Publications

Dukler N, Mughal MR, Ramani R, Huang Y-F, Siepel A. 2022. Extreme purifying selection against point mutations in the human genome. Nat Commun, 13, 4312.

Wu Y, Johnson L, Song B, Romay C, Stitzer M, Siepel A, Buckler E, Scheben A. 2022. A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants. Plant Genome, 15, e20204.

Abuhashem A, Chivu AG, Zhao Y, Rice EJ, Siepel A, Danko CG, Hadjantonakis A-K. 2022. RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription. Genes Dev. [Epub ahead of print].

Hejase HA, Ziyi M, Campagna L, Siepel A. A deep-learning approach for inference of selective sweep from ancestral recombination graph. Mol. Biol. Evol. 39:1, msab332.

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, 37:4727-4736.

Hutton HR, Vakoc CR, Siepel A. 2021. ACE: a probabilistic model for characterizing gene-level essentiality in CRISPR screens. Genome Biol. 22, 278.

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.