Principal Investigator

asiepel at cshl dot edu

Adam Siepel is a Professor in the Watson School of Biological Sciences and Chair of the Simons Center for Quantitative Biology. Adam initially studied engineering at Cornell University then worked in bioinformatic software development for several years, before attending graduate school in Computer Science at the University of New Mexico and UC Santa Cruz. He was a member of the faculty of the department of Biological Statistics and Computational Biology at Cornell University from 2006–2014 and has been at Cold Spring Harbor Laboratory since 2014. Adam has served on the editorial boards for Genome Research and PLOS Computational Biology, on review panels for the National Science Foundation and the National Institutes of Health, and on advisory committees for the National Human Genome Research Institute. He is a winner of a Guggenheim Fellowship, a Microsoft Research Faculty Fellowship, a Packard Fellowship, a National Science Foundation CAREER Award, and a Sloan Research Fellowship.  In his free time, Adam enjoys cycling, hiking, traveling, and spending time with his family.

Current Lab Members

Yifei Huang

Yifei Huang

Postdoc

yihuang at cshl dot edu

Yifei is a postdoc in the laboratory, who is interested in developing novel statistical models to study the mechanisms of evolution and gene expression. Before he joined Siepel Lab, Yifei finished his PhD training under the supervision of Dr. Brian Golding at McMaster University where he worked on inferring functionally important regions in proteins using statistical phylogenetics. He has a B.S. in Biotechnology and a M.S. in Bioinformatics from Zhengzhou University and Beijing Normal University. In his free time, Yifei enjoys reading and cooking.

Amit Blumberg

Amit Blumberg

Postdoc

ablumber at cshl dot edu

Amit is a postdoc in the lab, who is interested in understanding the role of enhancer RNA stability, by combining computational approaches and high-throughput molecular genetics experiments. Amit finished M.Sc. and PhD training at Ben Gurion University of the Negev, Israel, under the supervision of Prof. Dan Mishmar, where he worked on investigating the molecular basis underlying the complex regulation of human mitochondrial DNA (mtDNA) transcription. He has a B.S. in natural sciences from the Open University in Israel. In his free time, Amit enjoys hiking, reading and spending time with his wife and five kids.

Adrian Platts

Adrian Platts

Research Associate

aplatts at cshl dot edu

Adrian is a bioinformatician working jointly between CSHL and NYU on applying INSIGHT and fitCons approaches to plant species.  A Physics graduate, he initially worked on magnetic materials in the Harris lab before transitioning to a bioinformatics career, working with Stephen Krawetz on gene regulation during human reproduction.  In the 6 yrs prior to joining the Siepel lab he worked with Mathieu Blanchette at McGill and Stephen Wright at the University of Toronto in blending comparative and population genomics to  characterize the non-coding regulatory regions in dicot plants.

Ritika Ramani

Ritika Ramani

Programmer

rramani at cshl dot edu

Ritika is the lab programmer in charge of  developing and maintaining Phast and other lab tools. Before coming to the Siepel lab she spent two years developing Bioinformatics pipelines for analyzing microarray data at University of Mississippi Medical Center. She has a M.S in Bioinformatics from NJIT and a B.T. in Bioinformatics from Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, India. In her free time she likes to cook, wrestle polar bears, and read.

Noah Dukler

Noah Dukler

Ph.D. Student

ndukler at cshl dot edu

Noah is a Ph.D. student in the Tri-Institute Computational Biology and Medicine program.  He is primarily located in the Siepel Lab at Cold Spring Harbor Laboratory but maintains close ties with Weill Cornell Medical College in NYC. Together with the Lis Lab at Cornell/Ithaca, Noah is studying the transcriptional response in mammalian cells to a therapeutically interesting small molecule called celastrol, which is derived from the Thunder God vine used in traditional Chinese medicine.  He is also developing new conditional-random-field-based methods for the prediction of transcription factor binding sites.  Noah has a B.S. in Biochemistry and B.A. in Mathematics from SUNY Geneseo. In his free time, he enjoys cycling, hiking, and cooking.

Brad Gulko

Brad Gulko

Ph.D. Student

bgulko at cs dot cornell dot edu

Brad is a Ph.D. candidate in Computer Science at Cornell, who is developing new methods for identifying functionally important noncoding sequences in the human genome based on population genetic theory. Recently, he has developed a novel Bayesian scoring system for identifying combinations of functional genomic assay results that pinpoint genomic positions with identifiable fitness consequence (“fitCons” scores), as estimated from patterns of human polymorphism and primate divergence. Brad also has interests in machine learning and decision theory and substantial experience in the software industry.  He has a B.A. in Physics and Mathematics and an M.S. in Computer Engineering from the University of California, Santa Cruz.  In his free time, he enjoys hiking, archery and wine tasting.

Melissa Hubisz

Melissa Hubisz

Ph.D. Student

mjhubisz at cornell dot edu

Melissa is a Ph.D. student in the Computational Biology program at Cornell, who is working on new methods for ancestral recombination graph inference and demographic reconstruction for human populations.  Before resuming her graduate work, she was the lead programmer and lab manager for the Siepel Lab from 2008-2014.  Melissa also has extensive experience in population genetics through previous work with Rasmus Nielsen (now at UC Berkeley) and Jonathan Pritchard (now at Stanford).  She has a B.S. in Engineering and Applied Science from Caltech, an MS in Biometry from Cornell, and an MS in Human Genetics from the University of Chicago.  In her free time, she enjoys running and spending time with her husband and two children.

Elizabeth Hutton

Elizabeth Hutton

Ph.D. Student

ehutton at cshl dot edu

As a Ph.D. student in the Watson School of Biological sciences, Lizzie is interested in gene regulation.  She has a B.A. from Princeton University in Molecular Biology, with a certificate in Quantitative and Computational Biology, and enjoys puzzles.

Lenore Pipes

Lenore Pipes

Ph.D. Student

lp364 at cornell dot edu

Lenore is a Ph.D. student in the Tri-Institute Computational Biology and Medicine program.  She is primarily located in Ithaca but is jointly advised by Chris Mason at Weill Cornell Medical College in NYC.  Lenore is focusing on the analysis of RNA-seq data from dozens of primate genomes, with the ultimate goal of studying the evolution of alternative splicing across the primate phylogeny.  In addition to her individual research, she is involved in several large-scale consortium projects. Lenore has a BA in Biology and Sociology/Anthropology from Swarthmore and an MS in Bioinformatics from Johns Hopkins. When she is not toiling away at her research, Lenore has a second life as a competitive cyclist.

Irene Gill

Irene Gill

Senior Scientific Administrator

gill at cshl dot edu

Irene is our Senior Scientific Administrator who keeps the Siepel Lab from descending into total chaos. She also provides administrative support for several other PIs and the Simons Center for Quantitative Biology as a whole. Irene has been at Cold Spring Harbor Laboratory since 2007. When she is not organizing QB activities, she enjoys long walks with her husband and dog, reading, and watching classic old movies.

Lab Alumni

Leonardo Arbiza (Postdoc, 2010–2013). Natural selection on transcription factor binding sites in recent human evolution. Leo was a joint postdoc between the Siepel and Keinan Labs at Cornell and is now finishing his postdoc with Alon Keinan, with a focus on X-vs.-autosome genetic variation.

Bronislava Brejova (Postdoc, 2006–2008). Comparative genomic methods for gene prediction. Brona is now an associate professor in the Department of Computer Science at Comenius University in Bratislava, Slovakia.

Sang Chul Choi (Postdoc, 2010–2013). Comparative genomics and transcriptomics of Streptococcus species. Sang Chul collaborated with Mike Stanhope at Cornell and Robert Burne at the University of Florida on various comparative and functional genomic analyses of pathogenic Streptococci. He is now a Bioinformatics/Genome Scientist at the University of Alaska, Fairbanks.

Omar Cornejo (Postdoc, 2009–2010). Population genetics of Streptococcus species. Omar contributed to a joint project involving the Siepel, Bustamante, and Stanhope labs before finishing his postdoc with Carlos Bustamante at Stanford. He is now an assistant professor of biology at Washington State University.

Charles Danko (Postdoc, 2009–2014). Computational and experimental research in transcriptional regulation, including estimation of transcription rates, prediction of enhancers, and comparative genomics of gene regulation in primates. Charles is now an assistant professor at the Baker Institute for Animal Health and the Department of Biomedical Sciences at Cornell. He continues to work with the Siepel and Lis Labs on analyses of GRO-seq and PRO-seq data.

Ilan Gronau (Postdoc, 2009–2014). Development of coalescent-based methods for demography inference (G-PhoCS) and probabilistic methods for measuring the influence of natural selection on dispersed genomic elements (INSIGHT). Ilan is now a senior lecturer at the School of Computer Science in the Interdisciplinary Center (IDC), Herzliya, Israel. He continues to collaborate with the Siepel Lab from Israel.

Carolin Kosiol (Postdoc, 2006–2008). Comparative genomics of mammals, including positive selection in primates. Carolin is now a Group Leader in Bioinformatics at the Institute for Population Genetics, University of Veterinary Medicine, Vienna.

Andre L. Martins (Ph.D. student, 2007–2014). Bioinformatic analysis of transcriptional regulation in mammals and Drosophila, in close collaboration with the Lis Lab. Andre has returned to his native Portugal but continues to work closely with the Siepel and Lis Labs as a consultant.

Jaaved Mohammed (Ph.D. student, 2009–2016). Molecular evolution of miRNAs in Drosophila. Jaaved was a joint member of the Siepel Lab and Eric Lai’s Laboratory at Memorial Sloan Kettering Cancer Center. He is now a postdoc with Joanna Wysocka at Stanford.

Matthew Rasmussen (Postdoc, 2011–2013). Genome-wide inference of ancestral recombination graphs. Matt is now a software engineer at Counsyl, Inc. in South San Francisco.  Occasionally, we still lure him into thinking about ancestral recombination graphs for old times’ sake.

Tomas Vinar (Postdoc, 2006–2008). Probabilistic models of gene cluster evolution. Tomas is now an assistant professor in the Department of Applied Informatics at Comenius University in Bratislava, Slovakia.

Other Alumni

Master’s students

Adam Diehl, Michael D. Phillips

Undergraduate researchers

Alexandra Denby, Tytus Mak, Alison Marklein, Joseph Porter, Renee Setter, and Daniel Sussman.