Adam Siepel

Adam Siepel

Cancer Center Program Co-Leader

Ph.D., University of California, Santa Cruz, 2005

asiepel@cshl.edu | 516-367-6922

Siepel Lab Website   Faculty Profile

I am a computer scientist who is fascinated by the challenge of making sense of vast quantities of genetic data. My research group focuses in particular on questions involving molecular evolution and transcriptional regulation, with applications to cancer and other diseases as well as to plant breeding and agriculture.

Modern genomic technologies make it relatively easy to generate rich data sets describing genome sequences, RNA expression, chromatin states, and many other aspects of the storage, transmission, and expression of genetic information. For many problems in genetics today, the limiting step is no longer in data generation, but in integrating, interpreting, and understanding the available data. Addressing these challenges requires expertise both in the practical arts of data analysis and in the theoretical underpinnings of statistics, computer science, and genetics.

My group focuses on a diverse collection of research questions in this interdisciplinary area, spanning applications in cancer biology, basic molecular biology, evolutionary genetics, infectious diseases, and agriculture. Over the years, our research has touched on topics including the identification of recombinant strains of HIV, the discovery of new human genes, the characterization of conserved regulatory elements in mammalian genomes, the identification of noncoding mutations important in cancer, and the discovery of ancient gene flow from humans to Neandertals. A general theme in our work is the development of precise mathematical models for the complex processes by which genomes evolve over time, and the use of these models, together with techniques from computer science and statistics, both to peer into the past, and to address questions of practical importance for human health. We collaborate closely with experimentalists in cancer biology, transcriptional regulation, plant breeding and many other areas.

John Simon Guggenheim Memorial Foundation Fellowship, 2012-2013
Alfred P. Sloan Foundation Research Fellowship, 2009-2011
David & Lucile Packard Foundation Fellowship for Science and Engineering, 2007
Microsoft Research Faculty Fellowship Program, 2007
National Science Foundation (NSF) CAREER Award, 2007

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All Publications

A Deep-Learning Approach for Inference of Selective Sweeps from the Ancestral Recombination Graph.

22 Nov 2021 | Molecular Biology and Evolution
Hejase, Hussein, Mo, Ziyi, Campagna, Leonardo, Siepel, Adam

ACE: a probabilistic model for characterizing gene-level essentiality in CRISPR screens.

23 Sep 2021 | Genome Biology | 22(1):278
Hutton, Elizabeth, Vakoc, Christopher, Siepel, Adam

Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells.

11 Aug 2021 | Bioinformatics
Zhao, Yixin, Dukler, Noah, Barshad, Gilad, Toneyan, Shushan, Danko, Charles, Siepel, Adam

Characterization of Gene Expression Signatures for the Identification of Cellular Heterogeneity in the Developing Mammary Gland.

14 May 2021 | Journal of Mammary Gland Biology and Neoplasia
Henry, Samantha, Trousdell, Marygrace, Cyrill, Samantha, Zhao, Yixin, Feigman, Mary, Bouhuis, Julia, Aylard, Dominik, Siepel, Adam, Dos Santos, Camila

Circadian immunity, sunrise time and the seasonality of respiratory infections.

31 Mar 2021 | medRxiv
Mo, Ziyi, Scheben, Armin, Steinberg, Joshua, Siepel, Adam, Martienssen, Robert

Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data.

15 Feb 2021 | BMC Biology | 19(1):30
Blumberg, Amit, Zhao, Yixin, Huang, Yi-Fei, Dukler, Noah, Rice, Edward, Chivu, Alexandra, Krumholz, Katie, Danko, Charles, Siepel, Adam

Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps

1 Dec 2020 | Proceedings of the National Academy of Sciences of USA | 117(48):30554-30565
Hejase, H, Salman-Minkov, A, Campagna, L, Hubisz, M, Lovette, I, Gronau, I, Siepel, A

Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus

9 Sep 2020 | BioRxiv
Scheben, Armin, Ramos, Olivia, Kramer, Melissa, Goodwin, Sara, Oppenheim, Sara, Becker, Daniel, Schatz, Michael, Simmons, Nancy, Siepel, Adam, McCombie, Richard

Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph

Aug 2020 | PLoS Genetics | 16(8):e1008895
Hubisz, M, Williams, A, Siepel, A

A Community-Maintained Standard Library of Population Genetic Models

23 Jun 2020 | eLife | 9
Adrion, J, Cole, C, Dukler, N, Galloway, J, Gladstein, A, Gower, G, Kyriazis, C, Ragsdale, A, Tsambos, G, Baumdicker, F, Carlson, J, Cartwright, R, Durvasula, A, Gronau, I, Kim, B, McKenzie, P, Messer, P, Noskova, E, Ortega-Del Vecchyo, D, Racimo, F, Struck, T, Gravel, S, Gutenkunst, R, Lohmueller, K, Ralph, P, Schrider, D, Siepel, A, Kelleher, J, Kern, A

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