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Publications:


Selected Recent Publications:


  • Elucidation of Signaling Pathways from Large-Scale Phosphoproteomic Data Using Protein Interaction Networks (with J.D. Rudolph, M. de Graauw, B. van de Water and T. Geiger)
    Journal: Cell Systems, 3:585-593, 2016: pdf

  • A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1 (with D. Hollander, M. Donyo, N. Atias, K. Mekahel, Z. Melamed, S. Yannai, G. Lev-Maor, A. Shilo, S. Schwartz, I. Barshackand and G. Ast)
    Journal: Genome Research, 26, pp. 541-553, 2016: pdf

  • Systematic Identification and Correction of Annotation Errors in the Genetic Interaction Map of Saccharomyces Cerevisiae (with N. Atias and M. Kupiec)
    Journal: Nucleic Acids Rsearch, 44:#e50, 2016: pdf

  • Translation of genotype to phenotype by a hierarchy of cell subsystems (with M. Yu, M. Kramer, J. Dutkowski, R. Srivas, K. Licon, J. Kreisberg, C. Ng, N. Krogan and T. Ideker)
    Journal: Cell Systems, 2, pp. 77-88, 2016: pdf

  • INDI: A computational framework for inferring drug interactions and their associated recommendations (with A. Gottlieb, G. Stein, Y. Oron and E. Ruppin)
    Journal: Molecular Systems Biology, 8:#592, 2012: pdf

  • Toward accurate reconstruction of functional protein networks (with N. Yosef, L. Ungar, E. Zalckvar, A. Kimchi, M. Kupiec and E. Ruppin)
    Journal: Molecular Systems Biology, 5, #248, 2009: pdf

  • 2017:


  • GLADIATOR: a global approach for elucidating disease modules (with Y. Silberberg and M. Kupiec)
    Journal: Genome Medicine, in press.

  • BeWith: A Between-Within Method for Module Discovery in Cancer using Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions (with P. Dao, Y.-A. Kim, D. Wojtowicz, S. Madan and T. Przytycka)
    Proceedings: RECOMB 2017, to appear.

  • Genome Rearrangement with ILP (with T. Hartmann, N. Wieseke, M. Middendorf and M. Bernt)
    Proceedings: APBC 2017, to appear.

  • 2016:


  • Elucidation of Signaling Pathways from Large-Scale Phosphoproteomic Data Using Protein Interaction Networks (with J.D. Rudolph, M. de Graauw, B. van de Water and T. Geiger)
    Journal: Cell Systems, 3:585-593, 2016: pdf

  • Quantifying deleterious effects of regulatory variants (with S. Li, R.V. Alvarez, D. Landsman and I. Ovcharenko)
    Journal: Nucleic Acid Research, doi:10.1093/nar/gkw1263, 2016: pdf

  • Utilizing yeast chemogenomic profiles for the prediction of pharmacogenomic associations in humans (with Y. Silberberg and M. Kupiec)
    Journal: Scientific Reports, 6:#23703, 2016: pdf

  • Systematic Identification and Correction of Annotation Errors in the Genetic Interaction Map of Saccharomyces Cerevisiae (with N. Atias and M. Kupiec)
    Journal: Nucleic Acids Rsearch, 44:#e50, 2016: pdf

  • Copy-Number Evolution Problems: Complexity and Algorithms (with M. El-Kebir, B. Raphael, R. Shamir, S. Zaccaria, M. Zehavi and R. Zeira)
    Proceedings: WABI, pp. 137-149, 2016.

  • An integer programming framework for inferring disease complexes from network data (with A. Mazza, K. Klockmeier and E. Wanker)
    Journal: Bioinformatics (ISMB'16), 32:i271-i277, 2016: pdf

  • A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1 (with D. Hollander, M. Donyo, N. Atias, K. Mekahel, Z. Melamed, S. Yannai, G. Lev-Maor, A. Shilo, S. Schwartz, I. Barshackand and G. Ast)
    Journal: Genome Research, 26, pp. 541-553, 2016: pdf

  • Metabolic network prediction of drug side effects (with I. Shaked, M. Oberhardt, N. Atias and E. Ruppin)
    Journal: Cell Systems, 2, pp. 209-213, 2016: pdf

  • Translation of genotype to phenotype by a hierarchy of cell subsystems (with M. Yu, M. Kramer, J. Dutkowski, R. Srivas, K. Licon, J. Kreisberg, C. Ng, N. Krogan and T. Ideker)
    Journal: Cell Systems, 2, pp. 77-88, 2016: pdf

  • Proteomic analysis of dynein-interacting proteins in Amyotrophic Lateral Sclerosis synaptosomes reveals alterations in the RNA-binding protein Staufen1 (with N. Gershoni-Emek, A. Mazza, M. Chein, T. Gradus-Pery, X. Xiang, K.W. Li and E. Perlson)
    Journal: Molecular and Cellular Proteomics, 15, pp. 506-522, 2016: pdf

  • Inference of personalized drug targets via network propagation (with O. Shnaps, E. Perry and D. Silverbush)
    Proceedings: Pacific Symposium on Biocomputing, pp. 156-167, 2016: pdf

  • 2015:


  • Network-based integration of disparate omic data to identify silent players in cancer (with M. Ruffalo and M. Koyuturk)
    Journal: PLoS Computational Biology, 11:#e1004595, 2015: pdf

  • Functional Alignment of Metabolic networks (with A. Mazza, A. Wagner and E. Ruppin)
    Proceedings: RECOMB, pp. 243-255, 2015: pdf
    Journal: J. of Computational Biology, 23, pp. 390-399, 2016: pdf

  • Prediction of human population responses to toxic compounds by a collaborative competition (with The NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration)
    Journal: Nature Biotechnology, 2015: pdf

  • Human protein interaction networks across tissues and diseases (with E. Yeger-Lotem)
    Journal: Frontiers in Genetics, 6:257, 2015: pdf

  • Regulation of Sec16 levels and dynamics links proliferation and secretion (with K.D. Tillmann, V. Reiterer, F. Baschieri, J. Hoffmann, V. Millarte, M.A. Hauser, A. Mazza, N. Atias, D.F. Legler, M. Weiss and H. Farhan)
    Journal: J. of Cell Science, 128, pp. 670-682, 2015: pdf

  • The effects of telomere shortening on cancer cells: Network model of proteomic and microRNA analysis (with O. Uziel et al.)
    Journal: Genomics, 105, pp. 5-16, 2015: pdf

  • 2014:


  • Experimental design schemes for learning Boolean network mdoels (with N. Atias, M. Gershenzon and K. Labazin)
    Journal: Bioinformatics (ECCB'14 special issue), 30, pp. I445-I452, 2014: pdf

  • Modelling the yeast interactome (with V. Janjic and N. Przulj)
    Journal: Scientific Reports, 4:#4273, 2014: pdf

  • Network orientation via shortest paths (with D. Silverbush)
    Journal: Bioinformatics, 30, pp. 1449-55, 2014: pdf

  • A method for predicting protein-protein interaction types (with Y. Silberberg and M. Kupiec)
    Journal: PLoS One, 9:#e90904, 2014: pdf

  • Elucidating Influenza inhibition pathways via network reconstruction (with A. Mazza and I. Gat-Viks)
    Journal: J. Computational Biology (Special issue of RECOMB Systems Genomics'13), 21, pp. 394-404, 2014: pdf

  • Pathways of Toxicity (t4 workshop report) (with A. Kleensang et al.)
    Journal: ALTEX, 31, pp. 53-61, 2014: pdf

  • 2013:


  • Pathway-based analysis of genomic variation data (with N. Atias and S.Istrail)
    Journal: Current Opinion in Genetics and Development, 23, pp. 622-626 , 2013: pdf

  • Toward a role model
    Journal: EMBO Reports, 14, p. 948, 2013: pdf

  • A method for inferring medical diagnoses from patient similarities (with A. Gottlieb, G. Stein, E. Ruppin and R. Altman)
    Journal: BMC Medicine, 11:#194, 2013: pdf.

  • Network-based interpretation of genomic variation data (with B. Halldorsson)
    Journal: J. of Molecular Biology, 425, pp. 3964-3969, 2013: pdf.

  • A minimum labeling approach for reconstructing protein networks across multiple conditions (with A. Mazza, I. Gat-Viks and H. Farhan)
    Proceedings: WABI, pp. 33-44, 2013.
  • Journal: Algorithms in Molecular Biology, 9:#1, 2014: pdf

  • Environmental stresses disrupt telomere length homeostasis (with G. Romano, Y. Harari, T. Yehuda, A. Podhorzer, L. Rubinstein, R. Shamir, A. Gottlieb, Y. Silberberg, D. Peer, E. Ruppin and M. Kupiec)
    Journal: PLoS Genetics, 9:#e1003721, 2013: pdf.

  • A genetic screen for high copy number suppressors of the synthetic lethality between Elg1 and Srs2 in yeast (with I. Gazy, B. Liefshitz, A. Bronstein, O. Parnas, N. Atias and M. Kupiec)
    Journal: G3, 3, pp. 917-926, 2013: pdf.

  • Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions (with Z. Melamed, A. Levy, R. Ashwal-Fluss, G. Lev-Maor, K. Mekahel, N. Atias, S. Gilad, C. Levy, S. Kadener and G. Ast)
    Journal: Molecular Cell, 50, pp. 869-881, 2013: pdf.

  • Simultaneous identification of multiple driver pathways in cancer (with M. Leiserson, D. Blokh and B. Raphael)
    Journal: PLoS Computational Biology, 9:#e1003054, 2013: pdf.

  • iPoint: an integer programming based algorithm for inferring protein subnetworks (with N. Atias)
    Journal: Molecular Biosystems, DOI: 10.1039/C3MB25432A, 2013: pdf.


  • 2012:


  • Enhancing the prioritization of disease-causing genes through tissue-specific protein interaction networks (with O. Magger, Y.Y. Waldman and E. Ruppin)
    Journal: PLoS Computational Biology, 8:#e1002690, 2012.: pdf

  • Met kinetic signature derived from the response to HGF/SF in a cellular model predicts breast cancer patient survival (with G.Y. Stein, N. Yosef, H. Reichman, J. Horev, A. Laser-Azogui, A. Berens, J. Resau, E. Ruppin and I. Tsarfaty),
    Journal: PLoS One, 7, #e45969, 2012: pdf.

  • INDI: A computational framework for inferring drug interactions and their associated recommendations (with A. Gottlieb, G. Stein, Y. Oron and E. Ruppin)
    Journal: Molecular Systems Biology, 8:#592, 2012: pdf

  • Estimating population size via line graph reconstruction (with B. Halldorsson and D. Blokh),
    Proceedings: WABI, Lecture Notes in Computer Science 7534, pp. 69-80, 2012 pdf
  • Journal: Algorithms for Molecular Biology, 8:#17, 2013: pdf

  • Sign assignment problems on protein networks (with S. Houri)
    Proceedings: WABI 2012, Lecture Notes in Computer Science 7534, pp 338-345, 2012 pdf

  • Comparative analysis of protein networks: Hard problems, practical solutions (with N. Atias)
    Journal: Communications of the ACM, 55, pp. 88-97, 2012 (cover story): pdf

  • Approximation algorithms and hardness results for shortest path based graph orientations (with D. Blokh and D. Segev)
    Proceedings: CPM 2012, Lecture Notes in Computer Science 7354, pp 70-82, 2012: pdf

  • Systematic identification of gene annotation errors in the widely used yeast mutation collections (with T. Ben-Shitrit, N. Yosef, K. Shemesh, E. Ruppin and M. Kupiec)
    Journal: Nature Methods, doi:10.1038/nmeth.1890, 2012: pdf

  • A Linearized constraint based approach for modeling signaling networks (with L. Vardi and E. Ruppin)
    Journal: J. Comput. Biol. (special issue of RECOMB Systems Biology’11), 19:232-240, 2012: pdf

  • Large scale elucidation of drug response pathways in humans (with Y. Silberberg, A. Gottlieb and E. Ruppin)
    Journal: J. Comput. Biol. (special issue of RECOMB Systems Biology’11), 19:163-174, 2012: pdf.

  • Reconstructing Boolean models of signaling (with R.M. Karp)
    Proceedings: RECOMB, pp. 261-271, 2012: pdf.
    Journal: J. Comput. Biol., 20, pp. 249-257, 2013: pdf.


  • 2011:


  • ANAT: A tool for constructing and analyzing functional protein networks ((with N. Yosef, E. Zalckvar, A.D. Rubinstein, M. Homilius, N. Atias, L. Vardi, I. Berman, H. Zur, A. Kimchi and E. Ruppin)
    Journal: Science Signaling, 4, pl1, 2011: pdf

  • PRINCIPLE: A tool for associating genes with diseases via network propagation (with A. Gottlieb, O. Magger, I. Berman and E. Ruppin)
    Journal: Bioinformatics, 27, pages 3325-6, 2011: pdf

  • Competitive and cooperative metabolic interactions in bacterial communities (with S. Freilich, R. Zarecki, O. Eilam, E. Shiftman-Segal, C.S. Henry, M. Kupiec, U. Gophna and E. Ruppin)
    Journal: Nature Communications, 2:#589, 2011: pdf

  • PREDICT: A method for inferring novel drug indications with application to personalized medicine (with A. Gottlieb, G.Y. Stein and E. Ruppin)
    Journal: Molecular Systems Biology, 7, #496, 2011: pdf

  • On the approximability of reachability preserving network orientations (with M. Elberfeld, V. Bafna, I. Gamzu, A. Medvedovsky, D. Segev, D. Silverbush and U. Zwick)
    Journal: Internet Mathematics, 7, pages 209-232, 2011: pdf

  • Gene expression in the rodent brain is associated with its regional connectivity (with L. Wolf, C. Goldberg, M. Manor and E. Ruppin)
    Journal: PLoS Computational Biology, 7, #e1002040, 2011: pdf

  • Approximation algorithms for orienting mixed graphs (with M. Elberfeld, D. Segev, C.R. Davidson and D. Silverbush)
    Proceedings: CPM, pages 416-428, 2011: pdf
    Journal: Theoretical Computer Science, 483, pp. 96-103, 2013: preprint; publisher-link

  • Optimally orienting physical networks (with D. Silverbush and M. Elberfeld)
    Proceedings: RECOMB, pages 424-436, 2011: pdf
    Journal: Journal of Computational Biology, 18, pages 1437-1448, 2011: pdf

  • Processes of fungal proteome evolution and gain of function: Gene duplication and domain rearrangement (with I. Cohen-Gihon and R. Nussinov)
    Journal: Physical Biology, 8, #035009, 2011: pdf

  • Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect (with T. Shlomi, T. Benyamini, E. Gottlieb and E. Ruppin)
    Journal: PLoS Computational Biology, 7, #e1002018, 2011: pdf

  • Evolution of domain promiscuity in eukaryotic genomes – perspective from the inferred ancestral domain architectures (with I. Cohen-Gihon, J.H. Fong, R. Nussinov, T.M. Przytycka and A.R. Panchenko)
    Journal: Molecular Biosystems, 7, pages 784-792, 2011: pdf


  • 2010:


  • Combining drug- and gene similarity measures for drug-target elucidation (with L. Perlman, A. Gottlieb, N. Atias and E. Ruppin)
    Journal: J. Computational Biology (Special issue of RECOMB Systems Biology’10), 18, pages 133-145, 2011: pdf.

  • A novel HMM-based method for detecting enriched transcription factor binding sites reveals RUNX3 as a potential target in pancreatic cancer biology (with L. Levkovitz, N. Yosef, E. Ruppin and Y. Oron)
    Journal: PLoS One, 5, #e14423, 2011: pdf.

  • Improved orientations of physical networks (with I. Gamzu and D. Segev)
    Proceedings: WABI'10, pp. 215-225, 2010: pdf

  • Transcriptional Regulation by CHIP/LDB Complexes (with R. Bronstein, L. Levkovitz, N. Yosef, M. Yanku, E. Ruppin, H. Westphal, B. Oliver and D. Segal)
    Journal: PLoS Genetics, 6:e1001063: pdf.

  • Expander: from expression microarrays to networks and functions (with I. Ulitsky, A. Maron-Katz, S. Shavit, D. Sagir, C. Linhart, R. Elkon, A. Tanay, Y. Shiloh and R. Shamir)
    Journal: Nature Protocols, 5, pages 303-322, 2010: pdf.

  • MAPK signaling to the early secretory pathway revealed by kinase/phosphatase functional screening (with H. Farhan, M.W. Wendeler, S. Mitrovic, E. Fava, Y. Silberberg, M. Zerial and H.-P. Hauri)
    Journal: Journal of Cell Biology, 189:997-1011, 2010: pdf.

  • The large scale organization of the bacterial ecological interaction network (with S. Freilich, A. Kreimer, U. Gophna and E. Ruppin)
    Journal: Nucleic Acids Research, 38:3857-68, 2010: pdf.

  • Translation efficiency in humans: tissue specificity, global considerations and differences between developmental stages (with Y. Waldman, T. Tuller, T. Shlomi and E. Ruppin)
    Journal: Nucleic Acids Research, doi:10.1093/nar/gkq009, 2010: pdf.

  • A systems level strategy for analyzing the cell death network: implication in exploring the apoptosis/autophagy connection (with E. Zalckvar, N. Yosef, S. Reef, Y. Ber, A. D. Rubinstein, E. Ruppin and A. Kimchi)
    Journal: Cell Death and Differentiation, doi:10.1038/cdd.2010.7, 2010: pdf.

  • Associating genes and protein complexes with disease via network propagation (with Oron Vanunu, Oded Magger, Eytan Ruppin and Tomer Shlomi)
    Journal: PLoS Computational Biology, 6, #e1000641, 2010: pdf.

  • Network-free inference of knockout effects in yeast (with Tal Peleg, Nir Yosef and Eytan Ruppin)
    Proceedings: RECOMB Systems Biology, accepted for oral presentation.
    Journal: PLoS Computational Biology, 6, #e1000635, 2010: pdf.

  • Decoupling environment-dependent and independent genetic robustness across bacterial species (with S. Freilich, A. Kreimer, E. Boirenstein, U. Gophna and E. Ruppin)
    Journal: PLoS Computational Biology, 6, #e1000690, 2010: pdf

  • Prediction of phenotype information from genotype data (with N. Yosef, J. Gramm, Q.-f. Wang, W.S. Noble and R. M. Karp)
    Journal: Communications in information and systems, 10, pages 99-114, 2010: pdf.

  • An algorithmic framework for predicting side-effects of drugs (with Nir Atias)
    Proceedings: RECOMB, pages 1-14, 2010: pdf.
    Journal: Journal of Computational Biology, 18, pages 207-218, 2011: pdf.
    Recipient of the Best Paper award at RECOMB’10


  • 2009:


  • A set-cover based approach for inexact graph matching (with M. Mongiovi, R. Di Natale, R. Giugno, A. Pulvirenti and A. Ferro)
    Proceedings: CSB, pages 81-90, 2009: pdf.
    Journal: Journal of Bioinformatics and Computational Biology, 8, pages 199-218, 2010: pdf.
    Recipient of the Best Paper Award at CSB’09.

  • Metabolic-network driven strategies of bacterial ecological strategies (with S. Freilich, A. Kreimer, E. Borenstein, N. Yosef, U. Gophna and E. Ruppin)
    Journal: Genome Biology, doi:10.1186/gb-2009-10-6-r61, 2009: pdf.

  • Increased microRNA activity in human cancers (with A. Israel, E. Ruppin and E. Galun)
    Journal: PLoS One, 6, #e6045, 2009: pdf.

  • TP53 cancerous mutations exhibit selection for translation efficiency (with Yedael Waldman, Tamir Tuller and Eytan Ruppin)
    Journal: Cancer Research, 69, pages 8807-13, 2009: pdf.

  • Torque: Topology-free querying of protein interaction networks (with S. Bruckner, F. Hueffner, R. M. Karp and R. Shamir)
    Journal: Nucleic Acids Research, doi:10.1093/nar/gkp474, 2009: pdf.

  • A complex-centric view of protein network evolution (with N. Yosef, M. Kupiec and E. Ruppin)
    Journal: Nucleic Acids Research, doi:10.1093/nar/gkp414, 2009: pdf.

  • A genome-wide screen yeast genes that affect telomere length maintenance (with L. Ungar, N. Yosef, Y. Sela, E. Ruppin and M. Kupiec)
    Journal: Nucleic Acids Research, doi:10.1093/nar/gkp259, 2009: pdf.

  • Identification of protein complexes from co-immunoprecipitation data (with G. Geva)
    Journal: Bioinformatics, 27, pages 111-117, 2011: pdf.

  • Toward accurate reconstruction of functional protein networks (with N. Yosef, L. Ungar, E. Zalckvar, A. Kimchi, M. Kupiec and E. Ruppin)
    Journal: Molecular Systems Biology, 5, #248, 2009: pdf.

  • Topology-free querying of protein interaction networks (with S. Bruckner, F. Huffner, R.M. Karp and R. Shamir)
    Proceedings: RECOMB'09, pages 74-89, 2009: pdf.
    Journal: Journal of Computational Biology, 17, pages 237-252, 2010: pdf.


  • 2008:


  • A network-based method for predicting disease-causing genes (with S. Karni and H. Soreq)
    Journal: Journal of Computational Biology (RECOMB Systems Biology special issue), 16, pp. 181-189, 2009: pdf.

  • Structural similarity of genetically interacting proteins (with O. Dror, D. Schneidman-Duhovny, A. Shulman-Peleg, R. Nussinov and H. Wolfson)
    Journal: BMC Systems Biology, 2:69, 2008: pdf.

  • A propagation based algorithm for inferring gene-disease associations (with O. Vanunu)
    Proceedings: GCB 2008, to appear: pdf.

  • An algorithm for orienting graphs based on cause-effect pairs and its application to orienting protein networks (with A. Medvedovsky, V. Bafna and U. Zwick)
    Proceedings: WABI 2008, pp. 222-232: pdf.

  • Improved network-based identification of protein orthologs (with N. Yosef and W. S. Noble)
    Journal: Bioinformatics (ECCB'08) 24, pp. i200-i206, 2008: pdf.

  • Protein networks in disease(with T. Ideker)
    Journal: Genome Research, 18, pages 644-652, 2008: pdf.

  • A Systems-level Approach to Mapping the Telomere-length Maintenance Gene Circuitry (with R. Shachar, L. Ungar, M. Kupiec and E. Ruppin)
    Journal: Molecular Systems Biology, 4:172, 2008: pdf.

  • NetworkBLAST: comparative analysis of protein networks (with M. Kalaev, M. Smoot and T. Ideker)
    Journal: Bioinformatics, 24, pages 594-6, 2008: pdf.

  • Fast and accurate alignment of multiple protein networks (with M. Kalaev and V. Bafn)
    Proceedings: RECOMB 2008, pp. 246-256: pdf.
    Journal: Journal of Computational Biology, 16, pages 989-999, 2009: pdf.


  • 2007:


  • Haplotyping with missing data via perfect path phylogenies (with J. Gramm, T. Nierhoff and T. Tantau)
    Journal: Discrete Applied Mathematics, 155, pages 788-805, 2007: pdf.

  • Pepitope: epitope mapping from affinity-selected peptides (with I. Mayrose et al.)
    Journal: Bioinformatics, 23, pages 3244-6, 2007: pdf.

  • Systematic condition-dependent annotation of metabolic genes (with T. Shlomi, M. Herrgard, V. Portnoy, E. Naim, B.O. Palsson and E. Ruppin)
    Journal: Genome research, 17, pages 1626-1633, 2007: pdf.

  • Constraint-based functional similarity of metabolic genes: going beyong network topology (with O. Rokhlenko, T. Shlomi, E. Ruppin and R.Y. Pinter)
    Journal: Bioinformatics, 23, pages 2139-2146, 2007: pdf.

  • Comprehensive analysis of co-occurring domain sets in yeast proteins (with I. Cohen-Gihon and R. Nussinov)
    Journal: BMC Genomics 8:161, 2007: pdf.

  • SPINE: A framework for signaling-regularoty pathway inference from cause-effect experiments (with O. Ourfali, T. Shlomi, T. Ideker and E. Ruppin)
    Journal: Bioinformatics 23 (ISMB'07), pp. I359-I366, 2007: pdf.

  • Genetic interactions in yeast: is robustness going bust (with M. Kupiec and E. Ruppin)
    Journal: Molecular Systems Biology 3:97, 2007: pdf.

  • Transcriptional regulation of protein complexes within and across species (with K. Tan, T. Shlomi, H. Feizi and T. Ideker)
    Journal: Proc. Natl. Acad. Sci. USA 104, pp. 1283-1288, 2007: pdf.

  • Medical sequencing at the extremes of human body mass (with N. Ahituv et al.)
    Journal: American Journal of Human Genetics 80, pp. 779-791, 2007: pdf.

  • A genome-scale computational study of the interplay between transcriptional regulation and metabolism (with T. Shlomi, Y. Eisenberg and E. Ruppin)
    Journal: Molecular Systems Biology 3:101, 2007: pdf.

  • Network-based prediction of protein function (with I. Ulitsky and R. Shamir)
    Journal: Molecular Systems Biology 3:88, 2007: pdf.

  • QNet: A tool for querying protein interaction networks (with B. Dost, T. Shlomi, N. Gupta, E. Ruppin and V. Bafna)
    Proceedings: RECOMB 2007, pp. 1-15: pdf.
    Journal: Journal of Computational Biology 15, pp. 913-925, 2008: pdf.


  • 2006:


  • Structural similarity is a prominent feature of genetic interactions (with O. Dror, D. Schneidman-Duhovny, A. Shulman-Peleg, R. Nussinov and H. Wolfson)
    Second Annual RECOMB Satellite Workshop on Systems Biology, accepted for oral presentation

  • Epitope mapping using combinatorial phage-display libraries: A graph-based algorithm (with I. Mayrose, T. Shlomi, N.D. Rubinstein, J.M. Gershoni, E. Ruppin and T. Pupko)
    Journal: Nucleic Acids Research, doi: 10.1093/nar/gkl975, 2006: pdf.

  • Gene loss rate: A probabilistic measure for the conservation of eukaryotic genes (with E. Borenstein, T. Shlomi and E. Ruppin)
    Journal: Nucleic Acids Research, doi: 10.1093/nar/gkl792, 2006: pdf.

  • On the complexity of SNP block partitioning under the perfect phylogeny model (with J. Gramm, T. Hartman, T. Nierhoff and T. Tantau)
    Proceedings: WABI 2006, pp. 92-102: pdf.
    Journal: Discrete Mathematics, in press: pdf.

  • Flux based vs. topology based similarity of metabolic genes (with O. Rokhlenko, T. Shlomi, E. Ruppin and R.Y. Pinter)
    Proceedings: WABI 2006, pp. 274-285: pdf.

  • Identification of conserved protein complexes based on a model of protein network evolution (with E. Hirsh)
    Journal: Bioinformatics 23 (ECCB'06), pp. e170-e176, 2007: pdf.

  • A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data (with N. Yosef, Z. Yakhini, A. Tsalenko, V. Kristensen, A.-L. Borresen-Dale and E. Ruppin)
    Journal: Bioinformatics 23 (ECCB'06), pp. e91-e98, 2007: pdf.

  • A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements (with S. Zhang, I. Borovok, Y. Aharonowitz and V. Bafna)
    Journal: Bioinformatics 22 (ISMB'06), pp. e557-e565: pdf.

  • QPath: a method for querying pathways in a protein-protein interaction network (with T. Shlomi, D. Segal and E. Ruppin)
    Journal: BMC Bioinformatics 7:199, 2006: pdf.

  • Genetic variation in putative regulatory loci controlling gene expression in breast cancer (with V. Kristensen, H. Edvardsen, A. Tsalenko, S. Nordgard, T. Sorlie, A. Vailaya, A. Ben-Dor, P.E. Lonning, S. Lien, S. Omholt, A.-C. Syvanen, Z. Yakhini and A.-L. Borresen-D)
    Journal: Proc. Natl. Acad. Sci. USA 103, pp. 7735-40, 2006: pdf.

  • Reconstructing chain functions in genetic networks (with I. Gat-Viks, R.M. Karp and R. Shamir)
    Journal: SIAM J. Discrete Mathematics 20, pp. 727-740, 2007: pdf.

  • Systematic identification of functional orthologs based on protein network comparison (with S. Bandyopadhyay and T. Ideker)
    Journal: Genome Research 16, pp. 428-435, 2006: pdf, Cover.

  • Comparison of protein-protein interaction confidence assignment schemes (with S. Suthram, T. Shlomi, E. Ruppin and T. Ideker)
    Proceedings: First Annual RECOMB Satellite Workshop on Systems Biology, LNBI 2043, pages 39-50, 2007: pdf.
    Journal: BMC Bioinformatics 7:360, 2006: pdf

  • A Note on Phasing Long Regions using Local Haplotype Predictions (with E. Eskin and E. Halperin)
    Journal: Journal of Bioinformatics and Computational Biology 4, pp. 639-647, 2006: pdf

  • Modeling cellular machinery through biological network comparison (with T. Ideker)
    Journal: Nature Biotechnology 24, pp. 427-433, 2006: pdf

  • 2005:


  • Analysis of SNP-Expression Association Matrices (with Anya Tsalenko, Hege Edvardsen, Vessela Kristensen, Anne-Lise Boressen-Dale, Amir Ben-Dor and Zohar Yakhini)
    Proceedings: CSB 2005, pp. 135-143: pdf.
    Journal: Journal of Bioinformatics and Computational Biology 4, pp. 259-274, 2006: pdf.

  • Effcient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks (with Jacob Scott, Trey Ideker and Richard Karp)
    Proceedings: RECOMB 2005, pp. 1-13: pdf.
    Journal: Journal of Computational Biology 13, pp. 133-144, 2006: pdf.

  • EXPANDER - an integrative program suite for microarray data analysis (with Ron Shamir, Adi Maron-Katz, Amos Tanay, Chaim Linhart, Israel Steinfeld, Yosef Shiloh and Ran Elkon)
    Journal: BMC Bioinformatics 6, p. 232, 2005: pdf.

  • Islands of Tractability for Parsimony Haplotyping (with Bjarni Halldorsson and Sorin Istrail)
    Proceedings: CSB 2005, pp. 65-72: pdf.
    Journal: IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press: pdf.

  • A Motif-Based Framework for Recognizing Sequence Families (with Gene Myers)
    Journal: Bioinformatics 21, Suppl. 1 (ISMB’05), pp. i387-i393, 2005: pdf.

  • Multiplexing Schemes for Generic SNP Genotyping Assays (with Jens Gramm, Zohar Yakhini and Amir Ben-Dor)
    Journal: Journal of Computational Biology 12, pp. 514-533, 2005: pdf.

  • Conserved Patterns of Protein Interaction in Multiple Species (with Silpa Suthram, Ryan Kelley, Tanja Kuhn, Scott McCuine, Peter Uetz, Taylor Sittler, Richard Karp and Trey Ideker)
    Journal: Proc. Natl. Acad. Sci. USA 102, pp. 1974-1979, 2005: pdf.

  • An Initial Blueprint for Myogenic differentiation (with Alexander Blais, Mary Tsikitis, Diego Acosta-Alvear, Yuval Kluger and Brian Dynlacht)
    Journal: Genes and Development 19, pp. 563-569, 2005: pdf.


  • 2004:


  • A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals (with Tzvika Hartman)
    Proceedings: WABI 2004, pages 50-61: pdf.
    Journal: Journal of Computer and System Sciences 70, pp. 300-320, 2005: pdf.

  • CREME: Cis-Regulatory Module Explorer for the human genome (with Asa Ben-Hur, Gabriela Loots and Ivan Ovcharenko)
    Proceedings: RECOMB 2005, pp. 1-13: pdf.
    Journal: Journal of Computational Biology 13, pp. 133-144, 2006: pdf.

  • PathBLAST: A tool for alignment of protein interaction networks (with Brian Kelley, Bingbing Yuan, Fran Lewitter, Brent Stockwell and Trey Ideker)
    Journal: Nucleic Acids Research 32, pp. W83-W88, 2004: pdf.

  • Bayesian Haplotype Inference via the Dirichlet Process (with Eric Xing and Michael Jordan)
    Proceedings: ICML 2004, pp. 879-886: pdf.
    Journal: Journal of Computational Biology, 14, pages 267-284, 2007: pdf.

  • Revealing Modularity and Organization in the Yeast Molecular Network by Integrated Analysis of Highly Heterogeneous Genome-wide Data (with Amos Tanay, Martin Kupiec and Ron Shamir)
    Journal: Proc. Natl. Acad. Sci. USA 101, pp. 2981-2986, 2004: pdf.

  • Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data (with Trey Ideker, Brian Kelley, Ron Shamir and Richard Karp)
    Proceedings: RECOMB 2004, pp. 282-289: pdf.
    Journal: Journal of Computational Biology 12, pp. 835-846, 2005: pdf.

  • A Discriminative Model for Identifying Spatial Cis-Regulatory Modules (with Eran Segal)
    Proceedings: RECOMB 2004, pp. 141-149: pdf.
    Journal: Journal of Computational Biology 12, pp. 822-834, 2005: pdf.
    Recipient of the Best Paper by a Young Scientist Award at RECOMB'04.

  • Incomplete Directed Perfect Phylogeny (with Itsik Pe'er, Tal Pupko and Ron Shamir)
    Journal: SIAM Journal on Computing, 33(3), pp. 590-607, 2004: pdf.

  • Optimal Fully Dynamic Algorithms for Cograph Recognition (with Ron Shamir)
    Journal: Discrete Applied Mathematics, 136, pp. 329-340, 2004: pdf.

  • Reconstructing Chain Functions in Genetic Networks (with Irit Gat-Viks, Ron Shamir and Richard Karp)
    Proceedings: PSB 2004, pp. 498-509: pdf.

  • Multiplexing Schemes for Generic SNP Genotyping Assays (with Amir Ben-Dor and Zohar Yakhini)
    Proceedings: PSB 2004, pp. 140-151: pdf.

  • On the Complexity of Haplotyping via Perfect Phylogeny (with Jens Gramm, Till Nierhoff and Till Tantau)
    Proceedings: Second RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotypes, LNBI, Springer, 2004 pdf.


  • 2003:


  • Conserved Pathways within Bacteria and Yeast as revealed by Global Protein Network Alignment (with Brian Kelley, Richard Karp, Taylor Sittler, David Root, Brent Stockwell and Trey Ideker)
    Journal: Proc. Natl. Acad. Sci. USA 100, pp. 11394-11399, 2003: pdf.

  • CREME: A Framework for Identifying Cis-Regulatory Modules in Human-Mouse Conserved Segments (with Ivan Ovcharenko, Asa Ben-Hur and Richard Karp)
    Proceedings: ISMB 2003, pp. 283-291: pdf.

  • Genome-wide In-silico Determination of Transcriptional Regulation Modules Controlling Cell Cycle in Human Cells (with Rani Elkon, Chaim Linhart, Ron Shamir and Yossi Shiloh)
    Journal: Genome Research 13, pp. 773-780, 2003: pdf.

  • Optimally Phasing Long Genomic Regions using Local Haplotype Predictions (with Eleazar Eskin and Eran Halperin)
    Proceedings: Second RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotypes, LNBI, Springer, 2004 pdf.
    Technical Report: LTR-2003-78, Leibniz Center, Hebrew University, 2003: pdf.

  • On the Complexity of Haplotyping via Perfect Phylogeny (with Jens Gramm, Till Nierhoff and Till Tantau)
    Proceedings: Second RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotypes, LNBI, Springer, 2004 pdf.

  • Identifying Blocks and Sub-Populations in Noisy SNP Data (with Gad Kimmel and Ron Shamir)
    Proceedings: WABI 2003, pp. 303-319: pdf.
    Journal: INFORMS Journal on Computing, Special Issue on Computational Biology, 16, pp. 360-370, 2004: pdf.

  • Towards Optimally Multiplexed Applications of Universal Arrays (with Amir Ben-Dor, Tzvika Hartman, Richard Karp, Benno Schwikowski and Zohar Yakhini)
    Proceedings: RECOMB 2003, pp. 48-56: pdf.
    Journal: Journal of Computational Biology, 11(2-3), pp. 476-492, 2004: pdf.

  • CLICK and EXPANDER: A System for Clustering and Visualizing Gene Expression Data (with Adi Maron-Katz and Ron Shamir)
    Journal: Bioinformatics 19, pp. 1787-1799, 2003: pdf.

  • Scoring Clustering Solutions by their Biological Relevance (with Irit Gat-Viks and Ron Shamir)
    Journal: Bioinformatics, 19, pp. 2381-2389, 2003: pdf.


  • 2002 and earlier:


  • Discovering Statistically Significant Patterns in Gene Expression Data (with Amos Tanay and Ron Shamir)
    Proceedings: ISMB 2002 (Bioinformatics 18, Supplement 1), pp. 136-144: pdf.

  • On the Generality of Phylogenies from Incomplete Directed Characters (with Itsik Pe'er and Ron Shamir)
    Proceedings: ISMB 2003, pp. 283-291: pdf.

  • Cluster Graph Modification Problems (with Dekel Tsur and Ron Shamir)
    Proceedings: WG 2002, pp. 379-390: pdf.
    Journal: Discrete Applied Mathematics 144, pp. 173-182, 2004: pdf.

  • A Chemical Distance Based Test for Positive Darwinian Selection (with T. Pupko, M. Hasegawa, R. Shamir and D. Graur)
    Proceedings: WABI 2001, pp. 142-155: pdf.
    Journal: Gene 319, pp. 127-135, 2003: pdf.

  • CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis (with Ron Shamir)
    Proceedings: ISMB 2000, pp. 307-316: pdf.

  • Incomplete Directed Perfect Phylogeny (with I. Pe'er and R. Shamir)
    Proceedings: CPM 2000, pp. 143-153: pdf.

  • A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs (with P. Hell and R. Shamir)
    Proceedings: ESA 1999, pp. 527-539: pdf.
    Journal: SIAM Journal on Computing, 31(1), pp. 289-305, 2002: pdf.

  • Complexity Classification of Some Edge Modification Problems (with A. Natanzon and R. Shamir)
    Proceedings: WG 1999, pp. 65-77: pdf.
    Journal: Discrete Applied Mathematics 113, pp. 109-128, 2001: pdf.

  • On the Complexity of Positional Sequencing by Hybridization (with A. Ben-Dor, I. Pe'er and R. Shamir)
    Proceedings: CPM 1999, pp. 88-100: pdf.
    Journal: Journal of Computational Biology 8(4), pp. 361-371, 2001: pdf.
    Full version: Electronic Colloquium on Computational Complexity, Technical report 01-054, 2001: pdf.

  • A Polynomial Approximation Algorithm for the Minimum Fill-In Problem (with A. Natanzon and R. Shamir)
    Proceedings: STOC 1998, pp. 41-47: pdf.
    Journal: Journal of Computational Biology 8(4), pp. 361-371, 2001: pdf.
    Journal: SIAM Journal on Computing 30(4), pp. 1067-1079, 2000: pdf.

  • A Polynomial Approximation Algorithm for the Minimum Fill-In Problem (with A. Natanzon and R. Shamir)
    Proceedings: STOC 1998, pp. 41-47: pdf.
    Journal: SIAM Journal on Computing 30(4), pp. 1067-1079, 2000: pdf.

  • A New NC Algorithm for Perfect Matching in Bipartite Cubic Graphs (with A. Wigderson)
    Proceedings: ISTCS 1996, pp. 202-207: pdf.

  • Book Chapters:


  • Global alignment of protein-protein interaction networks (with Misael Mongiovi)
    Book: Data mining for systems biology: Methods and protocols, Mamitsuka et al. eds., Springer, 2013: pdf

  • Cross-species analysis of protein-protein interaction networks (with N. Yosef and E. Ruppin)
    Book: In Protein-protein interactions and networks: identification, analysis and prediction, 2008.

  • Biclustering Algorithms: A Survey (with A, Tanay and R. Shamir)
    Book: In Handbook of Computational Molecular Biology, Edited by Srinivas Aluru, Chapman & Hall/CRC, Computer and Information Science Series, 2005: pdf.

  • Algorithmic Approaches to Clustering Gene Expression Data (with R. Shamir)
    Book: Current Topics in Computational Biology, T. Jiang, T. Smith, Y. Xu, M.Q. Zhang eds., MIT Press, pp. 269-299, 2002: pdf.

  • Cluster Analysis and its Applications to Gene Expression Data (with R. Elkon and R. Shamir)
    Book: Ernst Schering workshop on Bioinformatics and Genome Analysis, Springer Verlag, 2001: pdf.


  • Theses:


  • Graph Modification Problems and their Applications to Genomic Research
    Ph.D. Thesis, School of Computer Science, Tel-Aviv University, 2002.

  • Perfect Matching in Parallel Computation
    M.Sc. Thesis, School of Computer Science, Hebrew University, 1995.