Cohen Lab Home Page

Publications

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

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 for Gli binding affinity, competition, and cooperativity. Sci. Signal. 4:ra38

Mogno, I., Vallania, F., Mitra, R.D., and Cohen, B.A. (2010) TATA is a modular component of synthetic promoters. Genome 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.

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.

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

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 laboratory. Genetics 177: 449-456.

Zeigler, R.D., Gertz, J., and Cohen, B.A. (2007) A cis-regulatory logic simulator. BMC 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.

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 Elements. BMC Bioinformatics 7:266.

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 Genomics. Genome 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 Networks. Mol. 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 Expression. Nat.Genet. 26:183-186.

*These authors contributed equally to this work.

Colas, P., Cohen, B.A., Ferrigno, P.K., Silver, P.A., and Brent, R. (2000) Targeted Modification and Transportation of Cellular Proteins. Proc. 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. USA 95: 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.
*These authors contributed equally to this work.

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.

Last updated 1/4/2010 by LLK.