Barak A. Cohen, PhD

Alvin Goldfarb Distinguished Professor of Computational Biology

Molecular Genetics and Genomics Program
Computational and Systems Biology Program

  • 314-362-3674

  • 314-362-3679

  • Couch Building, Room 4308



  • Genomics, Genetic Variation, High-Throughput Technologies, Single-Cell Regulatory Genomics, Computational Biology

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

Research Abstract:

Most disease-causing genetic variation resides in the 98% of the genome that does not code for protein. Underlying this disease risk are variants in enhancers, the cis-regulatory sequences that control when, where, and to what extent genes are expressed. Because the human genome may contain as many as 1,000,000 enhancer sequences, identifying disease-causing enhancer variants will require robust high-throughput approaches.

The Cohen Lab's quest to understand enhancer biology relies on new high-throughput technologies we have developed to study gene regulation. These technologies are both wet (single cell methods for assessing enhancer activity) and dry (machine learning and biophysical frameworks for modeling enhancer function). Our ultimate goal is to build accurate and quantitative models of enhancers that guide the interpretation of genetic variation in the human genome.

Mentorship and Commitment to Diversity Statement:
The Cohen Lab is committed to training the next generation of independent, interdisciplinary, broad-thinking, genome scientists. Because we never know where the next great idea will come from, making progress requires diversity in both thought and approach. Our lab is strengthened by the diverse histories, interests, and expertise of our members. We strive to maintain a lab culture that fosters creativity and invites contributions from anyone who shares our passion for exploration. Finally, the Cohen Lab is committed to ensuring access to family planning services for all of its members.

Selected Publications:

Hansen, J.L., Loell, K.J., Cohen, B.A. (2022). The pioneer factor hypothesis is not necessary to explain ectopic liver gene activation. Elife 11, e73358.

Hong, C.K.Y. and Cohen, B.A. (2022) Genomic environments scale the activities of diverse core promoters. Genome Res. 32:85-96.

Friedman, R.Z., Granas, D.M., Myers, C.A., Corbo, J.C., Cohen, B.A. and White, M.A. (2021) Information Content Differentiates Enhancers from Silencers in Mouse Photoreceptors. ELife 10, e67403.

Staller, M.V, Ramirez, E., Holehouse, A.S., Pappu, R.V., and Cohen, B.A. (2021) Design principles of acidic transcriptional activation domains. Cell Systems Biol. 6:1-12

Maricque, Brett B., Chaudhari, Hemangi G., and Cohen, B. A. (2019) A massively parallel reporter assay dissects the influence of chromatin structure on cis-regulatory activity. Nat Biotechnol. 37:90-95

Staller, M.V., Holehouse, A.S., Swain-Lenz, D., Das, R.K., Pappu, R.V., and Cohen, B.A. (2018). A high-throughput mutational scan of an intrinsically disordered acidic transcriptional activation domain. Cell Systems Biol. 6:1-12

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

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

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: 7/20/2022 3:46:12 PM

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