kuhlwilm M, ... ... Siepel A, et al. Identification of constrained sequence elements across 239 primate genomes. Nature. PMID 38030727 DOI: 10.1038/s41586-023-06798-8 |
0.531 |
|
| 2023 |
Scheben A, Mendivil Ramos O, Kramer M, Goodwin S, Oppenheim S, Becker DJ, Schatz MC, Simmons NB, Siepel A, McCombie WR. Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats. Genome Biology and Evolution. 15. PMID 37728212 DOI: 10.1093/gbe/evad148 |
0.365 |
|
| 2022 |
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. Author Correction: Comparative and demographic analysis of orang-utan genomes. Nature. PMID 35962045 DOI: 10.1038/s41586-022-04799-7 |
0.78 |
|
| 2022 |
Dukler N, Mughal MR, Ramani R, Huang YF, Siepel A. Extreme purifying selection against point mutations in the human genome. Nature Communications. 13: 4312. PMID 35879308 DOI: 10.1038/s41467-022-31872-6 |
0.531 |
|
| 2022 |
Wu Y, Johnson L, Song B, Romay C, Stitzer M, Siepel A, Buckler E, Scheben A. A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants. The Plant Genome. e20204. PMID 35416423 DOI: 10.1002/tpg2.20204 |
0.413 |
|
| 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 |
0.412 |
|
| 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 |
0.569 |
|
| 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 |
0.656 |
|
| 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 |
0.496 |
|
| 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 |
0.844 |
|
| 2020 |
Hubisz M, Siepel A. Inference of Ancestral Recombination Graphs Using ARGweaver. Methods of Molecular Biology. 2090: 231-266. PMID 31975170 DOI: 10.1007/978-1-0716-0199-0_10 |
0.428 |
|
| 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 |
0.395 |
|
| 2019 |
Siepel A. Challenges in funding and developing genomic software: roots and remedies Genome Biology. 20: 1-14. PMID 31358028 DOI: 10.1186/S13059-019-1763-7 |
0.448 |
|
| 2019 |
Huang Y, Siepel A. Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease Genome Research. 29: 1310-1321. PMID 31249063 DOI: 10.1101/Gr.245522.118 |
0.576 |
|
| 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 |
0.751 |
|
| 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 |
0.813 |
|
| 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 |
0.448 |
|
| 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 |
0.423 |
|
| 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 |
0.434 |
|
| 2017 |
Kondo S, Vedanayagam J, Mohammed J, Eizadshenass S, Kan L, Pang N, Aradhya R, Siepel A, Steinhauer J, Lai EC. New genes often acquire male-specific functions but rarely become essential in Drosophila. Genes & Development. 31: 1841-1846. PMID 29051389 DOI: 10.1101/Gad.303131.117 |
0.326 |
|
| 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 |
0.347 |
|
| 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 |
0.834 |
|
| 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 |
0.774 |
|
| 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 |
0.43 |
|
| 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 |
0.438 |
|
| 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 |
0.468 |
|
| 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 |
0.384 |
|
| 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 |
0.416 |
|
| 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 |
0.815 |
|
| 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 |
0.401 |
|
| 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 |
0.361 |
|
| 2014 |
Couger MB, 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 and Computation : Practice & Experience. 26: 2157-2166. PMID 25294974 DOI: 10.1002/Cpe.3231 |
0.508 |
|
| 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 |
0.507 |
|
| 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 |
0.309 |
|
| 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 |
0.317 |
|
| 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 |
0.794 |
|
| 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 |
0.431 |
|
| 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 |
0.413 |
|
| 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 |
0.485 |
|
| 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 |
0.718 |
|
| 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 |
0.31 |
|
| 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 |
0.833 |
|
| 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 |
0.381 |
|
| 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 |
0.321 |
|
| 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 |
0.569 |
|
| 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 |
0.543 |
|
| 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 |
0.753 |
|
| 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 |
0.406 |
|
| 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 |
0.686 |
|
| 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 |
0.823 |
|
| 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 |
0.831 |
|
| 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 |
0.809 |
|
| 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 |
0.477 |
|
| 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 |
0.34 |
|
| 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 |
0.582 |
|
| 2011 |
Suzuki H, Lefébure T, Hubisz MJ, Pavinski Bitar P, Lang P, Siepel A, Stanhope MJ. Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution. Genome Biology and Evolution. 3: 168-85. PMID 21282711 DOI: 10.1093/Gbe/Evr006 |
0.529 |
|
| 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 |
0.621 |
|
| 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 |
0.816 |
|
| 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 |
0.436 |
|
| 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 |
0.485 |
|
| 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 |
0.39 |
|
| 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 |
0.657 |
|
| 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 |
0.447 |
|
| 2009 |
Siepel A. Phylogenomics of primates and their ancestral populations Genome Research. 19: 1929-1941. PMID 19801602 DOI: 10.1101/Gr.084228.108 |
0.499 |
|
| 2009 |
Siepel A. Darwinian alchemy: Human genes from noncoding DNA. Genome Research. 19: 1693-1695. PMID 19797681 DOI: 10.1101/Gr.098376.109 |
0.436 |
|
| 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 |
0.749 |
|
| 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 |
0.459 |
|
| 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 |
0.583 |
|
| 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 |
0.536 |
|
| 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 |
0.749 |
|
| 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 |
0.655 |
|
| 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 |
0.86 |
|
| 2007 |
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Siepel A, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874 |
0.847 |
|
| 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 |
0.78 |
|
| 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 |
0.35 |
|
| 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 |
0.84 |
|
| 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 |
0.826 |
|
| 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 |
0.84 |
|
| 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 |
0.796 |
|
| 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 |
0.617 |
|
| 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 |
0.829 |
|
| 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 |
0.817 |
|
| 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 |
0.461 |
|
| 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 |
0.693 |
|
| 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 |
0.697 |
|
| 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 |
0.555 |
|
| 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 |
0.459 |
|
| 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 |
0.558 |
|
| 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 |
0.313 |
|
| 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 |
0.722 |
|
| 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 |
0.428 |
|
| 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 |
0.496 |
|
| 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 |
0.519 |
|
| 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 |
0.517 |
|
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