Graduate Group in Genomics and Computational Biology

Yoseph Barash, Ph.D.

faculty photo
Assistant Professor of Genetics
Department: Genetics

Contact information
1409 Blockley Hall
423 Guardian Drive
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

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.

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.

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

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

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.

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., 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: 04/15/2015
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