Postdoctoral Positions in Computational Genomics at Cold Spring Harbor Laboratory

Cold Spring Harbor Laboratory
Job Location
Cold Spring Harbor, New York,

Comprehensive benefits

Job Description

Postdoctoral Positions in Computational Genomics

Postdoctoral positions are available in Dr. Adam Siepel’s research group in its new location at the Simons Center for Quantitative Biology at Cold Spring Harbor Laboratory, starting in September, 2014.

The Siepel group specializes in the development of probabilistic models, algorithms for inference, prediction methods, and application of these methods in large-scale genomic data analysis. Of particular interest is research relevant to existing, NIH-supported projects in (1) human population genomics, including demography inference using Bayesian coalescent-based methods, inference of natural selection on regulatory and other noncoding sequences, and prediction of fitness consequences for noncoding mutations; and (2) transcriptional regulation in mammals and Drosophila, including the estimation of rates and patterns of transcriptional elongation from GRO-seq data, prediction of transcription factor binding sites from DNase-seq data, and regulatory network inference based on joint patterns of transcription and binding in inducible systems. The research on transcriptional regulation will continue to be carried out in close collaboration with Dr. John Lis at Cornell University.

Relevant recent papers include the following:

Rasmussen MD, Hubisz MJ, Gronau I, Siepel A. Genome-wide inference of ancestral recombination graphs. PLOS Genet. 10(5): e1004342, 2014.

Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, et al. (30 co-authors). Genome sequencing highlights the dynamic early history of dogs. PLOS Genet. 10(1):e1004016, 2014.

Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A. A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PLOS Genet. 9(8):e1003684, 2013.

Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B, Keinan A, Siepel A. Genome-wide inference of natural selection on human transcription factor binding sites. Nature Genetics 45(7):723-729, 2013.

Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol. Cell 50(2):212-222, 2013.

Gronau I, Arbiza L, Mohammed J, Siepel A. Inference of natural selection from interspersed genomic elements based on polymorphism and divergence. Mol. Biol. Evol. 30(5):1159-1171, 2013.

Guertin MJ, Martins AL, Siepel A, Lis JT. Accurate prediction of inducible transcription factor binding intensities in vivo. PLOS Genetics, 8(3):e1002610, 2012.

Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. Bayesian inference of ancient human demography from individual genome sequences. Nature Genetics 43(10):1031-1034, 2011.


The ideal candidate will be enthusiastic, highly motivated and independent; will have a strong background in comparative genomics, population genomics, or transcriptional regulation, a serious interest in molecular biology and genetics combined with good skills in mathematics and computer science, and a strong record of accomplishment in research. Postdoctoral associates in the group are expected to participate in both methods development and data analysis, to be comfortable in a fast-moving, interactive, and collaborative research environment, and to actively publish and present results.

Required Qualifications:

• Ph.D. in bioinformatics, computer science, statistics, genetics, molecular biology, applied mathematics, or a related field.
• Research experience (with first-author publications) in computational genomics or a closely related field.
• Fluency in probabilistic modeling and computational statistics.
• Proficiency in programming, ideally in C or C++ as well as in scripting languages such as python, Perl, mat lab, or R. Should be comfortable in a Linux environment, with large data sets, computer clusters, and databases.

The term for these positions is flexible but most likely will be 2-3 years. The proposed start date is September 2014.

To Apply:
Please submit a CV, a short description of research interests and experience, and contact information for three references by e-mail to Informal inquiries are welcome.

Adam Siepel, Ph.D.
Cold Spring Harbor Laboratory
One Bungtown Road
Cold Spring Harbor, NY 11724

Please note that interested candidates must also apply via the CSHL careers website at

Cold Spring Harbor Laboratory is a world-renowned research and educational institution with programs in cancer, neuroscience, plant biology, genomics and bioinformatics. The Laboratory is recognized internationally for its excellence in research and educational activities.

For more information about CSHL, please visit us at

CSHL is an EO/AA Employer. All qualified applicants will receive consideration for employment and will not be discriminated against on the basis of race, color, religion, sex, sexual orientation, national origin, age, disability or protected veteran status….

How to Apply

Please submit a CV, a short description of research interests and experience, and contact information for three references by e-mail to Informal inquiries are welcome.

Adam Siepel, Ph.D.
Cold Spring Harbor Laboratory
One Bungtown Road
Cold Spring Harbor, NY 11724

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