Research Articles

• Amir EA, Davis KL, Tadmor MD, Simonds EF, Levine JH, Bendall SC, Shenfeld DK, Krishnaswamy S, Nolan GP, Pe'er D viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Nat Biotechnol. 2013 May 19
  paper software

• Kreimer A, Litvin O, Hao K, Molony C, Pe'er D, Pe'er I. Inference of modules associated to eQTLs. Nucleic Acids Res. 2012 Mar 24
  [PDF]

• Wolpaw AJ, Shimada K, Skouta R, Welsch ME, Akavia UD, Pe'er D, Shaik F, Bulinski JC, Stockwell BR. Modulatory profiling identifies mechanisms of small molecule-induced cell death. Proc Natl Acad Sci U S A. 2011 Sep 27
  [PDF]

• Bendall SC, Simonds EF, Qiu P, Amir el-AD, Krutzik PO, Finck R, Bruggner RV, Melamed R, Trejo A, Ornatsky OI, Balderas RS, Plevritis SK, Sachs K, Pe'er D, Tanner SD, Nolan GP. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science. 2011 May 6
  [PDF]

• Pe'er D., Hacohen N., Principles and Strategies for Developing Network Models in Cancer. Cell. 2011 Mar 18
  [PDF]

• Akavia U.D., Litvin O., Kim J., Sanchez-Garcia F., Kotliar D., Causton H.C., Pochanard P., Mozes E., Garraway L.A., Pe'er D., An integrated approach to uncover drivers of cancer. Cell. 2010 Dec 10
  [PDF] [Software]

• Sanchez-Garcia F., Akavia U.D., Mozes E., Pe'er D., JISTIC: identification of significant targets in cancer BMC Bioinformatics. 2010 Apr 14
  [PDF] [Software]

• Patwardhan R.P., Lee C., Litvin O., Young D.L., Pe'er D., Shendure J., High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis Nat Biotechnol. 2009 Dec 27
  [PDF]

• Chen BJ., Causton H.C., Mancenido D., Goddard N.L., Perlstein E.O., Pe'er D., Harnessing gene expression to identify the genetic basis of drug resistance Mol Syst Biol. 2009 Oct 13
  [PDF] [Supplementary Material]

• Litvin O., Causton H., Chen BJ., Pe'er D., Modularity and interactions in the genetics of gene expression Proc Natl Acad Sci. 2009 Feb 17
  [PDF] [Supplementary Material]

• Lee S., Dudley A., Drubin D., Silver P., Krogan N., Pe'er D. and Koller D., Learning a Prior on Regulatory Potential from eQTL Data, PLoS Genet 5 (1), e1000358, 2009.
  [PDF]

• Sachs K., Itani S., Carlisle J., Nolan G., Pe'er D. and Lauffenburger D., Learning Signaling Network Structures with Sparsely Distributed Data, Journal of Computational Biology, 2009.
  [PDF]

• 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.
  [PDF]

• 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.
  [PDF]

• 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]