Zhao Y, Dukler N, Barshad G, Toneyan S, Danko CG, and Siepel A. 2021. Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. Bioinformatics, btab582, [Online ahead of print].
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. PLOS 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.