Yoseph Barash, Ph.D.

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Associate 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

Vaquero-Garcia J., Barrera A., Gazzara, M. González-Vallinas J., Lahens N., Hogenesch J., Lynch K., Barash Y.: A new view of transcriptome complexity and regulation through the lens of local splicing variations. ELife 5: e11752, Feb 2016.

Sotillo E., Barrett D., Black K., Bagashev A., Oldridge D., Wu G., Sussman R., Lanauze C., Gazzara M, Martinez N., Ruella M., Harrington C., Chung E., Perazzelli J., Hofmann T., Maude S., Raman P., Barrera A., Gill S., Lacey S., Melenhorst J., Allman D., Jacoby E., Fry T., Mackall C., Barash Y., Lynch K., Maris J, Grupp S.,Thomas-Tikhonenko A.: Convergence of acquired mutations and alternative splicing of CD19 enables resistance to CART-19 immunotherapy. Cancer Discovery 5(12): 1282-95, December 2015 Notes: Contribution: Dr. Barash lab detected novel splicing variations in patients RNASeq, predicted splice regulator using the lab's algorithms. This led to the main result of identifying SRFS3 expression as promoting CART19 escape and relapse.

Martinez N, Agosto L., Qiu J., Mallory M., Gazarra M., Barash Y., Fu X., Lynch K. : Widespread JNK-dependent alternative splicing induces a positive feedback loop through CELF2-mediated regulation of MKK7 during T-cell activation. Genes & Development 29(19): 2054-66, Oct 2015 Notes: Contribution: Dr. Barash guided the genome wide analysis of JNK signaling and CELF2 coregulation of alternative splicing in T-Cell.

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 347(6218): 1254806, Jan 2015 Notes: Prediction algorithm and analysis pipeline was developed with help from Dr. Barash and his code.

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 Notes: All work was done by Barash lab. Sole corresponding author. Project was initiated as a postdoc and Frey lab member helped with preliminary dataset and algorithm.

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.

Barash, Y., Blencowe, B. J., Frey, B. J.: Model-based detection of alternative splicing signals. Bioinformatics 26(12): i325-33, Jun 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, Sep 2011.

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

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, May 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, Aug 2008 Notes: co-corresponding first author.

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 Notes: co-corresponding first author.

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, Oct 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. J Comput Biol 9(2): 169-91, Apr 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). ACM, Page: 28-37, 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). ACM, Page: 28-37, 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: 01/19/2024
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