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

Single-Cell Transcription Mapping of Murine and Human Mammary Organoids Responses to Female Hormones

30 Jan 2024 | Journal of Mammary Gland Biology and Neoplasia | 29(1):3
Ortiz, Jenelys, Lewis, Steven, Ciccone, Michael, Chatterjee, Deeptiman, Henry, Samantha, Siepel, Adam, Dos Santos, Camila

DNA-sequence and epigenomic determinants of local rates of transcription elongation

23 Dec 2023 | bioRxiv
Liu, Lingjie, Zhao, Yixin, Siepel, Adam

Identification of constrained sequence elements across 239 primate genomes

29 Nov 2023 | Nature
Kuderna, Lukas, Ulirsch, Jacob, Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony, Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew, Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike, Kuhlwilm, Martin, Orkin, Joseph, Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rouselle, Marjolaine, Silva, Felipe, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss, Horvath, Julie, Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua, de Melo, Fabiano, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément, Zaramody, Alphonse, Jolly, Clifford, Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe, Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius, Knauf, Sascha, Le, Minh, Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea, Lee, Jessica, Tan, Patrick, Lim, Weng, Kitchener, Andrew, Zinner, Dietmar, Gut, Ivo, Melin, Amanda, Guschanski, Katerina, Schierup, Mikkel, Beck, Robin, Karakikes, Ioannis, Wang, Kevin, Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean, Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marques Bonet, Tomas, Farh, Kyle

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

7 Nov 2023 | PLoS Genetics | 19(11):e1011032
Mo, Ziyi, Siepel, Adam, Schrider, Daniel

Utility of AlphaMissense predictions in Asparagine Synthetase deficiency variant classification

2 Nov 2023 | bioRxiv
Staklinski, Stephen, Scheben, Armin, Siepel, Adam, Kilberg, Michael

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

27 Oct 2023 | Nucleic Acids Research (NAR)
Zhao, Yixin, Liu, Lingjie, Hassett, Rebecca, Siepel, Adam

Single-cell transcription mapping of murine and human mammary organoids responses to female hormones

29 Sep 2023 | bioRxiv
Ortiz, Jenelys, Lewis, Steven, Ciccone, Michael, Chatterjee, Deeptiman, Henry, Samantha, Siepel, Adam, Dos Santos, Camila

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

6 Sep 2023 | bioRxiv
Mo, Ziyi, Siepel, Adam

Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats

4 Sep 2023 | Genome Biology and Evolution | 15(9)
Scheben, Armin, Mendivil Ramos, Olivia, Kramer, Melissa, Goodwin, Sara, Oppenheim, Sara, Becker, Daniel, Schatz, Michael, Simmons, Nancy, Siepel, Adam, McCombie, W, Pfeifer, Susanne

Teosinte Pollen Drive guides maize domestication and evolution by RNAi

3 Aug 2023 | bioRxiv
Berube, Benjamin, Ernst, Evan, Cahn, Jonathan, Roche, Benjamin, de Santis Alves, Cristiane, Lynn, Jason, Scheben, Armin, Siepel, Adam, Ross-Ibarra, Jeffrey, Kermicle, Jerry, Martienssen, Robert

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