Selected Publications

Kuhlwilm M., Gronau I., Hubisz M.J., de Filippo C., Prado 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., and Castellano S. 2016. Ancient gene flow from early modern humans into Eastern Neanderthals. Nature, 530 (7591): 429–433.

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., and Siepel, A. 2015. Identification of active transcriptional regulatory elements from GRO-seq data. Nat. Methods, 12 (5): 433–438.

Gulko, B., Hubisz, M. J., 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, E. C. 2014. Diverse modes of evolutionary emergence and flux of conserved microRNA clusters. RNA, 20 (12): 1850–1863.

Core, L. J., Martins, A. L., Danko, C. G., Waters, C. T., Siepel, A., and Lis, J. T.  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, M. D., Hubisz, M. J., Gronau, I., and Siepel, A. 2014. Genome–wide inference of ancestral recombination graphs. PLOS Genet., 10 (5): e1004342.

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

Arbiza, L., Gronau, I., Aksoy, B. A., Hubisz, M. J., 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, J. A., Hubisz, M. J., Kostka, D., Pollard, K. S., 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, C. G., Hah, N., Luo, X., Martins, A. L., Core, L., Lis, J. T., Siepel, A., and Kraus, W. L. 2013. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol. Cell, 50: 212–222.

Guertin, M. J., Martins, A. L., Siepel, A., and Lis, J. T. 2012. Accurate prediction of inducible transcription factor binding intensities in vivo. PLOS Genet., 8 (3): e1002610.

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

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

Pollard, K. S., Hubisz, M. J., Rosenbloom, K. R., 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, R. R., Hubisz, M. J., Bustamante, C. D., 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, C. L. G., 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, J. S., Hinrichs, A. S., 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.