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Barak A. Cohen - Publications

Affiliations: 
Biology & Biomedical Sciences (Computational Biology) Washington University, Saint Louis, St. Louis, MO 
Area:
Bioinformatics, Molecular Biology
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53 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Shepherdson JL, Friedman RZ, Zheng Y, Sun C, Oh IY, Granas DM, Cohen BA, Chen S, White MA. Pathogenic variants in CRX have distinct -regulatory effects on enhancers and silencers in photoreceptors. Genome Research. PMID 38355306 DOI: 10.1101/gr.278133.123  0.317
2024 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. 20: e1011802. PMID 38227575 DOI: 10.1371/journal.pcbi.1011802  0.379
2022 Du AY, Zhuo X, Sundaram V, Jensen NO, Chaudhari HG, Saccone NL, Cohen BA, Wang T. Functional characterization of enhancer activity during a long terminal repeat's evolution. Genome Research. PMID 36192170 DOI: 10.1101/gr.276863.122  0.338
2022 Hansen JL, Loell KJ, Cohen BA. The pioneer factor hypothesis is not necessary to explain ectopic liver gene activation. Elife. 11. PMID 34984978 DOI: 10.7554/eLife.73358  0.372
2020 King DM, Hong CKY, Shepherdson JL, Granas DM, Maricque BB, Cohen B. Synthetic and genomic regulatory elements reveal aspects of -regulatory grammar in Mouse Embryonic Stem Cells. Elife. 9. PMID 32043966 DOI: 10.7554/Elife.41279  0.493
2019 King DM, Hong CKY, Shepherdson JL, Granas DM, Maricque BB, Cohen BA. Author response: Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in mouse embryonic stem cells Elife. DOI: 10.7554/Elife.41279.Sa2  0.361
2019 Mulvey B, Cohen B, Dougherty J. 15 TOWARD AN IN VIVO METHOD FOR CELL-TYPE SPECIFIC, MULTIPLEX ASSAYS OF NEUROPSYCHIATRIC-TRAIT ASSOCIATED TRANSCRIPTIONAL ELEMENTS European Neuropsychopharmacology. 29: S66-S67. DOI: 10.1016/J.Euroneuro.2019.07.156  0.367
2018 Maricque BB, Chaudhari HG, Cohen BA. A massively parallel reporter assay dissects the influence of chromatin structure on cis-regulatory activity. Nature Biotechnology. PMID 30451991 DOI: 10.1038/Nbt.4285  0.465
2018 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. PMID 29525204 DOI: 10.1016/J.Cels.2018.01.015  0.336
2018 Cottrell KA, Chaudhari HG, Cohen BA, Djuranovic S. PTRE-seq reveals mechanism and interactions of RNA binding proteins and miRNAs. Nature Communications. 9: 301. PMID 29352242 DOI: 10.1038/S41467-017-02745-0  0.357
2018 Chaudhari HG, Cohen BA. Local sequence features that influence AP-1 cis-regulatory activity. Genome Research. PMID 29305491 DOI: 10.1101/Gr.226530.117  0.451
2017 Swain-Lenz D, Nikolisky I, Cheng J, Sudarsanam P, Nayler D, Staller MV, Cohen BA. Causal Genetic Variation Underlying Metabolome Differences. Genetics. PMID 28652377 DOI: 10.1534/Genetics.117.203752  0.366
2017 Sundaram V, Choudhary MN, Pehrsson E, Xing X, Fiore C, Pandey M, Maricque B, Udawatta M, Ngo D, Chen Y, Paguntalan A, Ray T, Hughes A, Cohen BA, Wang T. Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. Nature Communications. 8: 14550. PMID 28348391 DOI: 10.1038/Ncomms14550  0.515
2017 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. 45: e16. PMID 28204611 DOI: 10.1093/Nar/Gkw942  0.443
2016 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. PMID 27924017 DOI: 10.1093/nar/gkw942  0.336
2016 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. 17: 1247-1254. PMID 27783940 DOI: 10.1016/J.Celrep.2016.09.066  0.795
2016 Fiore C, Cohen BA. Interactions between pluripotency factors specify cis-regulation in embryonic stem cells. Genome Research. PMID 27197208 DOI: 10.1101/Gr.200733.115  0.497
2015 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. 1: 315-325. PMID 26623441 DOI: 10.1016/J.Cels.2015.10.011  0.396
2015 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. PMID 26486725 DOI: 10.1101/Gr.191593.115  0.715
2014 Lorenz K, Cohen BA. Causal variation in yeast sporulation tends to reside in a pathway bottleneck. Plos Genetics. 10: e1004634. PMID 25211152 DOI: 10.1371/Journal.Pgen.1004634  0.361
2014 Vallania FL, Sherman M, Goodwin Z, Mogno I, Cohen BA, Mitra RD. Origin and consequences of the relationship between protein mean and variance. Plos One. 9: e102202. PMID 25062021 DOI: 10.1371/Journal.Pone.0102202  0.334
2014 Kwasnieski JC, Fiore C, Chaudhari HG, Cohen BA. High-throughput functional testing of ENCODE segmentation predictions. Genome Research. 24: 1595-602. PMID 25035418 DOI: 10.1101/Gr.173518.114  0.777
2014 Sherman MS, Cohen BA. A computational framework for analyzing stochasticity in gene expression. Plos Computational Biology. 10: e1003596. PMID 24811315 DOI: 10.1371/Journal.Pcbi.1003596  0.341
2014 Sudarsanam P, Cohen BA. Single nucleotide variants in transcription factors associate more tightly with phenotype than with gene expression. Plos Genetics. 10: e1004325. PMID 24784239 DOI: 10.1371/Journal.Pgen.1004325  0.464
2014 Zeigler RD, Cohen BA. Discrimination between thermodynamic models of cis-regulation using transcription factor occupancy data. Nucleic Acids Research. 42: 2224-34. PMID 24288374 DOI: 10.1093/Nar/Gkt1230  0.785
2013 Mogno I, Kwasnieski JC, Cohen BA. Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants. Genome Research. 23: 1908-15. PMID 23921661 DOI: 10.1101/Gr.157891.113  0.809
2013 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. Proceedings of the National Academy of Sciences of the United States of America. 110: 11952-7. PMID 23818646 DOI: 10.1073/Pnas.1307449110  0.414
2012 Kwasnieski JC, Mogno I, Myers CA, Corbo JC, Cohen BA. Complex effects of nucleotide variants in a mammalian cis-regulatory element. Proceedings of the National Academy of Sciences of the United States of America. 109: 19498-503. PMID 23129659 DOI: 10.1073/Pnas.1210678109  0.805
2012 White MA, Parker DS, Barolo S, Cohen BA. A model of spatially restricted transcription in opposing gradients of activators and repressors. Molecular Systems Biology. 8: 614. PMID 23010997 DOI: 10.1038/Msb.2012.48  0.492
2012 Lorenz K, Cohen BA. Small- and large-effect quantitative trait locus interactions underlie variation in yeast sporulation efficiency. Genetics. 192: 1123-32. PMID 22942125 DOI: 10.1534/Genetics.112.143107  0.342
2012 Sherman MS, Cohen BA. Thermodynamic state ensemble models of cis-regulation. Plos Computational Biology. 8: e1002407. PMID 22479169 DOI: 10.1371/Journal.Pcbi.1002407  0.444
2011 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. 4: ra38. PMID 21653228 DOI: 10.1126/Scisignal.2002077  0.483
2010 Gerke J, Lorenz K, Ramnarine S, Cohen B. Gene-environment interactions at nucleotide resolution Plos Genetics. 6. PMID 20941394 DOI: 10.1371/Journal.Pgen.1001144  0.771
2010 Mogno I, Vallania F, Mitra RD, Cohen BA. TATA is a modular component of synthetic promoters. Genome Research. 20: 1391-7. PMID 20627890 DOI: 10.1101/Gr.106732.110  0.529
2010 Gertz J, Gerke JP, Cohen BA. Epistasis in a quantitative trait captured by a molecular model of transcription factor interactions. Theoretical Population Biology. 77: 1-5. PMID 19818800 DOI: 10.1016/J.Tpb.2009.10.002  0.773
2009 Gertz J, Cohen BA. Environment-specific combinatorial cis-regulation in synthetic promoters. Molecular Systems Biology. 5: 244. PMID 19225457 DOI: 10.1038/Msb.2009.1  0.736
2009 Gerke J, Lorenz K, Cohen B. Genetic interactions between transcription factors cause natural variation in yeast Science. 323: 498-501. PMID 19164747 DOI: 10.1126/Science.1166426  0.787
2009 White MA, Riles L, Cohen BA. A systematic screen for transcriptional regulators of the yeast cell cycle. Genetics. 181: 435-46. PMID 19033152 DOI: 10.1534/Genetics.108.098145  0.371
2009 Gertz J, Siggia ED, Cohen BA. Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature. 457: 215-8. PMID 19029883 DOI: 10.1038/Nature07521  0.747
2008 Chen CT, Gottlieb DI, Cohen BA. Ultraconserved elements in the Olig2 promoter. Plos One. 3: e3946. PMID 19079603 DOI: 10.1371/Journal.Pone.0003946  0.666
2007 Zeigler RD, Gertz J, Cohen BA. A cis-regulatory logic simulator. Bmc Bioinformatics. 8: 272. PMID 17662143 DOI: 10.1186/1471-2105-8-272  0.758
2007 Witten JT, Chen CT, Cohen BA. Complex genetic changes in strains of Saccharomyces cerevisiae derived by selection in the laboratory. Genetics. 177: 449-56. PMID 17660538 DOI: 10.1534/Genetics.107.077859  0.724
2007 Chen CT, Wang JC, Cohen BA. The strength of selection on ultraconserved elements in the human genome. American Journal of Human Genetics. 80: 692-704. PMID 17357075 DOI: 10.1086/513149  0.614
2006 Gerke JP, Chen CT, Cohen BA. Natural isolates of Saccharomyces cerevisiae display complex genetic variation in sporulation efficiency. Genetics. 174: 985-97. PMID 16951083 DOI: 10.1534/Genetics.106.058453  0.748
2006 Gertz J, Fay JC, Cohen BA. Phylogeny based discovery of regulatory elements. Bmc Bioinformatics. 7: 266. PMID 16716228 DOI: 10.1186/1471-2105-7-266  0.716
2005 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. 15: 1145-52. PMID 16077013 DOI: 10.1101/Gr.3859605  0.728
2003 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. 301: 71-76. PMID 12775844 DOI: 10.1126/Science.1084337  0.384
2002 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. 13: 1608-14. PMID 12006656 DOI: 10.1091/Mbc.01-10-0472  0.447
2000 Colas P, Cohen B, Ferrigno PK, Silver PA, Brent R. Targeted modification and transportation of cellular proteins Proceedings of the National Academy of Sciences of the United States of America. 97: 13720-13725. PMID 11106396 DOI: 10.1073/Pnas.97.25.13720  0.308
2000 Cohen BA, Mitra RD, Hughes JD, Church GM. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nature Genetics. 26: 183-6. PMID 11017073 DOI: 10.1038/79896  0.368
1998 Cohen BA, Colas P, Brent R. An artificial cell-cycle inhibitor isolated from a combinatorial library Proceedings of the National Academy of Sciences of the United States of America. 95: 14272-14277. PMID 9826690 DOI: 10.1073/Pnas.95.24.14272  0.355
1996 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. 380: 548-550. PMID 8606778 DOI: 10.1038/380548A0  0.331
1994 Goodwin SB, Cohen BA, Fry WE. Panglobal distribution of a single clonal lineage of the Irish potato famine fungus Proceedings of the National Academy of Sciences of the United States of America. 91: 11591-11595. PMID 7972108 DOI: 10.1073/Pnas.91.24.11591  0.327
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