1. BulletBayesian prediction of tissue-regulated splicing using RNA sequence and cellular context
    Hui Yuan Xiong* , Yoseph Barash* and Brendan Frey
    Bininformatics, 2011, in press

  2. BulletPredicting Tissue-Dependent Alternative Splicing Using Bayesian Neural Networks
    Hui Yuan Xiong , Yoseph Barash* and Brendan Frey*
    MLCB, 2010

  3. BulletAn illuminated view of molecular biology
    Yoseph Barash*, Xinchen Wang
    Genome Biology , 11:307, August 2010

  4. Bullet Model-Based Detection of Alternative Splicing Signals
    Yoseph Barash*, Benjamin J. Blencowe & Brendan J. Frey*
    Bioinofrmatics, Vol. 26 p. i325-333, 2010
    Also, presented at the 18th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2010

  5. BulletDeciphering the splicing code
    Yoseph Barash*, John A. Calarco*, Weijun Gao, Qun Pan, Xinchen Wang, Ofer Shai, Benjamin J. Blencowe, and Brendan J. Frey
    Nature, Vol 465|6, May 2010

  6. BulletA 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
    I Aznarez*, Y Barash*, O Shai, D He, J Zielenski, LC Tsui, J Parkinson, B Frey, JM Rommens, B Blencowe
    Genome Res. Aug;18(8):1247-58, 2008

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

  8. BulletSfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression
    with R.M. Marion, A. Regev, E. Segal, D. Koller, N. Friedman and E.K. O'Shea.
    Proc. National Academy of Sciences USA, 101:14315-22, 2004.

  9. BulletCIS: Compound Importance Sampling Method for Protein-DNA Binding Site p-value Estimation
    Yoseph Barash, Gal Elidan, Tommy Kaplan, Nir Friedman.
    *     Bioinofrmatics,2004 Apr 12;20(6):839-46.
    *     12th International Conference on Intelligent Systems for Molecular Biology (ISMB 04)
          (shorter version)

  10. BulletComparative Analysis of Algorithms for Signal Quantitation from Oligonucleotide Microarrays
    Y. Barash, E. Dehan, M.Krupsky, W. Franklin, M. Geraci,N. Friedman and N. Kaminski.
    Bioinofrmaitcs,2004 Apr 12;20(6):839-46.

  11. BulletModeling Dependencies in Protein-DNA Binding Sites
    Yoseph Barash     Gal Elidan, Nir Friedman and Tommy Kaplan.
    Proc. Seventh Annual Inter. Conf. on Computational Molecular Biology (RECOMB), 2003.
    PostScript, PDF, Web Supplement.  

  12. BulletContext-Specific Bayesian Clustering for Gene Expression Data
    Yoseph Barash and     Nir Friedman.
    Journal of Computational Biology, 9:169-191, 2002. PostScript, PDF.

  13. BulletFrom Promoter Sequence to Expression: A Probabilistic Framework
    E. Segal, Yoseph Barash, I. Simon,     Nir Friedman and D. Koller.
    Proc. Sixth Annual Inter. Conf. on Computational Molecular Biology (RECOMB), 2002.
    PostScript, PDF.  

  14. BulletA simple hyper-geometric approach for discovering putative transcription factor binding sites
    Yoseph Barash,     G. Bejerano and Nir Friedman.
    Algorithms in Bioinformatics: Proc. First International Workshop, 2001. PostScript, PDF.

  15. BulletContext-Specific Bayesian Clustering for Gene Expression Data
    Yoseph Barash and     Nir Friedman.
    Proc. Fifth Annual Inter. Conf. on Computational Molecular Biology (RECOMB), 2001.
    PostScript, PDF.