Research Articles

  • Lee S*., Pe'er D*. Dudley A., Church G., and Koller, D. (*equal contribution), Identifying Regulatory Mechanisms and their Individual Variation Reveals Key Role of Chromatin Modification, Proc Natl Acad Sci.2006 Sep 19;103(38):14062-7.
    [PDF] [PNAS] [Supplementary Material]

  • Pe'er D, Regev, A. and Tanay, A. Minreg: A Scalable Algorithm for Learning Parsimonious Regulatory networks in Yeast and Mammals, Journal of Machine Learning Research, 7:167--189, Feb 2006.

  • Pe'er D. Bayesian network analysis of signaling networks: a primer, Science STKE, 281:pl4, April 2005
    [PDF] [STKE] [Breakthrough of year]

  • Sachs, K*., Perez, O*., Pe'er D*., Lauffenburger, D., and Nolan, G., (*equal contribution), Causal protein-signaling networks derived from multiparameter single-cell data, Science 308:523-529, April 2005.
    [PDF] [Science] [Supporting Material and Data] [Perspective]

  • Segal, E., Pe'er D., Regev, A. Koller, D. and Friedman N., Learning Module Networks, Journal of Machine Learning , 6:557-588, April 2005.

  • Segal, E*., Shapira, M., Regev, A*., Pe'er, D.*, Botstein, D., Koller, D. and Friedman, N., (*equal contribution), Module networks: identifying regulatory modules and their condition specific regulators from gene expression data, Nature Genetics 34:166-176, June 2003.
    [PDF] [Nature Genetics] [Web Supplement]

  • Pe'er, D., Regev, A. and Tanay, A., Minreg: Inferring an active regulator set, Bioinformatics 18:S258-S267, 2002
    [PDF] [Web Supplement]

  • Pe'er,D. , Regev, A., Elidan, G., and Friedman N., Inferring Subnetworks from Preturbed Expression Profiles Bioinformatics 17:S215-S224, 2001
    [PDF] [Web Supplement]

  • Friedman, N., Linial, M., Nachman, I, and Pe'er D., Using Bayesian networks to analyze expression data, Journal of Computational Biology, 7:601-620, 2000.
    [PDF] [Web Supplement] [Technical Supplement]

From Gene expression to Molecular Pathways
(Ph.D. Disseration)