Yoseph Barash, Ph.D.

faculty photo
Assistant Professor of Genetics
Department: Genetics

Contact information
Richards Building D205
3700 Hamilton Walk
Philadelphia, PA 19104
Office: 215-746-8683
Fax: 215-573-3111
B.Sc. (Computer Science and Physics)
Hebrew University, Jerusalem, Israel., 1998.
Ph.D. (Machine learning, computational biology)
School of Computer Science & Engineering Hebrew University, Jerusalem, Israel, 2006.
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Description of Research Expertise

Research Interests:
The lab develops machine learning algorithms that integrate high-throughput data (RNASeq, CLIPSeq , PIPSeq, etc.) to infer RNA biogenesis and function, followed by experimental verifications of inferred mechanisms.

Machine learning, probabilistic graphical models, computational biology, RNA splicing, post-transcriptional regulation, genomics, high-throughput sequencing analysis.

Selected Publications

Xiong Hui Y, Alipanahi Babak, Lee Leo J, Bretschneider Hannes, Merico Daniele, Yuen Ryan K C, Hua Yimin, Gueroussov Serge, Najafabadi Hamed S, Hughes Timothy R, Morris Quaid, Barash Yoseph, Krainer Adrian R, Jojic Nebojsa, Scherer Stephen W, Blencowe Benjamin J, Frey Brendan J: The human splicing code reveals new insights into the genetic determinants of disease. Science (New York, N.Y.) 347(6218): 1254806, Jan 2015.

Gazzara Matthew R, Vaquero-Garcia Jorge, Lynch Kristen W, Barash Yoseph: In silico to in vivo splicing analysis using splicing code models. Methods (San Diego, Calif.) 67(1): 3-12, May 2014.

Yoseph Barash, Jorge Vaquero-Garcia, Juan González-Vallinas, Hui Yuan Xiong, Weijun Gao, Leo J Lee and Brendan J Frey: AVISPA: a web tool for the prediction and analysis of alternative splicing. Genome Biology 14(10), 2013.

Xiong, Hui Yuan, Barash, Yoseph, Frey, Brendan J.: Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context. Bioinformatics 27(18): 2554-2562, 2011.

Barash, Y., Calarco, J. A., Gao, W., Pan, Q., Wang, X., Shai, O., Blencowe, B. J., Frey, B. J.: Deciphering the splicing code. Nature 465(7294): 53-9, 2010.

Barash, Y., Blencowe, B. J., Frey, B. J.: Model-based detection of alternative splicing signals. Bioinformatics 26(12): i325-33, 2010.

Barash, Y., Wang, X.: An illuminated view of molecular biology. Genome biology 11(8): 307, 2010.

Aznarez, I., Barash, Y., Shai, O., He, D., Zielenski, J., Tsui, L. C., Parkinson, J., Frey, B. J., Rommens, J. M., Blencowe, B. J.: A systematic analysis of intronic sequences downstream of 5'' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation. Genome research 18(8): 1247-58, 2008.

Fagnani, M., Barash, Y., Ip, J. Y., Misquitta, C., Pan, Q., Saltzman, A. L., Shai, O., Lee, L., Rozenhek, A., Mohammad, N., Willaime-Morawek, S., Babak, T., Zhang, W., Hughes, T. R., van der Kooy, D., Frey, B. J., Blencowe, B. J.: Functional coordination of alternative splicing in the mammalian central nervous system. Genome biology 8(6): R108, 2007.

Marion, R. M., Regev, A., Segal, E., Barash, Y., Koller, D., Friedman, N., O'Shea, E. K.: Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression. Proceedings of the National Academy of Sciences of the United States of America 101(40): 14315-22, 2004.

Barash, Y., Elidan, G., Kaplan, T., Friedman, N.: CIS: compound importance sampling method for protein-DNA binding site p-value estimation. Bioinformatics 21(5): 596-600, 2005.

Barash, Y., Friedman, N.: Context-specific Bayesian clustering for gene expression data. Journal of computational biology : a journal of computational molecular cell biology 9(2): 169-91, 2002.

Barash, Y., Elidan, G., Kaplan, T., Friedman, N.: "Modeling Dependencies in Protein-DNA Binding Sites" Proceedings of the Seventh Annual International Conference on Computational Molecular Biology (RECOMB) 2003.

Segal, E., Barash, Y., Simon, I., Friedman, N, Koller, D.: "From Promoter Sequence to Expression: A Probabilistic Framework" Proceedings of the 6th International Conference on Computational Molecular Biology (RECOMB) 2002.

Barash, Yoseph, Bejerano, Gill, Friedman, Nir: A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites Algorithms in Bioinformatics. Springer Berlin / Heidelberg, 2149: 278-293, 2001.

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Last updated: 09/06/2015
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