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Challenges in funding and developing genomic software: roots and remedies.

Siepel A.

Genome Biol. 2019 Jul 29;20(1):147. doi: 10.1186/s13059-019-1763-7.


Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease.

Huang YF, Siepel A.

Genome Res. 2019 Aug;29(8):1310-1321. doi: 10.1101/gr.245522.118. Epub 2019 Jun 27.


Erratum: Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus.

Mohammed J, Flynt AS, Panzarino AM, Mondal MMH, DeCruz M, Siepel A, Lai EC.

Genome Res. 2019 May;29(5):881. doi: 10.1101/gr.250654.119. No abstract available.


An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences.

Gulko B, Siepel A.

Nat Genet. 2019 Feb;51(2):335-342. doi: 10.1038/s41588-018-0300-z. Epub 2018 Dec 17. Erratum in: Nat Genet. 2019 Mar;51(3):577.


PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP.

Ramani R, Krumholz K, Huang YF, Siepel A.

Bioinformatics. 2019 Jul 1;35(13):2320-2322. doi: 10.1093/bioinformatics/bty966.


Dynamic evolution of regulatory element ensembles in primate CD4+ T cells.

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.

Nat Ecol Evol. 2018 Mar;2(3):537-548. doi: 10.1038/s41559-017-0447-5. Epub 2018 Jan 29.


Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution.

Fang H, Huang YF, Radhakrishnan A, Siepel A, Lyon GJ, Schatz MC.

Cell Syst. 2018 Feb 28;6(2):180-191.e4. doi: 10.1016/j.cels.2017.12.007. Epub 2018 Jan 17.


Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus.

Mohammed J, Flynt AS, Panzarino AM, Mondal MMH, DeCruz M, Siepel A, Lai EC.

Genome Res. 2018 Jan;28(1):52-65. doi: 10.1101/gr.226068.117. Epub 2017 Dec 12. Erratum in: Genome Res. 2019 May;29(5):881.


New genes often acquire male-specific functions but rarely become essential in Drosophila.

Kondo S, Vedanayagam J, Mohammed J, Eizadshenass S, Kan L, Pang N, Aradhya R, Siepel A, Steinhauer J, Lai EC.

Genes Dev. 2017 Sep 15;31(18):1841-1846. doi: 10.1101/gad.303131.117.


Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol.

Dukler N, Booth GT, Huang YF, Tippens N, Waters CT, Danko CG, Lis JT, Siepel A.

Genome Res. 2017 Nov;27(11):1816-1829. doi: 10.1101/gr.222935.117. Epub 2017 Oct 12.


Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data.

Huang YF, Gulko B, Siepel A.

Nat Genet. 2017 Apr;49(4):618-624. doi: 10.1038/ng.3810. Epub 2017 Mar 13.


Is a super-enhancer greater than the sum of its parts?

Dukler N, Gulko B, Huang YF, Siepel A.

Nat Genet. 2016 Dec 28;49(1):2-3. doi: 10.1038/ng.3759. No abstract available.


Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs.

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, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Marques-Bonet T, Ostrander EA, Wayne RK, Novembre J.

PLoS Genet. 2016 Mar 4;12(3):e1005851. doi: 10.1371/journal.pgen.1005851. eCollection 2016 Mar.


Ancient gene flow from early modern humans into Eastern Neanderthals.

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, Marques-Bonet T, Andrés AM, Viola B, Pääbo S, Meyer M, Siepel A, Castellano S.

Nature. 2016 Feb 25;530(7591):429-33. doi: 10.1038/nature16544. Epub 2016 Feb 17.


Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation.

Campagna L, Gronau I, Silveira LF, Siepel A, Lovette IJ.

Mol Ecol. 2015 Aug;24(16):4238-51. doi: 10.1111/mec.13314. Epub 2015 Aug 3.


GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters.

Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT.

PLoS Genet. 2015 Mar 27;11(3):e1005108. doi: 10.1371/journal.pgen.1005108. eCollection 2015 Mar.


Identification of active transcriptional regulatory elements from GRO-seq data.

Danko CG, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, Siepel A.

Nat Methods. 2015 May;12(5):433-8. doi: 10.1038/nmeth.3329. Epub 2015 Mar 23.


A method for calculating probabilities of fitness consequences for point mutations across the human genome.

Gulko B, Hubisz MJ, Gronau I, Siepel A.

Nat Genet. 2015 Mar;47(3):276-83. doi: 10.1038/ng.3196. Epub 2015 Jan 19.


The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease.

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, Berlin AM, Lara M, Russell P, Swofford R, Turner-Maier J, Young S, Hourlier T, Aken B, Searle S, Sun X, Yi Y, Suresh M, Tumpey TM, Siepel A, Wisely SM, Dessimoz C, Kawaoka Y, Birren BW, Lindblad-Toh K, Di Palma F, Engelhardt JF, Palermo RE, Katze MG.

Nat Biotechnol. 2014 Dec;32(12):1250-5. doi: 10.1038/nbt.3079. Epub 2014 Nov 17.


Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.

Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT.

Nat Genet. 2014 Dec;46(12):1311-20. doi: 10.1038/ng.3142. Epub 2014 Nov 10.


Diverse modes of evolutionary emergence and flux of conserved microRNA clusters.

Mohammed J, Siepel A, Lai EC.

RNA. 2014 Dec;20(12):1850-63. doi: 10.1261/rna.046805.114. Epub 2014 Oct 20.


Enabling large-scale next-generation sequence assembly with Blacklight.

Couger MB, Pipes L, Squina F, Prade R, Siepel A, Palermo R, Katze MG, Mason CE, Blood PD.

Concurr Comput. 2014 Sep 10;26(13):2157-2166.


Cis-regulatory elements and human evolution.

Siepel A, Arbiza L.

Curr Opin Genet Dev. 2014 Dec;29:81-9. doi: 10.1016/j.gde.2014.08.011. Epub 2014 Sep 16. Review.


Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines.

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, Lai EC.

Genome Res. 2014 Jul;24(7):1236-50. doi: 10.1101/gr.161554.113.


Adaptive evolution of testis-specific, recently evolved, clustered miRNAs in Drosophila.

Mohammed J, Bortolamiol-Becet D, Flynt AS, Gronau I, Siepel A, Lai EC.

RNA. 2014 Aug;20(8):1195-209. doi: 10.1261/rna.044644.114. Epub 2014 Jun 18.


Contrasting X-linked and autosomal diversity across 14 human populations.

Arbiza L, Gottipati S, Siepel A, Keinan A.

Am J Hum Genet. 2014 Jun 5;94(6):827-44. doi: 10.1016/j.ajhg.2014.04.011. Epub 2014 May 15.


Genome-wide inference of ancestral recombination graphs.

Rasmussen MD, Hubisz MJ, Gronau I, Siepel A.

PLoS Genet. 2014 May 15;10(5):e1004342. doi: 10.1371/journal.pgen.1004342. eCollection 2014.


Genome sequencing highlights the dynamic early history of dogs.

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, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Wilton A, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Ostrander EA, Marques-Bonet T, Wayne RK, Novembre J.

PLoS Genet. 2014 Jan;10(1):e1004016. doi: 10.1371/journal.pgen.1004016. Epub 2014 Jan 16. Erratum in: PLoS Genet. 2014 Aug;10(8):e1004631. Wilton, Alan [added].


Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii).

Ma X, Kelley JL, Eilertson K, Musharoff S, Degenhardt JD, Martins AL, Vinar T, Kosiol C, Siepel A, Gutenkunst RN, Bustamante CD.

PLoS One. 2013 Oct 23;8(10):e77175. doi: 10.1371/journal.pone.0077175. eCollection 2013.


A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes.

Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A.

PLoS Genet. 2013;9(8):e1003684. doi: 10.1371/journal.pgen.1003684. Epub 2013 Aug 15.


The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution.

Mohammed J, Flynt AS, Siepel A, Lai EC.

RNA. 2013 Sep;19(9):1295-308. doi: 10.1261/rna.039248.113. Epub 2013 Jul 23.


Genome-wide inference of natural selection on human transcription factor binding sites.

Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B, Keinan A, Siepel A.

Nat Genet. 2013 Jul;45(7):723-9. doi: 10.1038/ng.2658. Epub 2013 Jun 9.


Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans.

Zeng L, Choi SC, Danko CG, Siepel A, Stanhope MJ, Burne RA.

PLoS One. 2013;8(3):e60465. doi: 10.1371/journal.pone.0060465. Epub 2013 Mar 28.


Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells.

Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL.

Mol Cell. 2013 Apr 25;50(2):212-22. doi: 10.1016/j.molcel.2013.02.015. Epub 2013 Mar 21. Erratum in: Mol Cell. 2013 Jun 6;50(5):778.


Inference of natural selection from interspersed genomic elements based on polymorphism and divergence.

Gronau I, Arbiza L, Mohammed J, Siepel A.

Mol Biol Evol. 2013 May;30(5):1159-71. doi: 10.1093/molbev/mst019. Epub 2013 Feb 5.


Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans.

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.

Mol Biol Evol. 2013 Apr;30(4):881-93. doi: 10.1093/molbev/mss278. Epub 2012 Dec 10.


Replacing and additive horizontal gene transfer in Streptococcus.

Choi SC, Rasmussen MD, Hubisz MJ, Gronau I, Stanhope MJ, Siepel A.

Mol Biol Evol. 2012 Nov;29(11):3309-20. doi: 10.1093/molbev/mss138. Epub 2012 May 21.


Accurate prediction of inducible transcription factor binding intensities in vivo.

Guertin MJ, Martins AL, Siepel A, Lis JT.

PLoS Genet. 2012;8(3):e1002610. doi: 10.1371/journal.pgen.1002610. Epub 2012 Mar 29.


The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome.

Kostka D, Hubisz MJ, Siepel A, Pollard KS.

Mol Biol Evol. 2012 Mar;29(3):1047-57. doi: 10.1093/molbev/msr279. Epub 2011 Nov 10.


A high-resolution map of human evolutionary constraint using 29 mammals.

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, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M.

Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530.


Bayesian inference of ancient human demography from individual genome sequences.

Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A.

Nat Genet. 2011 Sep 18;43(10):1031-4. doi: 10.1038/ng.937.


Three periods of regulatory innovation during vertebrate evolution.

Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D.

Science. 2011 Aug 19;333(6045):1019-24. doi: 10.1126/science.1202702. Erratum in: Science. 2011 Nov 11;334(6057):761.


Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing.

Gottipati S, Arbiza L, Siepel A, Clark AG, Keinan A.

Nat Genet. 2011 Jul 24;43(8):741-3. doi: 10.1038/ng.877.


A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells.

Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL.

Cell. 2011 May 13;145(4):622-34. doi: 10.1016/j.cell.2011.03.042. Epub 2011 May 5. Erratum in: Cell. 2011 Jun 24;145(7):1156.


Error and error mitigation in low-coverage genome assemblies.

Hubisz MJ, Lin MF, Kellis M, Siepel A.

PLoS One. 2011 Feb 14;6(2):e17034. doi: 10.1371/journal.pone.0017034.


Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution.

Suzuki H, Lefébure T, Hubisz MJ, Pavinski Bitar P, Lang P, Siepel A, Stanhope MJ.

Genome Biol Evol. 2011;3:168-85. doi: 10.1093/gbe/evr006. Epub 2011 Jan 31.


PHAST and RPHAST: phylogenetic analysis with space/time models.

Hubisz MJ, Pollard KS, Siepel A.

Brief Bioinform. 2011 Jan;12(1):41-51. doi: 10.1093/bib/bbq072. Epub 2010 Dec 21.


Comparative and demographic analysis of orang-utan genomes.

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, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK.

Nature. 2011 Jan 27;469(7331):529-33. doi: 10.1038/nature09687.


Widespread regulatory activity of vertebrate microRNA* species.

Yang JS, Phillips MD, Betel D, Mu P, Ventura A, Siepel AC, Chen KC, Lai EC.

RNA. 2011 Feb;17(2):312-26. doi: 10.1261/rna.2537911. Epub 2010 Dec 22.

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