2022       2021       2020       2019       2018       2017       2016       2015       2014       2013

2012       2011       2010          2009          2008          2007          2006          2005 and before

*These authors contributed equally to this work


Zhao S, Hong CKY, Granas DM, Cohen BA (2021) A single-cell massively parallel reporter assay detects cell type specific cis-regulatory activity. bioRxiv. DOI: 10.1101/2021.11.11.468308.

Hansen JL, Loell KJ, Cohen BA (2022). The pioneer factor hypothesis is not necessary to explain ectopic liver gene activation. Elife 11, e73358.

Hong CKY, Cohen BA (2022). Genomic environments scale the activities of diverse core promotersGenome Res. 32, 85-96.

Staller MV, Ramirez E, Holehouse AS, Pappu RV, Cohen BA (2022). Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains. Cell Systems, in press.


Friedman RZ, Granas GM, Myers CA, Corbo JC, Cohen BA, White MA (2021). Information Content Differentiates Enhancers From Silencers in Mouse Photoreceptors. Elife 10, e67403.

Rockwell N, Yang W, Warrington N, Griffith M, Griffith O, Gurnett C, Cohen BA, Baldridge D, Rubin J (2021). p53 mutations exhibit sex specific gain-of-function activity in gliomagenesis. Cancer Res. Commun.1(3), pp.148-163.

Zhao S, Pincus Z, Cohen BA (2021). Modular effects of gene promoters and chromatin environments on noise in gene expressionbioRxiv, 2021.04.29.441875.


King DM, Hong CKY, Shepherdson JL, Granas DM, Maricque BB, Cohen BA (2020). Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in mouse embryonic stem cells. Elife 9, e41279.

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Maricque BB*, Chaudhari HG*, Cohen BA. (2019) A massively parallel reporter assay dissects the influence of chromatin structure on cis-regulatory activity. Nature Biotech. 37(1), 90-95.

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Staller MV, Holehouse AS, Swain-Lenz D, Das RK, Pappu RV, Cohen BA. (2018). A High-Throughput Mutational Scan of an Intrinsically Disordered Acidic Transcriptional Activation Domain. Cell Systems 6(4), 444-455.

Cottrell KA, Chaudhari HG, Cohen BA, Djuranovic S. (2018). PTRE-seq reveals mechanism and interactions of RNA binding proteins and miRNAs. Nat. Commun.19;9(1):301.

Chaudhari HG, Cohen BA. (2018). Local sequence features that influence AP-1 cis-regulatory activity.Genome Res., 28(2), 171-181.

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Cohen B.A. (2017). Point of View: How should novelty be valued in science? eLife. 2017;6:e28699

Swain-Lenz D., Nikolisky I., Cheng J., Sudarsanam P., Nayler D., Staller M.V., Cohen B.A. (2017). Causal Genetic Variation Underlying Metabolome Differences. Genetics. 206(4):2199-2206.

Maricque, B.B., Dougherty, J.D. and  Cohen, B.A. (2017). A genome-integrated massively parallel reporter assay reveals DNA sequence determinants of cis-regulatory activity in neural cells. Nucleic Acids Res. 45 (4): e16.

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White, M.A., Kwasnieski, J.C., Myers, C.A., Shen, S.Q., Corbo, J.C. and Cohen, B.A. (2016). A Simple Grammar Defines Activating and Repressing cis-Regulatory Elements in Photoreceptors. Cell Reports. 17(5):1247-1254

Fiore, C. and Cohen, B.A. (2016). Interactions between pluripotency factors specify cis-regulation in embryonic stem cellsGenome Res. 26:1–9

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Sherman M.S., Lorenz, K., Lanier, M.H. and Cohen, B.A. (2015) Cell-to-cell variability in the propensity to transcribe explains correlated fluctuations in gene expression. Cell Systems. 1(25) : 315-325

            Also see Preview by  Quincey A. Justman  : An Explicit Source for Extrinsic Noise.

White M.A. (2015) Understanding how cis-regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequencesGenomics. 106(3):165-70

Savic D., Roberts B.S., Carleton J.B., Partridge E.C., White M.A., Cohen B.A., Cooper G.M., Gertz J., Myers R.M. (2015) Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites.Genome Res. 25(12):1791-800

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Lorenz, K. and Cohen, B.A. (2014) Causal variation in yeast sporulation tends to reside in a pathway bottleneckPLoS Genet. 10(9): e1004634

*Kwasnieski, J.C., *Fiore, C., Chaudhari, H.G., Cohen, B.A.(2014) High-throughput functional testing of ENCODE segmentation predictions. Genome Res. 24: 1595-1602 

Vallania, F.L.M., Sherman, M, Goodwin, Z., Mogno, I., Cohen, B.A., and Mitra, R.D (2014) Origin and consequences of the relationship between protein mean and variance. PLoS ONE. 9(7):e102202

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

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

Zeigler, R.D., Cohen, B.A.(2014)Discrimination between thermodynamic models of cis-regulation using transcription factor occupancy data. Nucleic Acids Res. 42(4):2224-34

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*Mogno, I., *Kwasnieski, J.C., Cohen, B.A.(2013) Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants.Genome Res.23(11):1908-15

White, M.A., Myers, C.A., Corbo, J.C., and Cohen, B.A.(2013) Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks.Proc Natl Acad Sci U S A.110:11952-11957

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*Kwasnieski, J.C., *Mogno, I., Myers, C.A., Corbo, J.C. and Cohen, B.A. (2012) Complex Effects of Nucleotide Variants in a Mammalian cis-Regulatory Element. Proc Natl Acad Sci U S A.109(47):19498-503

Lorenz, K., and Cohen, B.A. (2012) Small- and large-effect quantitative trait locus interactions underlie variation in yeast sporulation efficiency.Genetics. 192(3):1123-32

White, M., Parker,D., Barolo, S. & Cohen, B.A. (2012) A model of spatially restricted transcription in opposing gradients of activators and repressors. Molecular Systems Biology 8 Article number: 614

Sherman MS and Cohen BA (2012) Thermodynamic State Ensemble Models of cis-Regulation. PLoS Comput Biol 8(3): e1002407

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*Parker, D.S., *White, M.A., Ramos, A. I., Cohen, B.A., and Barolo, S. (2011) The cis-regulatory logic of Hedgehog gradient responses: Key roles forGli binding affinity, competition, and cooperativity.  Sci. Signal. 4:ra38

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Mogno, I., Vallania, F., Mitra, R.D., and Cohen, B.A. (2010) TATA is a modular component of synthetic promotersGenome Res. 20:1391-1397.

Gerke J,  Lorenz K,  Ramnarine S,  and Cohen B.A. (2010) Gene–Environment Interactions at Nucleotide Resolution. PLoS Genet 6(9): e1001144.

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Gertz, J., Gerke, P., and Cohen, B. (2009)Epistasis in a quantitative trait captured by a molecular model of transcription factor interactions.Theoretical Population Biology 77 (2010), pp. 1-5.

White, M.A., Riles, L., and Cohen, B.A. (2009) A systematic screen for transcriptional regulators of the yeast cell cycle. Genetics, 181 435-446.

Gertz, J. and Cohen, B.A (2009) Environment-Specific Combinatorial cis-Regulation in Synthetic Promoters. Mol. Sys. Biol., 5 244.

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

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

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Chen C.T.L, Gottlieb D.I, and Cohen B.A. (2008) Ultraconserved Elements in the Olig2 Promoter. PLoS ONE 3(12): e3946.

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Witten, J.T., Chen, C.T.L., and Cohen, B.A. (2007) Complex genetic changes in strains of Saccharomyces cerevisiae derived by selection in the laboratoryGenetics 177: 449-456.

Zeigler, R.D., Gertz, J., and Cohen, B.A. (2007) A cis-regulatory logic simulatorBMC Bioinformatics 8:272.

Chen, C.T.L., Wang, J.C., and Cohen, B.A. (2007) The strength of selection on ultraconserved elements in the human genome. Am J Hum Genet.80:692-704.

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Gerke, J.P., Chen, C.T.L., Cohen, B.A. (2006) Natural Isolates of Saccharomyces cerevisiae Display Complex Genetic Variation In Sporulation Efficiency. Genetics 174:985-997.

Gertz, J., Fay, J.A., Cohen, B.A. (2006) Phylogeny Based Discovery of Regulatory ElementsBMC Bioinformatics 7:266.

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2005 and before

Gertz, J., Riles, L., Turnbaugh, P., Ho, S., Cohen, B.A. (2005) Discovery, Validation, and Genetic Dissection of Transcription Factor Binding Sites By Comparative and Functional GenomicsGenome Res. 15:1145-1152.

Cliften, P., Sudarsanam, P., Desikan, A., Fulton, L., Fulton, B., Majors, J., Waterston, R., Cohen, B.A. and Johnston, M. (2003) Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting. Science 301:71-76.

Cohen, B.A., Pilpel, Y., Mitra, R.D., and Church, G.M. (2002) Discrimination Between Paralogs Using Microarray Analysis: Application to the Yap1p and Yap2p Transcriptional NetworksMol. Biol. Cell 13:1608-1614.

*Cohen, B.A., *Mitra, R.D., Hughes, J., and Church, G.M. (2000) A Computational Analysis of Whole-Genome Expression Data Reveals Chromosomal Domains of Gene ExpressionNat.Genet. 26:183-186. Colas, P.,

Cohen, B.A., Ferrigno, P.K., Silver, P.A., and Brent, R. (2000) Targeted Modification and Transportation of Cellular ProteinsProc. Natl. Acad. Sci. USA 97:13720-13725.

Cohen, B.A., Colas, P., and Brent, R. (1998) An Artificial Cell-Cycle Inhibitor Isolated From a Combinatorial Library. Proc. Natl. Acad. Sci. USA95: 14272-14277.

*Colas, P., *Cohen, B.A., Jessen, T., Grishina, I., McCoy, J., and Brent, R. (1996) Genetic Selection of Peptide Aptamers That Recognize and Inhibit Cyclin-dependent kinase 2. Nature 380: 548-550.

Goodwin, S.B., Cohen, B. A., and Fry, W.E. (1994) Panglobal Distribution of a Single Clonal Lineage of the Irish Potato Famine Fungus. Proc. Natl. Acad. Sci. USA 91:11591-11595.

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