Cohen Lab


* These authors contributed equally to this work.


Shepherdson JL, Granas DM, Li J, Shariff Z, Plassmeyer SP, Holehouse AS, White MA, Cohen BA Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain. bioRχiv (2024) [doi: 10.1101/2024.03.21.585809]

Shepherdson JL*, Friedman RZ*, Zheng Y, Sun C, Oh IY, Granas DM, Cohen BA, Chen S, White MA Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors. Genome Research (2024) [doi: 10.1101/gr.278133.123]

Loell KJ, Friedman RZ, Myers CA, Corbo JC, Cohen BA, White MA Transcription factor interactions explain the context-dependent activity of CRX binding sites. PLOS Computational Biology (2024) [doi: 10.1371/journal.pcbi.1011802]


Friedman RZ, Ramu A, Lichtarge S, Myers CA, Granas DM, Gause M, Corbo JC, Cohen BA, White MA Active learning of enhancer and silencer regulatory grammar in photoreceptors. bioRχiv (2023) [doi: 10.1101/2023.08.21.554146]

Ramu A and Cohen BA Transcription factor fluctuations underlie cell-to-cell variability in a signaling pathway response. Genetics (2023) [doi: 10.1093/genetics/iyad094]

Rockweiler NB, Ramu A, Nagirnaja L, Wong WH, Noordam MJ, Drubin CW, Huang N, Miller B, Todres EZ, Vigh-Conrad KA, Zito A, Small KS, Ardlie KG, Cohen BA, Conrad DF The origins and functional effects of postzygotic mutations throughout the human life span. Science (2023) [doi: 10.1126/science.abn7113]

Zhao S, Hong CKY, Myers CA, Granas DM, White MA, Corbo JC, Cohen BA A single-cell massively parallel reporter assay detects cell-type-specific gene regulation. Nature Genetics (2023) [doi: 10.1038/s41588-022-01278-7]


Hong CKY, Erickson AA, Li J, Federico AJ, and Cohen BA Massively parallel characterization of insulator activity across the genome. bioRχiv (2022) [doi: 10.1101/2022.11.29.518444]

Hansen JL and Cohen BA A quantitative metric of pioneer activity reveals that HNF4A has stronger in vivo pioneer activity than FOXA1. Genome Biology (2022) [doi: 10.1186/s13059-022-02792-x]

Hong CKY*, Ramu A*, Zhao S*, Cohen BA Effect of genomic and cellular environments on gene expression noise. bioRχiv (2022) [doi: 10.1101/2022.08.31.506082]

Loell K, Wu Y, Staller MV, Cohen BA Activation domains can decouple the mean and noise of gene expression. Cell Reports (2022) [doi: 10.1016/j.celrep.2022.111118]

Staller MV, Ramirez E, Kotha SR, Holehouse AS, Pappu RV, Cohen BA Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains. Cell Systems (2022) [doi: 10.1016/j.cels.2022.01.002]

Hansen JL, Loell KJ, Cohen BA A test of the pioneer factor hypothesis using ectopic liver gene activation. eLife (2022) [doi: 10.7554/eLife.73358]

Hong CKY, Cohen BA Genomic environments scale the activities of diverse core promoters. Genome Research (2022) [doi: 10.1101/gr.276025.121]


Zhao S, Pincus Z, Cohen BA Modular effects of gene promoters and chromatin environments on noise in gene expression. bioRχiv (2021) [doi: 10.1101/2021.04.29.441875]

Friedman RZ, Granas DM, Myers CA, Corbo JC, Cohen BA, White MA Information content differentiates enhancers from silencers in mouse photoreceptors. eLife (2021) [doi: 10.7554/eLife.67403]

Rockwell NC, Yang W, Warrington NM, Staller MV, Griffith M, Griffith OL, Gurnett CA, Cohen BA, Baldridge D, Rubin JB Sex- and Mutation-Specific p53 Gain-of-Function Activity in Gliomagenesis. Cancer Research Communications (2021) [doi: 10.1158/2767-9764.CRC-21-0026]


King DM, Hong CKY, Shepherdson JL, Granas DM, Maricque BB, Cohen BA Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in mouse embryonic stem cells. eLife (2020) [doi: 10.7554/eLife.41279]


Maricque BB*, Chaudhari HG*, Cohen BA A massively parallel reporter assay dissects the influence of chromatin structure on cis-regulatory activity. Nature Biotechnology (2019) [doi: 10.1038/nbt.4285]


Cottrell KA, Chaudhari HG, Cohen BA, Djuranovic S PTRE-seq reveals mechanism and interactions of RNA binding proteins and miRNAs. Nature Communications (2018) [doi: 10.1038/s41467-017-02745-0]

Chaudhari HG, Cohen BA Local sequence features that influence AP-1 cis-regulatory activity. Genome Research (2018) [doi: 10.1101/gr.226530.117]

Staller MV, Holehouse AS, Swain-Lenz D, Das RK, Pappu RV, Cohen BA A High-Throughput Mutational Scan of an Intrinsically Disordered Acidic Transcriptional Activation Domain. Cell Systems (2018) [doi: 10.1016/j.cels.2018.01.015]


Cohen BA Point of View: How should novelty be valued in science?. eLife (2017) [doi: 10.7554/eLife.28699]

Swain-Lenz D, Nikolskiy I, Cheng JY, Sudarsanam P, Nayler D, Staller MV, Cohen BA Causal Genetic Variation Underlying Metabolome Differences. Genetics (2017) [doi: 10.1534/genetics.117.203752]

Maricque BB, Dougherty JD, Cohen BA A genome-integrated massively parallel reporter assay reveals DNA sequence determinants of cis-regulatory activity in neural cells. Nucleic Acids Research (2017) [doi: 10.1093/nar/gkw942]


White MA, Kwasnieski JC, Myers CA, Shen SQ, Corbo JC, Cohen BA A Simple Grammar Defines Activating and Repressing cis-Regulatory Elements in Photoreceptors. Cell Reports (2016) [doi: 10.1016/j.celrep.2016.09.066]

Fiore C, Cohen BA Interactions between pluripotency factors specify cis-regulation in embryonic stem cells. Genome Research (2016) [doi: 10.1101/gr.200733.115]


Savic D, Roberts BS, Carleton JB, Partridge EC, White MA, Cohen BA, Cooper GM, Gertz J, Myers RM Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/enhancer-binding protein beta binding sites. Genome Research (2015) [doi: 10.1101/gr.191593.115]

White MA Understanding how cis-regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequences. Genomics (2015) [doi: 10.1016/j.ygeno.2015.06.003]

Sherman MS, Lorenz K, Lanier MH, Cohen BA Cell-to-Cell Variability in the Propensity to Transcribe Explains Correlated Fluctuations in Gene Expression. Cell Systems (2015) [doi: 10.1016/j.cels.2015.10.011]


Sudarsanam P, Cohen BA Single Nucleotide Variants in Transcription Factors Associate More Tightly with Phenotype than with Gene Expression. PLOS Genetics (2014) [doi: 10.1371/journal.pgen.1004325]

Vallania FLM, Sherman M, Goodwin Z, Mogno I, Cohen BA, Mitra RD Origin and Consequences of the Relationship between Protein Mean and Variance. PLOS One (2014) [doi: 10.1371/journal.pone.0102202]

Zeigler RD, Cohen BA Discrimination between thermodynamic models of cis-regulation using transcription factor occupancy data. Nucleic Acids Research (2014) [doi: 10.1093/nar/gkt1230]

Sherman MS, Cohen BA A Computational Framework for Analyzing Stochasticity in Gene Expression. PLOS Computational Biology (2014) [doi: 10.1371/journal.pcbi.1003596]

Kwasnieski JC*, Fiore C*, Chaudhari HG, Cohen BA High-throughput functional testing of ENCODE segmentation predictions. Genome Research (2014) [doi: 10.1101/gr.173518.114]

Lorenz K, Cohen BA Causal Variation in Yeast Sporulation Tends to Reside in a Pathway Bottleneck. PLOS Genetics (2014) [doi: 10.1371/journal.pgen.1004634]


White MA, Myers CA, Corbo JC, Cohen BA Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks. PNAS (2013) [doi: 10.1073/pnas.1307449110]

Mogno I*, Kwasnieski JC*, Cohen BA Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants. Genome Research (2013) [doi: 10.1101/gr.157891.113]


Sherman MS, Cohen BA Thermodynamic State Ensemble Models of cis-Regulation. PLOS Computational Biology (2012) [doi: 10.1371/journal.pcbi.1002407]

White MA, Parker DS, Barolo S, Cohen BA A model of spatially restricted transcription in opposing gradients of activators and repressors. Molecular Systems Biology (2012) [doi: 10.1038/msb.2012.48]

Lorenz K, Cohen BA Small- and Large-Effect Quantitative Trait Locus Interactions Underlie Variation in Yeast Sporulation Efficiency. Genetics (2012) [doi: 10.1534/genetics.112.143107]

Kwasnieski JC*, Mogno I*, Myers CA, Corbo JC, Cohen BA Complex effects of nucleotide variants in a mammalian cis-regulatory element. PNAS (2012) [doi: 10.1073/pnas.1210678109]


Parker DS*, White MA*, Ramos AI, Cohen BA, Barolo S The cis-Regulatory Logic of Hedgehog Gradient Responses: Key Roles for Gli Binding Affinity, Competition, and Cooperativity. Science Signaling (2011) [doi: 10.1126/scisignal.2002077]


Mogno I, Vallania F, Mitra RD, Cohen BA TATA is a modular component of synthetic promoters. Genome Research (2010) [doi: 10.1101/gr.106732.110]

Gertz J, Gerke JP, Cohen BA Epistasis in a quantitative trait captured by a molecular model of transcription factor interactions. Theoretical Population Biology (2010) [doi: 10.1016/j.tpb.2009.10.002]

Gerke J, Lorenz K, Ramnarine S, Cohen B Gene-Environment Interactions at Nucleotide Resolution. PLOS Genetics (2010) [doi: 10.1371/journal.pgen.1001144]


Gertz J, Siggia ED, Cohen BA Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature (2009) [doi: 10.1038/nature07521]

White MA, Riles L, Cohen BA A Systematic Screen for Transcriptional Regulators of the Yeast Cell Cycle. Genetics (2009) [doi: 10.1534/genetics.108.098145]

Gerke J, Lorenz K, Cohen B Genetic Interactions Between Transcription Factors Cause Natural Variation in Yeast. Science (2009) [doi: 10.1126/science.1166426]

Gertz J, Cohen BA Environment-specific combinatorial cis-regulation in synthetic promoters. Molecular Systems Biology (2009) [doi: 10.1038/msb2009.1]


Chen CTL, Gottlieb DI, Cohen BA Ultraconserved Elements in the Olig2 Promoter. PLOS One (2008) [doi: 10.1371/journal.pone.0003946]


Chen CTL, Wang JC, Cohen BA The strength of selection on ultraconserved elements in the human genome. American Journal Of Human Genetics (2007) [doi: 10.1086/513149]

Witten JT, Chen CTL, Cohen BA Complex genetic changes in strains of Saccharomyces cerevisiae derived by selection in the laboratory. Genetics (2007) [doi: 10.1534/genetics.107.077859]

Zeigler RD, Gertz J, Cohen BA A cis-regulatory logic simulator. BMC Bioinformatics (2007) [doi: 10.1186/1471-2105-8-272]


Gerke JP, Chen CTL, Cohen BA Natural isolates of Saccharomyces cerevisiae display complex genetic variation in sporulation efficiency. Genetics (2006) [doi: 10.1534/genetics.106.058453]

Gertz J, Fay JC, Cohen BA Phylogeny based discovery of regulatory elements. BMC Bioinformatics (2006) [doi: 10.1186/1471-2105-7-266]

2005 and earlier

Gertz J, Riles L, Turnbaugh P, Ho SW, Cohen BA Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics. Genome Research (2005) [doi: 10.1101/gr.3859605]

Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science (2003) [doi: 10.1126/science.1084337]

Cohen BA, Pilpel Y, Mitra RD, Church GM Discrimination between paralogs using microarray analysis: Application to the Yap1p and Yap2p transcriptional networks. Molecular Biology Of The Cell (2002) [doi: 10.1091/mbc.01-10-0472]

Colas P, Cohen B, Ferrigno PK, Silver PA, Brent R Targeted modification and transportation of cellular proteins. PNAS (2000) [doi: 10.1073/pnas.97.25.13720]

Cohen BA*, Mitra RD*, Hughes JD, Church GM A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nature Genetics (2000) [doi: 10.1038/79896]

Cohen BA, Colas P, Brent R An artificial cell-cycle inhibitor isolated from a combinatorial Library. PNAS (1998) [doi: 10.1073/pnas.95.24.14272]

Colas P*, Cohen B*, Jessen T, Grishina I, McCoy J, Brent R Genetic selection of peptide aptamers that recognize and inhibit cyclin-dependent kinase 2. Nature (1996) [doi: 10.1038/380548a0]

Goodwin SB, Cohen BA, Fry WE Panglobal Distribution of a Single Clonal Lineage of the Irish Potato Famine Fungus. PNAS (1994) [doi: 10.1073/pnas.91.24.11591]