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 human evolution and transcriptional regulation.
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, genetics, and evolutionary biology.
My group focuses on a diverse collection of research questions in this interdisciplinary area. 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, and the estimation of the times in early human history when major population groups first diverged. 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. Recently, we have increasingly concentrated on research at the interface of population genomics and phylogenetics, with a particular focus on humans and the great apes. We also have an active research program in computational modeling and analysis of transcriptional regulation in mammals and Drosophila, in close collaboration with Prof. John Lis at Cornell University.
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.
A science writer’s quest to understand heredity
May 30, 2018
LabDish Blog At this very moment, there is more Neanderthal DNA on Earth than there was when Neanderthals were alive. Bits of their DNA, inherited tens of thousands of years ago, persist in many of our genomes today. This astounding legacy is one of many revelations that renowned science writer Carl Zimmer uses to burst...
Evolving sets of gene regulators explain some of our differences from other primates
January 29, 2018
Cold Spring Harbor, NY — Today, biologists add an important discovery to a growing body of data explaining why we’re different from chimps and other primate relatives, despite the remarkable similarity of our genes. The new evidence has to do with the way genes are regulated. It’s the result of a comprehensive genome-wide computational analysis...
A lesson in class
December 15, 2017
Base Pairs podcast Base Pairs is a podcast about “the power of genetic information.” And there’s no better example of that power than how genome sequencing has changed our understanding of biology. In this episode, experts from three very different fields in the life sciences share stories from their own research that showcase this change....
August 15, 2016
Base Pairs podcast Few people today would take kindly to being called a Neanderthal. The name of this extinct human species has become synonymous with “stupid and rude,” and it’s not hard to see why. When we stand in front of museum dioramas depicting Neanderthals wearing little or no clothing, their hairy bodies crouched in...
Neanderthals mated with modern humans much earlier than previously thought, study finds
February 12, 2016
First genetic evidence of modern human DNA in a Neanderthal individual Cold Spring Harbor, NY — Using several different methods of DNA analysis, an international research team has found what they consider to be strong evidence of an interbreeding event between Neanderthals and modern humans that occurred tens of thousands of years earlier than any...
Harnessing data from Nature’s great evolutionary experiment
January 21, 2015
Scientists develop a computational method to estimate the importance of each letter in the human genome Cold Spring Harbor, NY — There are 3 billion letters in the human genome, and scientists have endlessly debated how many of them serve a functional purpose. There are those letters that encode genes, our hereditary information, and those...
New senior faculty join CSHL
November 10, 2014
LabDish blog This fall, the Lab welcomes six new faculty members. They’re a diverse group—a mix of junior and senior investigators, with research spanning across Biology. Want to know a little more? We’ll be featuring brief profiles all week. So check back for more! Professor Douglas Fearon, Cancer Where are you from? The University of...
Re-learning how to read a genome
November 10, 2014
Study suggests a unified model for how DNA is read, offering insight into how genes evolve Cold Spring Harbor, NY — There are roughly 20,000 genes and thousands of other regulatory “elements” stored within the three billion letters of the human genome. Genes encode information that is used to create proteins, while other genomic elements...
CSHL receives $50 million to establish Simons Center for Quantitative Biology
July 7, 2014
Cold Spring Harbor Laboratory (CSHL) today announced a $50 million gift from Jim and Marilyn Simons to establish the Simons Center for Quantitative Biology. Cold Spring Harbor, NY — Cold Spring Harbor Laboratory (CSHL) today announced a $50 million gift from Jim and Marilyn Simons to establish the Simons Center for Quantitative Biology. The Center...
Kuhlwilm, M. and Gronau, I. and Hubisz, M. J. and de Filippo, C. and Prado-Martinez, J. and Kircher, M. and Fu, Q. and Burbano, H. A. and Lalueza-Fox, C. and de la Rasilla, M. and Rosas, A. and Rudan, P. and Brajkovic, D. and Kucan, Z. and Gusic, I. and Marques-Bonet, T. and Andres, A. M. and Viola, B. and Paabo, S. and Meyer, M. and Siepel, A. and Castellano, S. (2016) Ancient gene flow from early modern humans into Eastern Neanderthals. Nature, 530(7591) pp. 429-433.
Gulko, B. and Hubisz, M. J. and Gronau, I. and Siepel, A. (2015) A method for calculating probabilities of fitness consequences for point mutations across the human genome. Nature Genetics, 47(3) pp. 276-283.
Rasmussen, M. D. and Hubisz, M. J. and Gronau, I. and Siepel, A. (2014) Genome-wide inference of ancestral recombination graphs. PLoS Genetics, 10(5) pp. e1004342.
Gronau, I. and Hubisz, M. J. and Gulko, B. and Danko, C. G. and Siepel, A. (2011) Bayesian inference of ancient human demography from individual genome sequences. Nat Genet, 43(10) pp. 1031-4.
Pollard, K. S. and Hubisz, M. J. and Rosenbloom, K. R. and Siepel, A. (2010) Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res, 20(1) pp. 110-21.Additional materials of the author at
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