Selected Publications

Blumberg A, Zhao Y, Huang Y-F, Dukler N, Rice EJ, Krumholz K, Danko CG, and Siepel A. 2021. Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. BMC Biol. 19: 30.

Hejase HA, Salman-Minkov A, Campagna L, Hubisz MJ, Lovette IJ, Grounau I, and Siepel A. 2020. Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. Proc Natl Acad Sci USA, 117: 30554-30565.

Hubisz MJ, Williams AL, and Siepel A. 2020. Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. POS Genet., 16: e1008895.

Dukler N, Huang Y-F, and Siepel A. 2020. Phylogenetic modeling of regulatory element turnover based on epigenomic data. Mol Biol Evol., 37: 2137-2152.

Joly-Lopez Z, Platts AE, Gulko B, Choi JY, Groen SC, Zhong X, Siepel A., and Purgganan MD. 2020. An inferred fitness consequence map of the rice genome. Nat Plants, 6: 119-130.

Huang Y-F, and Siepel A. 2019. Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease. Genome Res., 29: 1310-1321.

Ramani R, Krumholz K, Huang Y-F, and Siepel A. 2019. Phastweb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phlyoP Bioinformatics, 35: 2320-2322.

Gulko B, and Siepel A. 2019. An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences. Nat. Genet. 51 (2): 335–42.

Danko CG, Choate LA, Marks BA, Rice EJ, Zhong W, Chu T, Martins AL, Dukler N, Coonrod SA, Wojno EDT, Lis JT, Kraus WL, and Siepel A. 2018. Dynamic evolution of regulatory element ensembles in primate CD4+ T-cells Nat Ecol Evol., 2: 537–548.

Fang H, Huang YF, Radhakrishnan A, Siepel A, Lyon GJ, and Schatz MC. 2018. Scikit-ribo enables accurate estimation and robust modeling of translation dynamics at codon resolutionCell Syst. 6 (2): 180–91. e4.

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

Kuhlwilm M, Gronau I, Hubisz MJ, de Filippo C, Prado J, Kircher M, Fu Q, Burbano HA, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajkovic D, Kucan Z, Gusic I, Marques-Bonet T, Andres AM, Viola B, Paabo S, Meyer M, Siepel A, and Castellano S. 2016. Ancient gene flow from early modern humans into Eastern Neanderthals. Nature, 530 (7591): 429–433.

Danko CG, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, and Siepel A. 2015. Identification of active transcriptional regulatory elements from GRO-seq data. Nat. Methods, 12 (5): 433–438.

Gulko B, Hubisz MJ, Gronau I, and Siepel A. 2015. A method for calculating probabilities of fitness consequences for point mutations across the human genome. Nat. Genet., 47 (3): 276–283.

Mohammed J, Siepel A, Lai EC. 2014. Diverse modes of evolutionary emergence and flux of conserved microRNA clusters. RNA, 20 (12): 1850–1863.

Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, and Lis JT.  2014. Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat. Genet., 46: 1311–1320.

Siepel A and Arbiza L. 2014. Cis–regulatory elements and human evolution. Curr. Opin. Genet. Dev., 29C: 81–89.

Rasmussen MD, Hubisz MJ, Gronau I, and Siepel A. 2014. Genome–wide inference of ancestral recombination graphs. PLOS Genet., 10 (5): e1004342.

Mohammed J, Flynt AS, Siepel A, and Lai EC. 2013. The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution. RNA, 19 (9): 1295–1308.

Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B, Keinan A, and Siepel A. 2013. Genome–wide inference of natural selection on human transcription factor binding sites. Nat. Genet.,  45: 723–729.

Gronau I, Arbiza L, Mohammed J, and Siepel A. 2013. Inference of Natural Selection from Interspersed Genomic Elements Based on Polymorphism and Divergence. Mol. Biol. Evol., 30 (5): 1159–1171.

Capra JA, Hubisz MJ, Kostka D, Pollard KS, and Siepel A. 2013. A Model–Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes. PLOS Genet., 9 (8): e1003684.

Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, and Kraus WL. 2013. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol. Cell, 50: 212–222.

Guertin MJ, Martins AL, Siepel A, and Lis JT. 2012. Accurate prediction of inducible transcription factor binding intensities in vivo. PLOS Genet., 8 (3): e1002610.

Gronau I, Hubisz MJ, Gulko B, Danko CG, and Siepel A. 2011. Bayesian inference of ancient human demography from individual genome sequences. Nat. Genet., 43: 1031–1034.

Hubisz MJ, Pollard KS, and Siepel A. 2011. PHAST and RPHAST: phylogenetic analysis with space/time models.  Brief. Bioinform., 12 (1): 41–51.

Pollard KS, Hubisz MJ, Rosenbloom KR, and Siepel A. 2010. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res., 20: 110–121.

Siepel A. 2009. Phylogenomics of primates and their ancestral populations. Genome Res., 19 (11): 1929–1941.

Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, Siepel A. 2008. Patterns of positive selection in six Mammalian genomes. PLOS Genet., 4 (8): e1000144.

Siepel A, Diekhans M, Brejova B, Langton L, Stevens M, Comstock CLG, et al. 2007. Targeted discovery of novel human exons by comparative genomics. Genome Res., 17 (12): 1763–1773.

Rhesus Macaque Genome Sequencing and Analysis Consortium. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science, 316 (5822): 222–234.

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res., 15 (8): 1034–1050.

Siepel A and  Haussler D. 2004. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol. Biol. Evol., 21: 468–488.