Barak A. Cohen, Ph.D.

Alvin Goldfarb Distinguished Professor of Computational Biology

Molecular Genetics and Genomics Program
Computational and Systems Biology Program

  • 314-362-3674

  • 314-362-3679

  • 8232

  • MRB - McKinley Research Building, Room 4308



  • systems biology, enhancers and gene regulatory networks, non-coding genetic variation, computational biology, genomics, quantitative genetics, thermodynamics,

  • Genomic analyses of regulatory networks, Non-coding disease variants

Research Abstract:

Non-coding DNA makes up 98% of the genome. Some of these non-coding sequences regulate when, where, and to what levels genes are expressed. Genetic variation in regulatory DNA contributes to phenotypic differences between individuals, including differences in disease susceptibility, by influencing gene expression

My lab uses high-throughput genomics and quantitative models to better understand how regulatory DNA functions in the genome. We aim to develop the experimental and computational tools that will allow us to predict which sequences in the genome regulate gene expression and how genetic variants in these sequences alter gene expression.

Selected Publications:

Maricque, B. B., Dougherty, J. D., & Cohen, B.A. (2016) A genome-integrated massively-parallel reporter assay reveals DNA sequence determinants of cis-regulatory activity in neural cells. Nucleic Acids Res. 45(4):e16 PMCID:PMC5389540

White M.A., Kwasnieski, J. C., Myers, C. A., Shen, S. Q., Corbo, J. C., & Cohen, B.A. (2016) A simple regulatory grammar distinguishes activating from repressing cis-regulatory elements in photoreceptors. Cell Reports. 17(5):1247-1254. PMCID: PMC123866

Kwasnieski, J.C., Fiore, C., Chaudhari, H.G., & Cohen B.A. (2014) High-throughput functional testing of ENCODE segmentation predictions. Genome Res. 10:1595-602. PMCID: PMC4199366

Fiore, C. & Cohen, B.A. (2016). Interactions between pluripotency factors specify cis-regulation in embryonic stem cells. Genome Res. 26:1–9. PMCID: PMC4889965

Sherman, M., Lorenz, K., Lanier, H. M., & Cohen, B.A. (2015) Cell-to-cell variability in the propensity to transcribe explains correlated fluctuations in gene expression. Cell Systems. 1, 315-325. PMCID: PMC4662655

Sudarsanam, P. & Cohen, B.A. (2014) Single nucleotide variants in transcription factors associate more tightly with phenotype than with gene expression. Plos Genet. 10(5):e1004325 PMCID: PMC4006743

Sherman, M. & Cohen, B.A. (2014) A computational framework for analyzing stochasticity in gene expression. PLoS Comp. Biol. 10(5):e1003596 PMCID: PMC4014403

White, M.A, Parker, D.S., Barolo, S. & Cohen, B.A. (2012) A model of spatially restricted transcription in opposing gradients of activators and repressors. Mol. Sys. Biol., 8:614. PMCID: PMC3472688

Gertz, J., Siggia, E., & Cohen, B.A. (2009) Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature, 457: 215-218. PMCID: PMC2677908

Gerke, J.P., Lorenz, K. & Cohen, B.A. (2009) Genetic interactions between transcription factors cause natural variation in yeast. Science, 323:498-501 PMCID: PMC4984536

Last Updated: 7/13/2017 10:54:00 AM

Competing thermodynamic models of a cis-regulatory system
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