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

Yixin Zhao

Yixin Zhao

Postdoc

yizhao at cshl dot edu

Yixin is a postdoc in the lab, who is interested in applying novel experimental techniques (e.g. PRO-seq) to study gene regulation, gene expression and intriguing evolutionary questions.

Before he joined the Siepel Lab, Yixin worked and finished his PhD training under the supervision of Prof. Chung-I Wu at Sun Yat-sen University (SYSU) where he focused on microRNA expression and function evolution using high-throughput sequencing data and molecular biology experiments. He also got his B.S. in Biotechnology in SYSU.

In his free time, Yixin enjoys going to the gym, walking and cooking.

Hussein (Hejase) Hijazi

Hussein (Hejase) Hijazi

Postdoc

hijazi at cshl dot edu

Hussein is a postdoc in the lab. He is interested in developing and applying machine learning techniques to understand and uncover the functional roles of genomes with complex evolutionary histories.

Prior to joining the Siepel lab in January of 2018, Hussein finished his PhD in computer science and engineering at Michigan State University (MSU) under the supervision of Dr. Kevin Liu, where he worked on scalable phylogenetic analysis and functional interpretation of genomes with complex evolutionary histories.

In his free time, Hussein loves reading, spending time with his wife, and following his beloved MSU’s basketball team.

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 six years 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.

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.

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, with a focus on X-vs.-autosome genetic variation.  Leonardo is currently a Computational Biology Research Scientist at Twist Bioscience, a startup company that has revolutionized massive high quality DNA synthesis.

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. Sang Chul is currently in the Department of Biotechnology at Sungshin Women’s University, Seoul, Republic of Korea.

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. Omar 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.

Brad Gulko (Ph.D. Student, 2010–2017). Developed a novel Bayesian scoring system for identifying combinations of functional genomic assay results that pinpoint genomic positions with identifiable fitness consequence (“fitCons” scores).

Carolin Kosiol (Postdoc, 2006–2008). Comparative genomics of mammals, including positive selection in primates. Carolin is currently a Lecturer in Bioinformatics at the School of Biology, University of St. Andrews, Fife, UK.

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 and is working in software development.

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.

Lenore Pipes (Ph.D. student, 2012-2017). Evolution of alternative splicing in primates. Lenore was a joint member of the Siepel Lab and Christopher Mason’s Laboratory at Cornell University. She is now a postdoc with Rasmus Nielsen at UC Berkeley.

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 associate 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.