Nir Friedman

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• Peer-Reviewed Journal Publications
• Invited Papers and Book Chapters
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• Peer-Reviewed Conference Proceedings
• Other Publications

Books

• Probabilistic Graphical Models: Principles and Techniques with D. Koller.
  MIT Press, 2009.
  
 

Peer-Reviewed Journal Publications

2017

• A synthetic biology approach to probing nucleosome symmetry with Y. Ichikawa, C.F. Connelly, A. Appleboim, T.C.R. Miller, H. Jacobi, N. A Abshiru, H. Chou, Y. Chen, U. Sharma, Y. Zheng, P. M Thomas, H. V Chen, V. Bajaj, C. W. Muller, N.L. Kelleher, D. NA Bolon, O.J. Rando, and P.D. Kaufman.
  eLife 6, 2017.
  
 

• Temporal profiling of redox-dependent heterogeneity in single cells with M. Radzinski, R. Fassler, O. Yogev, W. Breuer, J. Gutin, T. Ravid, M. Schuldiner, N. Shai, and D. Reichmann.
  bioRxiv:198408, 2017.
  
 

• Deciphering cis-regulatory logic with 100 million synthetic promoters with C. de Boer, R. Sadeh, and A. Regev.
  bioRxiv:224907, 2017.
  
 

2016

• Genome-wide histone modification patterns in Kluyveromyces Lactis reveal evolutionary adaptation of a heterochromatin-associated mark with A. Bean, A. Weiner, A. Hughes, E. Itskovits, and O.J. Rando.
  bioRxiv:039776, 2016.
  
 

• Perturb-seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens with A. Dixit, O. Parnas, B. Li, J. Chen, C.P. Fulco, L. Jerby-Arnon, N.D. Marjanovic, D. Dionne, T. Burks, R. Raychowdhury, B. Adamson, T.M. Norman, E.S. Lander, J.S. Weissman, and A. Regev.
  Cell 167:1853-1866. e17, 2016.
  
 

• Mapping the Landscape of a Eukaryotic Degronome with Y. Geffen, A. Appleboim, R.G. Gardner, R. Sadeh, and T. Ravid.
  Molecular Cell 63:1055-1065, 2016.
  
 

• Nuclear receptors control pro-viral and antiviral metabolic responses to hepatitis C virus infection with G. Levy, N. Habib, M.A. Guzzardi, D. Kitsberg, D. Bomze, E. Ezra, B.E. Uygun, K. Uygun, M. Trippler, J.F. Schlaak, O. Shibolet, E.H. Sklan, M. Cohen, J. Timm, and Y. Nahmias.
  Nature Chemical Biology 12:1037-1045, 2016.
  
 

• Elucidating Combinatorial Chromatin States at Single-Nucleosome Resolution with R. Sadeh, R. Launer-Wachs, H. Wandel, and A. Rahat.
  Molecular Cell 63:1080-1088, 2016.
  
 

2015

• Epigenomics and the structure of the living genome with O.J. Rando.
  Genome research 25:1482-1490, 2015.
  
 

• Condition-specific genetic interaction maps reveal crosstalk between the cAMP/PKA and the HOG MAPK pathways in the activation of the general stress response with J. Gutin, A. Sadeh, A. Rahat, and A. Aharoni.
  Molecular Systems Biology 11:829, 2015.
  
 

• Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C with T.H.S. Hsieh, A. Weiner, B. Lajoie, J. Dekker, and O.J. Rando.
  Cell 162:108-119, 2015.
  
 

• Clk post-transcriptional control denoises circadian transcription both temporally and spatially with I. Lerner, O. Bartok, V. Wolfson, J.S. Menet, U. Weissbein, S. Afik, D. Haimovich, C. Gafni, M. Rosbash, and S. Kadener .
  Nature Communications 6, 2015.
  
 

• Chromatin dynamics and the RNA exosome function in concert to regulate transcriptional homeostasis with M. Rege, V. Subramanian, C. Zhu, T.S. Hsieh, A. Weiner, S. Clauder-Munster, L.M. Steinmetz, O.J. Rando, L.A. Boyer, and C.L. Peterson.
  Cell Reports 13:1610-1622, 2015.
  
 

• High-Resolution Chromatin Dynamics during a Yeast Stress Response with A. Weiner, T.H.S. Hsieh, A. Appleboim, H.V. Chen, A. Rahat, I. Amit, and O.J. Rando.
  Molecular Cell 58:371-386, 2015.
  
 

2014

• Chromatin state dynamics during blood formation with D.Lara-Astiaso, A. Weiner, E. Lorenzo-Vivas, I. Zaretsky, D.A. Jaitin, E. David, H. Keren-Shaul,, A. Mildner, D. Winter, S. Jung, and I. Amit..
  Science 345:943-949, 2014.
  
 

• High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies with M. Rabani, R. Raychowdhury, M. Jovanovic, M. Rooney, D.J. Stumpo, A. Pauli, N. Hacohen, A.F. Schier, P.J. Blackshear, I. Amit, and A. Regev.
  Cell 159:1698-710, 2014.
  
 

• Single-cell RNA-seq reveals dynamic paracrine control of cellular variation with A. Shalek, R. Satija, J. Shuga, J.J. Trombetta, D. Gennert, D. Lu, P. Chen, R.S. Gertner, J.T. Gaublomme, N. Yosef, S. Schwartz, B. Fowler, S. Weaver, J. Wang, X. Wang, R. Ding, R. Raychowdhury, N. Hacohen,, H. Park, A.P. May, and A. Regev.
  Nature 510:363-369, 2014.
  
 

2013

• De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis with B.J. Haas, A. Papanicolaou, M. Yassour, M.G. Grabherr, P.D. Blood, J. Bowden, M.B. Couger, D. Eccles, B. Li, M. Lieber, MD. Macmanes, M. Ott, J. Orvis, N. Pochet, F. Strozzi, N. Weeks, R. Westerman, T. William, C.N. Dewey, R. Henschel, R.D. Leduc, and A. Regev.
  Nature Protocols 8(8):1494-512, 2013.
  
 

2012

• High-resolution view of the yeast meiotic program revealed by ribosome profiling with G.A. Brar, M. Yassour, A. Regev, N.T. Ingolia, and J.S. Weissman.
  Science, 2012.
  
 

• A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals with M. Garber, N. Yosef, A. Goren, R. Raychowdhury, A. Thielke, M. Guttman, J. Robinson, B. Minie, N. Chevrier, Z. Itzhaki, R. Blecher-Gonen, C. Bornstein, D. Amann-Zalcenstein, A. Weiner, D. Friedrich, J. Meldrim, O. Ram, C. Cheng, A. Gnirke, S. Fisher, B. Wong, B.E. Bernstein, C. Nusbaum, N. Hacohen, A. Regev, and I. Amit.
  Molecular Cell 47:810-22, 2012.
  
 

• A functional selection model explains evolutionary robustness despite plasticity in regulatory networks with N. Habib, I. Wapinski, H. Margalit, and A. Regev.
  Molecular Systems Biology 8:619, 2012.
  
 

• Systematic dissection of roles for chromatin regulators in a yeast stress response with A. Weiner, H.V. Chen, C.L. Liu, A. Rahat, A. Klien, L. Soares, M. Gudipati, J. Pfeffner, A. Regev, S. Buratowski, J. A Pleiss, and O.J. Rando.
  PLoS Biology 10:e1001369, 2012.
  
 

2011

• Substantial Histone Reduction Modulates Genomewide Nucleosomal Occupancy and Global Transcriptional Output with B. Celona, A. Weiner, F. Di Felice, F. Mancuso, E. Cesarini, R. Rossi, L. Gregory, D. Baban, G. Rossetti, P. Grianti, M. Pagani, T. Bonaldi, J. Ragoussis, G. Camilloni, M. Bianchi, and A. Agresti.
  PLoS Biology 9:e1001086, 2011.
  
 

• Full-length transcriptome assembly from RNA-Seq data without a reference genome with M.G. Grabherr, B.J. Haas, M. Yassour, J.Z. Levin, D.A. Thompson, I. Amit, X. Adiconis, L. Fan, R. Raychowdhury, Q. Zeng, Z. Chen, E. Mauceli, N. Hacohen, A. Gnirke, N. Rhind, F. di Palma, B.W. Birren, C. Nusbaum, K. Toh-Lindblad, and A. Regev.
  Nature Biotechnology, 2011.
  
 

• Densely interconnected transcriptional circuits control cell states in human hematopoiesis with N. Novershtern, A. Subramanian, L.N. Lawton, R.H. Mak, W.N. Haining, M.E. McConkey, N. Habib, N. Yosef, CY. Chang, T. Shay, G.M. Frampton, A.C. Drake, I. Leskov, B. Nilsson, F. Preffer, D. Dombkowski, J.W. Evans, T. Liefeld, J.S. Smutko, J. Chen, R.A. Young, T.R. Golub, A. Regev, and B.L. Ebert.
  Cell 144(2):296-309, 2011.
  
 

• Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells with M. Rabani, JZ. Levin, L. Fan, X. Adiconis, R. Raychowdhury, M. Garber, A. Gnirke, C. Nusbaum, N. Hacohen, I. Amit, and A. Regev.
  Nature Biotechnology 29:436-42, 2011.
  
 

• Dynamics of Sir3 spreading in budding yeast: secondary recruitment sites and euchromatic localization with M. Radman-Livaja, G. Ruben, A. Weiner, R. Kamakaka, and O.J. Rando.
  EMBO J30:1012-26, 2011.
  
 

• Patterns and mechanisms of ancestral histone protein inheritance in budding yeast with M. Radman-Livaja, K.F. Verzijlbergen, A. Weiner, T. van Welsem, O.J. Rando, and F. van Leeuwen.
  PLoS Biology 9:e1001075, 2011.
  
 

• Comparative functional genomics of the fission yeasts with N. Rhind, Z. Chen, M. Yassour, DA. Thompson, BJ. Haas, N. Habib, I. Wapinski, S. Roy, MF. Lin, DI. Heiman, SK. Young, K. Furuya, Y. Guo, A. Pidoux, HM. Chen, B. Robbertse, JM. Goldberg, K. Aoki, EH. Bayne, AM. Berlin, CA. Desjardins, E. Dobbs, L. Dukaj, L. Fan, MG. Fitzgerald, C. French, S. Gujja, K. Hansen, D. Keifenheim, JZ. Levin, RA. Mosher, CA. Muller, J. Pfiffner, M. Priest, C. Russ, A. Smialowska, P. Swoboda, SM. Sykes, M. Vaughn, S. Vengrova, R. Yoder, Q. Zeng, R. Allshire, D. Baulcombe, BW. Birren, W. Brown, K. Ekwall, M. Kellis, J. Leatherwood, H. Levin, H. Margalit, R. Martienssen, CA. Nieduszynski, JW. Spatafora, JZ. Dalgaard, P. Baumann, H. Niki, A. Regev, and C. Nusbaum.
  Science, 2011.
  
 

• Exploring Transcription Regulation through Cell-to-cell Variability with R. Rinott and A. Jaimovich.
  Proc. Natl. Acad. Sci. USA 108:6329-34, 2011.
  
 

• High Throughput Determination of TGFbeta1/SMAD3 Targets in A549 Lung Epithelial Cells with Y. Zhang, D. Handley, T. Kaplan, H. Yu, A.S. Bais, T. Richards, K.V. Pandit, Q. Zeng, P.V. Benos, O. Eickelberg, and N. Kaminski.
  PLoS One 6:e20319, 2011.
  
 

2010

• Parentally induced transgenerational environmental reporgramming of metabolic gene expression in mammals with B.R. Carone, L. Fauquier, N. Habib, J.M. Shea, C.E. Hart, R. Li, C. Bock, H. Gu, P.D. Zamore, A. Meissner, Z. Weng, H.A. Hofmann, and O.J. Rando.
  Cell 143(7):1084-96, 2010.
  
 

• Mean Field Variational Approximation for Continuous-Time Bayesian Networks with I. Cohn, T. El-Hay, and R. Kupferman.
  J. Machine Learning Research 11:2745-2738, 2010.
  PDF
 

• RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast with T.S. Kim, C.-L. Liu, M. Yassour, J. Holik, S. Buratowski, and O.J. Rando.
  Genome Biology 11(7):R75, 2010.
  
 

• Comprehensive comparative analysis of strand-specific RNA sequencing methods with J. Z. Levin, M. Yassour, X. Adiconis, C. Nusbaum, D. A. Thompson, A. Gnirke, and A. Regev.
  Nature Methods 7(9):709-15, 2010.
  
 

• Replication and Active Demethylation Represent Partially Overlapping Mechanisms for Erasure of H3K4me3 in Budding Yeast with M. Radman-Livaja, C.-L. Liu, S.L. Schreiber, and O.J. Rando.
  PLoS Genetics6:e1000837, 2010.
  
 

• Blood mononuclear cell gene expression signature of postpartum depression with R.H. Segman, T. Goltser-Dubner, I. Weiner, L. Canetti, E. Galili-Weisstub, A. Miliwidsky, V. Pavlov, and D. Hochner-Celnikier.
  Molecular Psychiatry 15:93-100, 2010.
  
 

• High-resolution nucleosome mapping reveals transcription-dependent promoter packaging with A. Weiner, A. Hughes, M. Yassour, and O.J. Rando.
  Genome Research 20:90-100, 2010.
  Web Supplement
 

• Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species with M. Yassour, J. Pfiffner, J. Z. Levin, X. Adiconis, A. Gnirke, C. Nusbaum, D. A. Thompson, and A. Regev.
  Genome Biology 11(8):R87, 2010.
  
 

2009

• Ab initio Construction of a Eukaryotic Transcriptome by Massively Parallel mRNA Sequencing with M. Yassour, T. Kaplan, H. B. Fraser, J. Z. Levin, J. Pfiffner, X. Adiconis, G. Schroth, S. Luo, I. Khrebtukova, A. Gnirke, C. Nusbaum, D. A. Thompson, and A. Regev.
  Proc. National Academy of Sciences USA, 106:3264-9, 2009.
  Web Supplement
 

2008

• Structure and function of a transcriptional network activated by the MAPK Hog1 with A. P. Capaldi, T. Kaplan, Y. Liu, N. Habib, A. Regev, and E. K. O'Shea.
  Nature Genetics, 40:1300-1306, 2008.
  PDF Web Supplement
 

• Mitochondrial processes are impaired in hereditary inclusion body myopathy with I. Eisenberg, N. Novershtern, Z. Itzhaki, M. Becker-Cohen, M. Sadeh, P. H. Willems, W. J. Koopman, and S. Mitrani-Rosenbaum.
  Hum. Mol. Genet., 17(22):3663-74, 2008.
  
 

• A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval with N. Habib, T. Kaplan, and H. Margalit.
  PLoS Comput Biol, 4(2):e1000010, 2008.
  PDF Web Supplement
 

• Physiological and molecular evidence of heat acclimation memory: A lesson from thermal responses and ischemic cross-tolerance in the heart with A. Tetievsky, O. Cohen, L. Eli-Berchoer, G. Gerstenblith, MD. Stern, I. Wapinski, and M. Horowitz.
  Physiological Genomics, 2008.
  
 

• Cell Cycle- and Chaperone-Mediated Regulation of H3K56ac Incorporation in Yeast with T. Kaplan, C.-L. Liu, J. A. Erkmann, J. Holik, M. Grunstein, P. D. Kaufman, and O.J. Rando.
  PLoS Genetics, 4(11):e1000270, 2008.
  PDF
 

2007

• Dynamics of Replication-Independent Histone Turnover in Budding Yeast with M.F. Dion, T. Kaplan, M. Kim, S. Buratowski, and O.J. Rando.
  Science 315(5817):1405-8, 2007.
  
 

• "Ideal parent" structure learning for continuous variable Bayesian networks with G. Elidan and I. Nachman.
  J. Machine Learning Research, 8:1799--1833 , 2007.
  PDF
 

• A Functional and Regulatory Map of Asthma with N. Novershtern, Z. Itzhaki, O. Manor, and N. Kaminski.
  American Journal of Respiratory and Cell Molecular Biology 38(3):324-336 , 2007.
  Web Supplement
 

• Natural history and evolutionary principles of gene duplication in fungi with I. Wapinski, A. Pfeffer, and A. Regev.
  Nature 449:54-61, 2007.
  Web Supplement
 

2006

• Towards an integrated protein-protein interaction network: a relational Markov network approach with A. Jaimovich, G. Elidan, and H. Margalit.
  J. Computational Biology 13:145-164, 2006.
  PDF
 

• Multivariate Information Bottleneck with N. Slonim and N. Tishby.
  Neural Computation 18:1739-89, 2006.
  
 

2005

• Learning hidden variable networks: The information bottleneck approach with G. Elidan.
  J. Machine Learning Research, 6:81--127, 2005.
  PDF
 

• Ab initio prediction of transcription factor targets using structural knowledge with T. Kaplan and H. Margalit.
  PLoS Comput Biol1(1):e1, 2005.
  Web Supplement
 

• Single-nucleosome mapping of histone modifications in S. cerevisiae with C.-L. Liu, T. Kaplan, M. Kim, S. Buratowski, S.L. Schreiber, and O.J. Rando.
  PLoS Biol 3(10):e328, 2005.
  
 

• Learning Module Networks with E. Segal, D. Pe'er, A. Regev, and D. Koller.
  J. Machine Learning Research, 6:557--588 , 2005.
  PDF
 

• Peripheral blood mononuclear cell gene expression profiles identify emergent post-traumatic stress disorder among trauma survivors with R.H. Segman, N. Shefi, T. Goltser-Dubner, N. Kaminski, and A.Y. Shalev.
  Molecular Psychiatry 10:500-13, 2005.
  PDF
 

2004

• Blood transcriptional signatures of multiple sclerosis: Unique gene expression of disease activity with A. Achiron, M. Gurevich, N. Kaminski, and M. Mandel.
  Annals of Neurology, 55:410-7, 2004.
  
 

• Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays with Y. Barash, E. Dehan, M. Krupsky, W. Franklin, M. Geraci, and N. Kaminski.
  Bioinformatics, 20:839-4, 2004.
  
 

• CIS: Compound importance sampling method for protein-DNA binding site p-value estimation with Y. Barash, G. Elidan, and T. Kaplan.
  Bioinformatics, 2004.
  Presentation Web Supplement
 

• Efficient exact p-value computation for small sample, sparse, and surprising categorical data with G. Bejerano and N. Tishby.
  J Computational Biology 11:867-886, 2004.
  PDF
 

• Stress-related genomic responses during the course of heat acclimation and its association with ischemic-reperfusion cross-tolerance with M. Horowitz, L. Eli-Berchoer, I. Wapinski, and E. Kodesh.
  Journal of Applied Physiology, 97:1496-507, 2004.
  
 

• Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression with R.M. Marion, A. Regev, E. Segal, Y. Barash, D. Koller, and E.K. O'Shea.
  Proc. National Academy of Sciences USA, 101:14315-22, 2004.
  
 

• A module map showing conditional activity of expression modules in cancer with E. Segal, D. Koller, and A. Regev.
  Nature Genetics, 36:1090-8, 2004.
  Web Supplement
 

2003

• Human and porcine early kidney precursors as a new source for transplantation with B. Dekel, T. Burakova, F.D. Arditti, S. Reich-Zeliger, O. Milstein, S. Aviel-Ronen, G. Rechavi, N. Kaminski, J.H. Passwell, and Y. Reisner.
  Nature Medicine 9:53-60, 2003.
  
 

• Being Bayesian about Network Structure: A Bayesian Approach toStructure Discovery in Bayesian Networks with D. Koller.
  Machine Learning, 50:95-126, 2003.
  PostScript PDF
 

• Module Networks: identifying regulatory modules and their condition- specific regulators from gene expression data with E. Segal, M. Shapira, A. Regev, D. Pe'er, D. Botstein, and D. Koller.
  Nature Genetics, 34:166-178, 2003.
  Web Supplement
 

2002

• Context-Specific Bayesian Clustering for Gene Expression Data with Y. Barash.
  Journal of Computational Biology 9:169-191, 2002.
  PostScript PDF
 

• A Structural EM Algorithm for Phylogenetic Inference with M. Ninio, I. Pe'er, and T. Pupko.
  Journal of Computational Biology, 9:331-353, 2002.
  PostScript PDF Presentation
 

• Learning probabilistic models of relational structure with L. Getoor, B. Taskar, and D. Koller.
  Journal of Machine Learning Research, 3:679-707, 2002.
  PostScript PDF
 

• A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites with T. Pupko, I. Pe'er, M. Hasegawa, and D. Graur.
  Bioinformatics, 18:1116-1123, 2002.
  PDF Web Supplement
 

2001

• On decision-theoretic foundations for defaults with R.I. Brafman.
  Artificial Intelligence, 133:1-33, 2001, 2001.
  
 

• Plausibility measures and default reasoning with J.Y. Halpern.
  Journal of the ACM, 48:648--685, -- --2001, 2001.
  PostScript PDF
 

2000

• Tissue Classification with Gene Expression Profiles with A. Ben-Dor, L. Bruhn, I. Nachman, M. Schummer, and Z. Yakhini.
  J. Computational Biology, 7: 559-584, 2000.
  PostScript PDF
 

• Conditional First-Order Logic Revisited with J.Y. Halpern and D. Koller.
  ACM Trans. Computational Logic, 1:175-207, 2000.
  PostScript PDF
 

• Using Bayesian Network to Analyze Expression Data with M. Linial, I. Nachman, and D. Pe'er.
  J. Computational Biology 7:601-620, 2000.
  PostScript PDF
 

1999

• Modeling beliefs in dynamic systesm. Part II: revision and update with J.Y. Halpern.
  Journal of AI Research 10:117-167, 1999.
  PostScript PDF
 

• Belief revision: A critique with J.Y. Halpern.
  Journal of Logic, Language, and Information 8:401-420, 1999.
  PostScript PDF
 

1997

• Bayesian network classifiers with D. Geiger and M. Goldszmidt.
  Machine Learning 29:131--163, 1997.
  PostScript PDF
 

• Modeling beliefs in dynamic systems. Part I: Foundations with J.Y. Halpern.
  Artificial Intelligence, 95:257--316, 1997.
  PostScript PDF
 

Invited Papers and Book Chapters

2013

• Comprehensive mapping of DNA damage: from static genetic maps to condition-specific maps
  Molecular Cell 49(2):234-6, 2013.
  
 

2012

• Gene expression: Running to stand still with T. Kaplan.
  Nature 484:171-2, 2012.
  
 

2010

• The DNA damage road map (Perspective) with M. Schuldiner.
  Science 330:1327-8, 2010.
  
 

• From large-scale assays to mechanistic insights: computational analysis of interactions with A. Jaimovich.
  Current Opinions in Biotechnology, 2010.
  
 

2005

• From signatures to models: Understanding cancer using microarrays with E. Segal, N. Kaminski, A. Regev, and D. Koller.
  Nature Genetics, 37 Suppl:S38-45, 2005.
  PDF
 

2004

• Inferring cellular networks using probabilistic graphical models
  Science. 303:799-805, 2004.
  
 

• Identifying regulatory networks: Lessons from yeast to humans with A. Regev.
  American Journal of Respiratory and Cell Molecular Biology, 31:125-132, 2004.
  PDF
 

2002

• Practical approaches to analyzing results of microarray experiments with N. Kaminski.
  American Journal of Respiratory and Cell Molecular Biology, 27:125-132, 2002.
  PDF
 

Peer-Reviewed Book Chapters

• Statistical methods for analyzing gene expression data for cancer research with N. Kaminski.
  H. W. Mewes, H. Seidel, and B. Weiss, eds. Ernest Schering Foundation Workshop: Volume 38: Bioinformatics and Genome Analysis, 2002.
  
 

• Learning probabilistic relational models with L. Getoor, D. Koller, and A. Pfeffer.
  S. Dvzeroski and N. Lavrac, eds. Relational Data Mining, Springer-Verlag, pp. 307-337, 2001.
  
 

• Learning Bayesian networks with local structure with M. Goldszmidt.
  M. I. Jordan ed. Learning and Inference in Graphical Models, 1998.
  PostScript PDF
 

Peer-Reviewed Conference Proceedings

2011

• Physical Module Networks: an integrative approach for reconstructing transcription regulation with N. Novershtern and A. Regev.
  Nineteenth Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB), appears in Bioinformatics 27:i177-185, 2011.
  
 

• An integrative clustering and modeling algorithm for dynamical gene expression data with J. Sivriver and N. Habib.
  Nineteenth Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB), appears in Bioinformatics 27:i392-400, 2011.
  
 

2010

• Continuous-Time Belief Propagation with T. El-Hay, I. Cohn, and R. Kupferman.
  Proc. Twenty Seventh International Conf. on Machine Learning (ICML 10), 2010.
  PDF
 

• Modularity and Directionality in Genetic Interaction Maps with A. Jaimovich, R. Rinott, M. Schuldiner, and H. Margalit.
  Eighteenth Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB), appears in Bioinformatics 26, 2010.
  Web Supplement
 

2009

• Mean Field Variational Approximation for Continuous-Time Bayesian Networks with I. Cohn, T. El-Hay, and R. Kupferman.
  Proc. Twenty Fifth Conf. on Uncertainty in Artificial Intelligence (UAI 09), 2009.
  PDF
 

• Identifying novel constrained elements by exploiting biased substitution patterns with M. Gerber, M. Guttman, M. Clamp, M.C. Zody, and X. Xie.
  Seventeenth Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB), appears in Bioinformatics 25:i54-i62, 2009.
  
 

• Convexifying the Bethe Free Energy with O. Meshi, A. Jaimovich, and A. Globerson.
  Proc. Twenty Fifth Conf. on Uncertainty in Artificial Intelligence (UAI 09), 2009.
  PDF
 

2008

• Gibbs Sampling in Factorized Continuous-Time Markov Processes with T. El-Hay and R. Kupferman.
  Proc. Twenty Fourth Conf. on Uncertainty in Artificial Intelligence (UAI 08), 2008.
  PDF Presentation
 

• Nucleosome Positioning from Tiling Microarray Data with M. Yassour, T. Kaplan, and A. Jaimovich.
  Sixteenth Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB), appears in Bioinformatics 24:i139-146, 2008, 2008.
  
 

2007

• Template Based Inference in Symmetric Relational Markov Random Fields with A. Jaimovich and O. Meshi.
  The 23rd Conference on Uncertainty in Artificial Intelligence (UAI'07), 2007.
  PDF
 

• Phylogeny Reconstruction: Increasing the Accuracy of Pairwise Distance Estimation Using Bayesian Inference of Evolutionary Rates with M. Ninio, E. Privman, and T. Pupko.
  European Conference on Computational Biology. Appeared in Bioinformatics 23(2):e136-41, 2007.
  PDF
 

• Automatic Genome-Wide Reconstruction of Phylogenetic Gene Trees with I. Wapinski, A. Pfeffer, and A. Regev.
  Fifteenth Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB), appeared in Bioinformatics 23:i549-58, 2007.
  PDF
 

2006

• Continuous Time Markov Networks with T. El-Hay, D. Koller, and R. Kupferman.
  Proc. Twenty Second Conf. on Uncertainty in Artificial Intelligence (UAI 06), 2006.
  PDF
 

• Dimension Reduction in Singularly Perturbed Continuous-Time Bayesian Networks with R. Kupferman.
  Proc. Twenty Second Conf. on Uncertainty in Artificial Intelligence (UAI 06), 2006.
  PDF
 

2005

• Towards an Integrated Protein-protein Interaction Network with A. Jaimovich, G. Elidan, and H. Margalit.
  Ninth Annual International Conference on Computational Molecular Biology, 2005.
  PDF
 

• Predicting transcription factor binding sites using structural knowledge with T. Kaplan and H. Margalit.
  Ninth Annual International Conference on Computational Molecular Biology, 2005.
  
 

• A Gamma mixture model better accounts for among site rate heterogeneity with I. Mayrose and T. Pupko.
  European Conference on Computational Biology. Appeared in Bioinformatics 21 Suppl 2:ii151-ii158, 2005.
  PDF
 

2004

• Ideal parent structure learning for continuous variable networks with I. Nachman and G. Elidan.
  Proc. Twentieth Conference on Uncertainty in Artificial Intelligence, 2004.
  PostScript PDF Presentation
 

• Inferring quantitative models of regulatory networks from expression data with I. Nachman and A. Regev.
  Eleventh Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB), Appeared in Bioinformatics. 20 Suppl. 1:I248-I256, 2004.
  PDF Presentation
 

• GeneXPress: A visualization and statistical analysis tool for gene expression and sequence data with E. Segal, R. Yelensky, A. Kaushal, T. Pham, A. Regev, and D. Koller.
  Eleventh Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB), 2004.
  PDF Presentation
 

2003

• Modeling Dependencies in Protein-DNA Binding Sites with Y. Barash, G. Elidan, and T. Kaplan.
  Proc. Seventh Annual Inter. Conf. on Computational Molecular Biology (RECOMB), 2003.
  PostScript PDF Presentation
 

• The Information Bottleneck EM Algorithm with G. Elidan.
  Proc. Nineteenth Conf. on Uncertainty in Artificial Intelligence (UAI), 2003.
  PostScript PDF Presentation
 

• Learning Module Networks with E. Segal, D. Pe'er, A. Regev, and D. Koller.
  Proc. Nineteenth Conf. on Uncertainty in Artificial Intelligence (UAI), 2003.
  PostScript PDF Presentation
 

2002

• Data perturbation for escaping local maxima in learning with G. Elidan, M. Ninio, and D. Schuurmans.
  Eighteenth National Conf. on Artificial Intelligence (AAAI), 2002.
  PostScript PDF Presentation Web Supplement
 

• From Promoter Sequence to Expression: A Probabilistic Framework with E. Segal, Y. Barash, I. Simon, and D. Koller.
  Proc. Sixth Annual Inter. Conf. on Computational Molecular Biology (RECOMB), 2002.
  PostScript PDF Presentation
 

• Robust temporal and spectral modeling for query by melody with S. Shwartz, S. Dobnov, and Y. Singer.
  Proc.25th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, 2002.
  
 

• Unsupervised Document Classification using Sequential Information Maximization with N. Slonim and N. Tishby.
  Proc.25th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, 2002.
  PostScript PDF
 

2001

• A simple hyper-geometric approach for discovering putative transcription factor binding sites with Y. Barash and G. Bejerano.
  Algorithms in Bioinformatics: Proc. First International Workshop, 2001.
  PostScript PDF Presentation
 

• Context-Specific Bayesian Clustering for Gene Expression Data with Y. Barash.
  Proc. Fifth Annual Inter. Conf. on Computational Molecular Biology (RECOMB), 2001.
  PostScript PDF Presentation
 

• Class Discovery in Gene Expression Data with A. Ben-Dor and Z. Yakhini.
  Proc. Fifth Annual Inter. Conf. on Computational Molecular Biology (RECOMB), 2001.
  PostScript PDF
 

• Incorporating Expressive Graphical Models in Variational Approximations: Chain-Graphs and Hidden Variables with T. El-Hay.
  Proc. Seventeenth Conf. on Uncertainty in Artificial Intelligence (UAI), 2001.
  PostScript PDF Presentation
 

• Learning the dimensionality of hidden variables with G. Elidan.
  Proc. Seventeenth Conf. on Uncertainty in Artificial Intelligence (UAI), 2001.
  PostScript PDF Presentation
 

• Multivariate Information Bottleneck with O. Mosenzon, N. Slonim, and N. Tishby.
  Proc. Seventeenth Conf. on Uncertainty in Artificial Intelligence (UAI), 2001.
  PostScript PDF Presentation
  Recipient of the Best Paper Award
 

• A Structural EM Algorithm for Phylogenetic Inference with M. Ninio, I. Pe'er, and T. Pupko.
  Proc. Fifth Annual Inter. Conf. on Computational Molecular Biology (RECOMB 2001), 2001.
  PostScript PDF Presentation
 

• Learning probabilistic models of relational structure with L. Getoor, B. Taskar, and D. Koller.
  Eighteenth International Conference on Machine Learning, 2001.
  PostScript PDF
 

• Inferring Subnetworks from Perturbed Expression Profiles with D. Pe'er, A. Regev, and G. Elidan.
  9th Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB), 2001. Appeared in Bioinformatics 17, suppl. 1 S215-24, 2001.
  PostScript PDF Presentation Web Supplement
  Recipient of the Best Paper Award
 

• Rich Probabilistic Models for Gene Expression with E. Segal, B. Taskar, A. Gasch, and D. Koller.
  9th Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB), 2001. Appeared as Bioinformatics, 17, suppl. 1: S243-52, 2001.
  PostScript PDF Presentation Web Supplement
 

• Agglomerative Multivariate Information Bottleneck with N. Slonim and N. Tishby.
  Neural Information Processing Systems (NIPS 01), 2001.
  PostScript PDF
 

2000

• Tissue Classification with Gene Expression Profiles with A. Ben-Dor, L. Bruhn, I. Nachman, M. Schummer, and Z. Yakhini.
  Proc. Fourth Annual Inter. Conf. on Computational Molecular Biology (RECOMB), 2000.
  PostScript PDF
 

• Discovering Hidden Variables: A Structure-Based Approach with G. Elidan, N. Lotner, and D. Koller.
  Neural Information Processing Systems, 2000, 2000.
  PostScript PDF Presentation
 

• Likelihood Computations Using Value Abstraction with D. Geiger and N. Lotner.
  Proc. Sixteenth Conf. on Uncertainty in Artificial Intelligence (UAI), 2000.
  PostScript PDF Presentation
 

• Being Bayesian about Network Structure with D. Koller.
  Proc. Sixteenth Conf. on Uncertainty in Artificial Intelligence (UAI), 2000.
  PostScript PDF Presentation
 

• Using Bayesian Network to Analyze Expression Data with M. Linial, I. Nachman, and D. Pe'er.
  Proc. Fourth Annual Inter. Conf. on Computational Molecular Biology (RECOMB 2000), 2000.
  PostScript PDF Presentation
 

• Gaussian Process Networks with I. Nachman.
  Proc. Sixteenth Conf. on Uncertainty in Artificial Intelligence (UAI), 2000.
  PostScript PDF Presentation
 

1999

• Discovering the Hidden Structure of Complex Dynamic Systems with X. Boyen and D. Koller.
  Proc. Fifteenth Conf. on Uncertainty in Artificial Intelligence (UAI), 1999.
  PostScript PDF
 

• Model-Based Bayesian Exploration with R. Dearden and D. Andre.
  Proc. Fifteenth Conf. on Uncertainty in Artificial Intelligence (UAI), 1999.
  PostScript PDF
 

• Learning Probabilistic Relational Models with L. Getoor, D. Koller, and A. Pfeffer.
  Sixteenth International Conf. on Artificial Intelligence (IJCAI), 1999.
  PostScript PDF
 

• On the Application of The Bootstrap for Computing Confidence Measureson Features of Induced Bayesian Networks with M. Goldszmidt and A. Wyner.
  Proc. Seventh International Workshop on Artificial Intelligence and Statistics, 1999.
  PostScript PDF
 

• Data Analysis with Bayesian Networks: A Bootstrap Approach with M. Goldszmidt and A. Wyner.
  Proc. Fifteenth Conf. on Uncertainty in Artificial Intelligence (UAI), 1999., 1999.
  PostScript PDF
 

• Efficient Learning using Constrained Sufficient Statistics with L. Getoor.
  Proc. Seventh International Workshop on Artificial Intelligence and Statistics, 1999 , 1999.
  PostScript PDF
 

• Learning Bayesian network structure from massive datasets: The ``SparseCandidate'' algorithm with D. Pe'er and I. Nachman.
  Proc. Fifteenth Conf. on Uncertainty in Artificial Intelligence (UAI), 1999.
  PostScript PDF Presentation
 

1998

• Belief Revision with Unreliable Observations with C. Boutilier and J.Y. Halpern.
  Fifteenth National Conf. on Artificial Intelligence (AAAI), 1998.
  PostScript PDF
 

• Bayesian Q-Learning with R. Dearden and S. Russell.
  Fifteenth National Conf. on Artificial Intelligence (AAAI), 1998.
  PostScript PDF
 

• Structured Representation of Complex Stochastic Systems with D. Koller and A. Pfeffer.
  Fifteenth National Conf. on Artificial Intelligence (AAAI), 1998.
  PostScript PDF
 

• Learning the Structure of Dynamic Probabilistic Networks with K. Murphy and S. Russell.
  Fourteenth Conf. on Uncertainty in Artificial Intelligence (UAI), 1998.
  PostScript PDF
 

• Efficient Bayesian parameter estimation in large discrete domains with Y. Singer.
  Neural Information Processing Systems (NIPS 98), 1998., 1998.
  PostScript PDF
 

• The Bayesian structural EM algorithm
  Fourteenth Conf. on Uncertainty in Artificial Intelligence (UAI), 1998.
  PostScript PDF
 

• Bayesian Network Classification with Continuous Attributes: Getting the Best of Both Discretization and Parametric Fitting with M. Goldszmidt and T. J. Lee.
  Fifteenth Inter. Conf. on Machine Learning (ICML), 1998.
  PostScript PDF
 

1997

• Generalized Prioritized Sweeping with D. Andre and R. Parr.
  Neural Information Processing Systems., 1997.
  PostScript PDF
 

• Challenge: Where is the Impact of Bayesian Networks in Learning? with D. Heckerman, M. Goldszmidt, and S. Russell.
  Proc. Fifteenth International Joint Conference on Artificial Intelligence (IJCAI). 1997. , 1997.
  PostScript PDF
 

• Learning belief networks in the presence of missing values and hidden variables
  Fourteenth Inter. Conf. on Machine Learning (ICML97), 1997.
  PostScript PDF
 

• Sequential update of Bayesian network structure with M. Goldszmidt.
  Proc. Thirteenth Conf. on Uncertainty in Artificial Intelligence (UAI 97), 1997.
  PostScript PDF
 

• Image Segmentation in Video Sequences: A Probabilistic Approach with S. Russell.
  Proc. Thirteenth Conf. on Uncertainty in Artificial Intelligence (UAI 97), 1997.
  PostScript PDF
 

1996

• Context-Specific Independence in Bayesian Networks with C. Boutilier, M. Goldszmidt, and D. Koller.
  Proc. Twelfth Conf. on Uncertainty in Artificial Intelligence (UAI), 1996.
  PostScript PDF
 

• Building classifiers using bayesian networks with M. Goldszmidt.
  Thirteenth National Conf. on Artificial Intelligence (AAAI96), 1996.
  PostScript PDF
 

• Discretizing continuous attributes while learning Bayesian networks with M. Goldszmidt.
  Thirteenth Inter. Conf. on Machine Learning (ICML96), 1996.
  PostScript PDF
 

• Learning Bayesian networks with local structure with M. Goldszmidt.
  Proc. Twelfth Conf. on Uncertainty in Artificial Intelligence (UAI 96), 1996.
  PostScript PDF
 

• Plausibility measures and default reasoning with J.Y. Halpern.
  Thirteenth National Conf. on Artificial Intelligence (AAAI96), 1996.
  PostScript PDF
 

• A qualitative Markov assumption and its implications for belief change with J.Y. Halpern.
  Proc. Twelfth Conf. on Uncertainty in Artificial Intelligence (UAI 96), 1996.
  PostScript PDF
 

• Belief revision: A critique with J.Y. Halpern.
  Fifth Inter. Conf. on Knowledge Representation and Reasoning (KR96), 1996.
  PostScript PDF
 

• Conditional first-order logic revisited with J.Y. Halpern and D. Koller.
  Thirteenth National Conf. on Artificial Intelligence (AAAI96), 1996.
  PostScript PDF
 

• On the Sample Complexity of Learning Bayesian Networks with Z. Yakhini.
  Proc. Twelfth Conf. on Uncertainty in Artificial Intelligence (UAI 96), 1996.
  PostScript PDF
 

1995

• On Decision-Theoretic Foundations for Defaults with R.I. Brafman.
  Fourteenth International Conf. on Artificial Intelligence (IJCAI 95), 1995.
  PostScript PDF
 

• Plausibility Measures: A User's Guide with J.Y. Halpern.
  Proc. Eleventh Conf. on Uncertainty in Artificial Intelligence (UAI 95), 1995.
  PostScript PDF
 

1994

• Conditional Logics of Belief Change with J.Y. Halpern.
  Proc. National Conference on Artificial Intelligence (AAAI '94), 915-921, 1994.
  PostScript PDF
 

• A Knowledge-Based framework for belief change. Part II: Revision and update with J.Y. Halpern.
  Principles of Knowledge Representation and Reasoning: Proc. Fourth International Conference (KR'94), 190-201, 1994.
  PostScript PDF
 

• On the Complexity of Conditional Logics with J.Y. Halpern.
  Principles of Knowledge Representation and Reasoning: Proc. Fourth International Conference (KR'94), 202-213., 1994.
  PostScript PDF
 

• A Knowledge-based framework for belief change. Part I: Foundations with J.Y. Halpern.
  Theoretical Aspects of Reasoning about Knowledge: Proc. Fifth Conference (TARK'94), 44-64, 1994.
  PostScript PDF
 

Other Publications

• Overabundance Analysis and Class Discovery in Gene Expression Data with A. Ben-Dor and Z. Yakhini.
  2002.
  PostScript PDF
 

• Modeling Beliefs in Dynamic Systems
  Phd Thesis, Stanford University, 1997.
  PostScript
 

• Nondeterministic Actions and the Frame Problem with C. Boutilier.
  Preliminary version appeared in Extending Theories of Actions, AAAI Spring Symposium., 1995.
  PostScript PDF
 

• On the power and complexity of knowledge-charts
  Master's Thesis, Weizmann Institute of Science, 1992.