Adam Siepel
Professor
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
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
How evolved is your knowledge?
January 26, 2023
Test your knowledge of evolution with this quiz, inspired by the March 2023 performances of Isabella Rossellini’s play, Darwin’s Smile, at CSHL.
Exposing the evolutionary weak spots of the human genome
September 22, 2022
Researchers built a computer program that tracks harmful mutations throughout human evolution. It may help uncover the origins of genetic diseases.
CSHL Ph.D. program: Graduating class of 2021
August 22, 2021
The CSHL School of Biological Sciences awarded Ph.D. degrees to seven students this year, who describe some of their experiences.
Birds of a feather do flock together
November 17, 2020
Researchers found a genetic mechanism for how brand new species acquire distinct traits.
Bridge to education
December 15, 2019
CSHL’s DNA Learning Center builds new bridges between unique science education and diverse groups.
Making sense of the genome…at last
December 6, 2019
Quantitative biologists like Cold Spring Harbor Laboratory’s Adam Siepel are finally making sense of the flood of data contained in the human genome.
The Lab partners with award-winning magazine
December 6, 2019
Nautilus, an award-winning science magazine, has partnered with CSHL to bring the story of the lab’s scientists and research to a brand-new audience.
Research profile: Adam Siepel
November 12, 2019
Adam Siepel, Chair of the Simons Center for Quantitative Biology, uses advanced computational methods to solve complex biological questions.
How does natural selection affect the genome?
December 18, 2018
Adam Siepel explains how natural selection can tell researchers how informative sifting through the complex human genome will be.
How much are we learning? Natural selection is science’s best critic
December 17, 2018
Researchers determine that natural selection and our evolutionary history may be the best guides for future research.
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