Adam Siepel

Adam Siepel

Cancer Center Program Co-Leader
Chair, Simons Center for Quantitative Biology

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

Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data.

1 Mar 2023 | bioRxiv
Mo, Ziyi, Siepel, Adam

Selective sweeps on different pigmentation genes mediate convergent evolution of island melanism in two incipient bird species

Nov 2022 | PLoS Genetics | 18(11):e1010474
Campagna, Leonardo, Mo, Ziyi, Siepel, Adam, Uy, J, Bierne, Nicolas

Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells

2022 | bioRxiv
Zhao, Yixin, Liu, Lingjie, Siepel, Adam

Author Correction: Comparative and demographic analysis of orang-utan genomes.

Aug 2022 | Nature | 608(7924):E36
Locke, Devin, Hillier, LaDeana, Warren, Wesley, Worley, Kim, Nazareth, Lynne, Muzny, Donna, Yang, Shiaw-Pyng, Wang, Zhengyuan, Chinwalla, Asif, Minx, Pat, Mitreva, Makedonka, Cook, Lisa, Delehaunty, Kim, Fronick, Catrina, Schmidt, Heather, Fulton, Lucinda, Fulton, Robert, Nelson, Joanne, Magrini, Vincent, Pohl, Craig, Graves, Tina, Markovic, Chris, Cree, Andy, Dinh, Huyen, Hume, Jennifer, Kovar, Christie, Fowler, Gerald, Lunter, Gerton, Meader, Stephen, Heger, Andreas, Ponting, Chris, Marques-Bonet, Tomas, Alkan, Can, Chen, Lin, Cheng, Ze, Kidd, Jeffrey, Eichler, Evan, White, Simon, Searle, Stephen, Vilella, Albert, Chen, Yuan, Flicek, Paul, Ma, Jian, Raney, Brian, Suh, Bernard, Burhans, Richard, Herrero, Javier, Haussler, David, Faria, Rui, Fernando, Olga, Darré, Fleur, Farré, Domènec, Gazave, Elodie, Oliva, Meritxell, Navarro, Arcadi, Roberto, Roberta, Capozzi, Oronzo, Archidiacono, Nicoletta, Della Valle, Giuliano, Purgato, Stefania, Rocchi, Mariano, Konkel, Miriam, Walker, Jerilyn, Ullmer, Brygg, Batzer, Mark, Smit, Arian, Hubley, Robert, Casola, Claudio, Schrider, Daniel, Hahn, Matthew, Quesada, Victor, Puente, Xose, Ordoñez, Gonzalo, López-Otín, Carlos, Vinar, Tomas, Brejova, Brona, Ratan, Aakrosh, Harris, Robert, Miller, Webb, Kosiol, Carolin, Lawson, Heather, Taliwal, Vikas, Martins, André, Siepel, Adam, RoyChoudhury, Arindam, Ma, Xin, Degenhardt, Jeremiah, Bustamante, Carlos, Gutenkunst, Ryan, Mailund, Thomas, Dutheil, Julien, Hobolth, Asger, Schierup, Mikkel, Ryder, Oliver, Yoshinaga, Yuko, de Jong, Pieter, Weinstock, George, Rogers, Jeffrey, Mardis, Elaine, Gibbs, Richard, Wilson, Richard

RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription

18 Aug 2022 | Genes and Development
Abuhashem, Abderhman, Chivu, Alexandra, Zhao, Yixin, Rice, Edward, Siepel, Adam, Danko, Charles, Hadjantonakis, Anna-Katerina

Extreme purifying selection against point mutations in the human genome

25 Jul 2022 | Nature Communications | 13(1):4312
Dukler, Noah, Mughal, Mehreen, Ramani, Ritika, Huang, Yi-Fei, Siepel, Adam

RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription

2022 | bioRxiv
Abuhashem, Abderhman, Chivu, Alexandra, Zhao, Yixin, Rice, Edward, Siepel, Adam, Danko, Charles, Hadjantonakis, Anna-Katerina

A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants

13 Apr 2022 | The Plant Genome | :e20204
Wu, Yaoyao, Johnson, Lynn, Song, Baoxing, Romay, Cinta, Stitzer, Michelle, Siepel, Adam, Buckler, Edward, Scheben, Armin

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

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