A New NCAlgorithm for Perfect Matching in Bipartite Cubic Graphs. - Roded Sharan; Avi Wigderson (ISTCS, 1996)

Incomplete Directed Perfect Phylogeny. - Itsik Pe'er; Ron Shamir; Roded Sharan (CPM, 2000)

Center CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis. - Roded Sharan; Ron Shamir (ISMB, 2000)

A Polynomial Approximation Algorithm for the Minimum Fill-In Problem. - Assaf Natanzon; Ron Shamir; Roded Sharan (SIAM J. Comput., 2000)

A Chemical-Distance-Based Test for Positive Darwinian Selection. - Tal Pupko; Roded Sharan; Masami Hasegawa; Ron Shamir; Dan Graur (WABI, 2001)

Complexity classification of some edge modification problems. - Assaf Natanzon; Ron Shamir; Roded Sharan (Discret. Appl. Math., 2001)

On the Complexity of Positional Sequencing by Hybridization - Piotr Berman; Amir Ben-Dor; Itsik Pe'er; Roded Sharan; Ron Shamir (Electron. Colloquium Comput. Complex., 2001)

A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs. - Pavol Hell; Ron Shamir; Roded Sharan (SIAM J. Comput., 2001)

Discovering statistically significant biclusters in gene expression data. - Amos Tanay; Roded Sharan; Ron Shamir (ISMB, 2002)

On the Generality of Phylogenies from Incomplete Directed Characters. - Itsik Pe'er; Ron Shamir; Roded Sharan (SWAT, 2002)

On the Complexity of Positional Sequencing by Hybridization. - Amir Ben-Dor; Itsik Pe'er; Ron Shamir; Roded Sharan (J. Comput. Biol., 2002)

Graph modification problems and their applications to genomic research - Roded Sharan (2002)

CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. - Roded Sharan; Ivan Ovcharenko; Asa Ben-Hur; Richard M. Karp (ISMB (Supplement of Bioinformatics), 2003)

Towards optimally multiplexed applications of universal DNA tag systems. - Amir Ben-Dor; Tzvika Hartman; Benno Schwikowski; Roded Sharan; Zohar Yakhini (RECOMB, 2003)

Identifying Blocks and Sub-populations in Noisy SNP Data. - Gad Kimmel; Roded Sharan; Ron Shamir (WABI, 2003)

Scoring clustering solutions by their biological relevance. - Irit Gat-Viks; Roded Sharan; Ron Shamir (Bioinform., 2003)

CLICK and EXPANDER: a system for clustering and visualizing gene expression data. - Roded Sharan; Adi Maron-Katz; Ron Shamir (Bioinform., 2003)

Bayesian haplo-type inference via the dirichlet process. - Eric P. Xing; Roded Sharan; Michael I. Jordan (ICML, 2004)

Multiplexing Schemes for Generic SNP Genotyping Assays. - Roded Sharan; Amir Ben-Dor; Zohar Yakhini (Pacific Symposium on Biocomputing, 2004)

A fully dynamic algorithm for modular decomposition and recognition of cographs. - Ron Shamir; Roded Sharan (Discret. Appl. Math., 2004)

Cluster graph modification problems. - Ron Shamir; Roded Sharan; Dekel Tsur (Discret. Appl. Math., 2004)

Computational Problems in Noisy SNP and Haplotype Analysis: Block Scores, Block Identification, and Population Stratification. - Gad Kimmel; Roded Sharan; Ron Shamir (INFORMS J. Comput., 2004)

Towards Optimally Multiplexed Applications of Universal Arrays. - Amir Ben-Dor; Tzvika Hartman; Richard M. Karp; Benno Schwikowski; Roded Sharan; Zohar Yakhini (J. Comput. Biol., 2004)

PathBLAST: a tool for alignment of protein interaction networks. - Brian P. Kelley; Bingbing Yuan; Fran Lewitter; Roded Sharan; Brent R. Stockwell; Trey Ideker (Nucleic Acids Res., 2004)

CREME: Cis-Regulatory Module Explorer for the human genome. - Roded Sharan; Asa Ben-Hur; Gabriela G. Loots; Ivan Ovcharenko (Nucleic Acids Res., 2004)

Incomplete Directed Perfect Phylogeny. - Itsik Pe'er; Tal Pupko; Ron Shamir; Roded Sharan (SIAM J. Comput., 2004)

A motif-based framework for recognizing sequence families. - Roded Sharan; Eugene W. Myers (ISMB (Supplement of Bioinformatics), 2005)

Comparison of Protein-Protein Interaction Confidence Assignment Schemes. - Silpa Suthram; Tomer Shlomi; Eytan Ruppin; Roded Sharan; Trey Ideker (Systems Biology and Regulatory Genomics, 2005)

EXPANDER - an integrative program suite for microarray data analysis. - Ron Shamir; Adi Maron-Katz; Amos Tanay; Chaim Linhart; Israel Steinfeld; Roded Sharan; Yosef Shiloh; Ran Elkon (BMC Bioinform., 2005)

A Discriminative Model for Identifying Spatial cis-Regulatory Modules. - Eran Segal; Roded Sharan (J. Comput. Biol., 2005)

Multiplexing Schemes for Generic SNP Genotyping Assays. - Roded Sharan; Jens Gramm; Zohar Yakhini; Amir Ben-Dor (J. Comput. Biol., 2005)

Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data. - Roded Sharan; Trey Ideker; Brian P. Kelley; Ron Shamir; Richard M. Karp (J. Comput. Biol., 2005)

A 1.5-approximation algorithm for sorting by transpositions and transreversals. - Tzvika Hartman; Roded Sharan (J. Comput. Syst. Sci., 2005)

A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. - Shaojie Zhang 001; Ilya Borovok; Yair Aharonowitz; Roded Sharan; Vineet Bafna (ISMB (Supplement of Bioinformatics), 2006)

Flux-Based vs. Topology-Based Similarity of Metabolic Genes. - Oleg Rokhlenko; Tomer Shlomi; Roded Sharan; Eytan Ruppin; Ron Y. Pinter (WABI, 2006)

QPath: a method for querying pathways in a protein-protein interaction network. - Tomer Shlomi; Daniel Segal; Eytan Ruppin; Roded Sharan (BMC Bioinform., 2006)

A direct comparison of protein interaction confidence assignment schemes. - Silpa Suthram; Tomer Shlomi; Eytan Ruppin; Roded Sharan; Trey Ideker (BMC Bioinform., 2006)

A Note on Phasing Long Genomic Regions Using Local Haplotype Predictions. - Eleazar Eskin; Roded Sharan; Eran Halperin (J. Bioinform. Comput. Biol., 2006)

Analysis of Snp-expression Association Matrices. - Anya Tsalenko; Roded Sharan; Vessela N. Kristensen; Hege Edvardsen; Anne-Lise Børresen-Dale; Amir Ben-Dor; Zohar Yakhini (J. Bioinform. Comput. Biol., 2006)

Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. - Jacob Scott; Trey Ideker; Richard M. Karp; Roded Sharan (J. Comput. Biol., 2006)

Reconstructing Chain Functions in Genetic Networks. - Irit Gat-Viks; Richard M. Karp; Ron Shamir; Roded Sharan (SIAM J. Discret. Math., 2006)

Islands of Tractability for Parsimony Haplotyping. - Roded Sharan; Bjarni V. Halldórsson; Sorin Istrail (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. - Oved Ourfali; Tomer Shlomi; Trey Ideker; Eytan Ruppin; Roded Sharan (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Identification of conserved protein complexes based on a model of protein network evolution. - Eitan Hirsh; Roded Sharan (Bioinform., 2007)

Pepitope: epitope mapping from affinity-selected peptides. - Itay Mayrose; Osnat Penn; Elana Erez; Nimrod D. Rubinstein; Tomer Shlomi; Natalia Tarnovitski Freund; Erez M. Bublil; Eytan Ruppin; Roded Sharan; Jonathan M. Gershoni; Eric Martz; Tal Pupko (Bioinform., 2007)

Constraint-based functional similarity of metabolic genes: going beyond network topology. - Oleg Rokhlenko; Tomer Shlomi; Roded Sharan; Eytan Ruppin; Ron Y. Pinter (Bioinform., 2007)

A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data. - Nir Yosef; Zohar Yakhini; Anya Tsalenko; Vessela N. Kristensen; Anne-Lise Børresen-Dale; Eytan Ruppin; Roded Sharan (Bioinform., 2007)

Haplotyping with missing data via perfect path phylogenies. - Jens Gramm; Till Nierhoff; Roded Sharan; Till Tantau (Discret. Appl. Math., 2007)

Bayesian Haplotype Inference via the Dirichlet Process. - Eric P. Xing; Michael I. Jordan; Roded Sharan (J. Comput. Biol., 2007)

Cross-Species Analysis of Protein-protein Interaction Networks. - Nir Yosef; Eytan Ruppin; Roded Sharan (Protein-protein Interactions and Networks, 2008)

Improved network-based identification of protein orthologs. - Nir Yosef; Roded Sharan; William Stafford Noble (ECCB, 2008)

A Propagation-based Algorithm for Inferring Gene-Disease Assocations. - Oron Vanunu; Roded Sharan (German Conference on Bioinformatics, 2008)

An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks. - Alexander Medvedovsky; Vineet Bafna; Uri Zwick; Roded Sharan (WABI, 2008)

NetworkBLAST: comparative analysis of protein networks. - Maxim Kalaev; Michael E. Smoot; Trey Ideker; Roded Sharan (Bioinform., 2008)

Structural similarity of genetically interacting proteins. - Oranit Dror; Dina Schneidman-Duhovny; Alexandra Shulman-Peleg; Ruth Nussinov; Haim J. Wolfson; Roded Sharan (BMC Syst. Biol., 2008)

QNet: A Tool for Querying Protein Interaction Networks. - Banu Dost; Tomer Shlomi; Nitin Gupta 002; Eytan Ruppin; Vineet Bafna; Roded Sharan (J. Comput. Biol., 2008)

On the complexity of SNP block partitioning under the perfect phylogeny model. - Jens Gramm; Tzvika Hartman; Till Nierhoff; Roded Sharan; Till Tantau (Discret. Math., 2009)

Fast and Accurate Alignment of Multiple Protein Networks. - Maxim Kalaev; Vineet Bafna; Roded Sharan (J. Comput. Biol., 2009)

A Network-Based Method for Predicting Disease-Causing Genes. - Shaul Karni; Hermona Soreq; Roded Sharan (J. Comput. Biol., 2009)

Torque: topology-free querying of protein interaction networks. - Sharon Bruckner; Falk Hüffner; Richard M. Karp; Ron Shamir; Roded Sharan (Nucleic Acids Res., 2009)

Improved Orientations of Physical Networks. - Iftah Gamzu; Danny Segev; Roded Sharan (WABI, 2010)

Prediction of Phenotype Information from Genotype Data. - Jens Gramm; Richard M. Karp; William S. Noble; Roded Sharan; Qianfei Wang; Nir Yosef (Commun. Inf. Syst., 2010)

Sigma: a Set-Cover-Based Inexact Graph Matching Algorithm. - Misael Mongiovì; Raffaele Di Natale; Rosalba Giugno; Alfredo Pulvirenti; Alfredo Ferro; Roded Sharan (J. Bioinform. Comput. Biol., 2010)

Topology-Free Querying of Protein Interaction Networks. - Sharon Bruckner; Falk Hüffner; Richard M. Karp; Ron Shamir; Roded Sharan (J. Comput. Biol., 2010)

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species. - Shiri Freilich; Anat Kreimer; Elhanan Borenstein; Uri Gophna; Roded Sharan; Eytan Ruppin (PLoS Comput. Biol., 2010)

Network-Free Inference of Knockout Effects in Yeast. - Tal Peleg; Nir Yosef; Eytan Ruppin; Roded Sharan (PLoS Comput. Biol., 2010)

Associating Genes and Protein Complexes with Disease via Network Propagation. - Oron Vanunu; Oded Magger; Eytan Ruppin; Tomer Shlomi; Roded Sharan (PLoS Comput. Biol., 2010)

Similarity-based methods to predict drug targets, indications and side-effects. - Roded Sharan (SISAP, 2011)

Identification of protein complexes from co-immunoprecipitation data. - Guy Geva; Roded Sharan (Bioinform., 2011)

PRINCIPLE: a tool for associating genes with diseases via network propagation. - Assaf Gottlieb; Oded Magger; Igor Berman; Eytan Ruppin; Roded Sharan (Bioinform., 2011)

On the Approximability of Reachability-Preserving Network Orientations. - Michael Elberfeld; Vineet Bafna; Iftah Gamzu; Alexander Medvedovsky; Danny Segev; Dana Silverbush; Uri Zwick; Roded Sharan (Internet Math., 2011)

An Algorithmic Framework for Predicting Side Effects of Drugs. - Nir Atias; Roded Sharan (J. Comput. Biol., 2011)

Combining Drug and Gene Similarity Measures for Drug-Target Elucidation. - Liat Perlman; Assaf Gottlieb; Nir Atias; Eytan Ruppin; Roded Sharan (J. Comput. Biol., 2011)

Optimally Orienting Physical Networks. - Dana Silverbush; Michael Elberfeld; Roded Sharan (J. Comput. Biol., 2011)

Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect. - Tomer Shlomi; Tomer Benyamini; Eyal Gottlieb; Roded Sharan; Eytan Ruppin (PLoS Comput. Biol., 2011)

Gene Expression in the Rodent Brain is Associated with Its Regional Connectivity. - Lior Wolf; Chen Goldberg; Nathan Manor; Roded Sharan; Eytan Ruppin (PLoS Comput. Biol., 2011)

Approximation Algorithms and Hardness Results for Shortest Path Based Graph Orientations. - Dima Blokh; Danny Segev; Roded Sharan (CPM, 2012)

Invited: From protein networks to disease mechanisms. - Roded Sharan (ICCABS, 2012)

Sign Assignment Problems on Protein Networks. - Shay Houri; Roded Sharan (WABI, 2012)

Comparative analysis of protein networks: hard problems, practical solutions. - Nir Atias; Roded Sharan (Commun. ACM, 2012)

Large-Scale Elucidation of Drug Response Pathways in Humans. - Yael Silberberg; Assaf Gottlieb; Martin Kupiec; Eytan Ruppin; Roded Sharan (J. Comput. Biol., 2012)

A Linearized Constraint-Based Approach for Modeling Signaling Networks. - Liram Vardi; Eytan Ruppin; Roded Sharan (J. Comput. Biol., 2012)

Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks. - Oded Magger; Yedael Y. Waldman; Eytan Ruppin; Roded Sharan (PLoS Comput. Biol., 2012)

Estimating population size via line graph reconstruction. - Bjarni V. Halldórsson; Dima Blokh; Roded Sharan (Algorithms Mol. Biol., 2013)

The Approximability of Shortest Path-Based Graph Orientations of Protein-Protein Interaction Networks. - Dima Blokh; Danny Segev; Roded Sharan (J. Comput. Biol., 2013)

Reconstructing Boolean Models of Signaling. - Roded Sharan; Richard M. Karp (J. Comput. Biol., 2013)

Simultaneous Identification of Multiple Driver Pathways in Cancer. - Mark D. M. Leiserson; Dima Blokh; Roded Sharan; Benjamin J. Raphael (PLoS Comput. Biol., 2013)

Approximation algorithms for orienting mixed graphs. - Michael Elberfeld; Danny Segev; Colin R. Davidson; Dana Silverbush; Roded Sharan (Theor. Comput. Sci., 2013)

A minimum-labeling approach for reconstructing protein networks across multiple conditions. - Arnon Mazza; Irit Gat-Viks; Hesso Farhan; Roded Sharan (Algorithms Mol. Biol., 2014)

Experimental design schemes for learning Boolean network models. - Nir Atias; Michal Gershenzon; Katia Labazin; Roded Sharan (Bioinform., 2014)

Network orientation via shortest paths. - Dana Silverbush; Roded Sharan (Bioinform., 2014)

Elucidating Influenza Inhibition Pathways via Network Reconstruction. - Arnon Mazza; Irit Gat-Viks; Roded Sharan (J. Comput. Biol., 2014)

Preface. - Roded Sharan (J. Comput. Biol., 2015)

Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer. - Matthew Ruffalo; Mehmet Koyutürk; Roded Sharan (PLoS Comput. Biol., 2015)

Inference of Personalized Drug Targets via Network Propagation. - Ortal Shnaps; Eyal Perry; Dana Silverbush; Roded Sharan (PSB, 2016)

Copy-Number Evolution Problems: Complexity and Algorithms. - Mohammed El-Kebir; Benjamin J. Raphael; Ron Shamir; Roded Sharan; Simone Zaccaria; Meirav Zehavi; Ron Zeira (WABI, 2016)

An integer programming framework for inferring disease complexes from network data. - Arnon Mazza; Konrad Klockmeier; Erich E. Wanker; Roded Sharan (Bioinform., 2016)

Functional Alignment of Metabolic Networks. - Arnon Mazza; Allon Wagner; Eytan Ruppin; Roded Sharan (J. Comput. Biol., 2016)

BeWith: A Between-Within Method for Module Discovery in Cancer using Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions (Extended Abstract). - Phuong Dao; Yoo-Ah Kim; Sanna Madan; Roded Sharan; Teresa M. Przytycka (RECOMB, 2017)

Complexity and algorithms for copy-number evolution problems. - Mohammed El-Kebir; Benjamin J. Raphael; Ron Shamir; Roded Sharan; Simone Zaccaria; Meirav Zehavi; Ron Zeira (Algorithms Mol. Biol., 2017)

ANAT 2.0: reconstructing functional protein subnetworks. - Yomtov Almozlino; Nir Atias; Dana Silverbush; Roded Sharan (BMC Bioinform., 2017)

BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions. - Phuong Dao; Yoo-Ah Kim; Damian Wójtowicz; Sanna Madan; Roded Sharan; Teresa M. Przytycka (PLoS Comput. Biol., 2017)

A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer. - Sushant Patkar; Assaf Magen; Roded Sharan; Sridhar Hannenhalli (PLoS Comput. Biol., 2017)

ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules. - Dana Silverbush; Simona Cristea; Gali Yanovich; Tamar Geiger; Niko Beerenwinkel; Roded Sharan (RECOMB, 2018)

A Dynamic Algorithm for Network Propagation. - Barak Sternberg; Roded Sharan (WABI, 2018)

An optimization framework for network annotation. - Sushant Patkar; Roded Sharan (Bioinform., 2018)

Genome Rearrangement with ILP. - Tom Hartmann; Nicolas Wieseke; Roded Sharan; Martin Middendorf; Matthias Bernt (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

A Sticky Multinomial Mixture Model of Strand-Coordinated Mutational Processes in Cancer. - Itay Sason; Damian Wójtowicz; Welles Robinson; Mark D. M. Leiserson; Teresa M. Przytycka; Roded Sharan (RECOMB, 2019)

Modeling clinical and molecular covariates of mutational process activity in cancer. - Welles Robinson; Roded Sharan; Mark D. M. Leiserson (Bioinform., 2019)

Session Introduction. - Mark D. M. Leiserson; Teresa M. Przytycka; Roded Sharan (PSB, 2020)

DNA Repair Footprint Uncovers Contribution of DNA Repair Mechanism to MutationalSignatures. - Damian Wójtowicz; Mark D. M. Leiserson; Roded Sharan; Teresa M. Przytycka (PSB, 2020)

A Mixture Model for Signature Discovery from Sparse Mutation Data. - Itay Sason; Yuexi Chen; Mark D. M. Leiserson; Roded Sharan (RECOMB, 2020)

A Robustness Analysis of Dynamic Boolean Models of Cellular Circuits. - Ariel Bruner; Roded Sharan (J. Comput. Biol., 2020)

Long reads capture simultaneous enhancer-promoter methylation status for cell-type deconvolution. - Sapir Margalit; Yotam Abramson; Hila Sharim; Zohar Manber; Surajit Bhattacharya; Yi-Wen Chen; Eric Vilain; Hayk Barseghyan; Ran Elkon; Roded Sharan; Yuval Ebenstein (Bioinform., 2021)

ANAT 3.0: a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches. - L. F. Signorini; T. Almozlino; Roded Sharan (BMC Bioinform., 2021)

An automated approach for determining the number of components in non-negative matrix factorization with application to mutational signature learning. - Gal Gilad; Itay Sason; Roded Sharan (Mach. Learn. Sci. Technol., 2021)

A data-driven approach for constructing mutation categories for mutational signature analysis. - Gal Gilad; Mark D. M. Leiserson; Roded Sharan (PLoS Comput. Biol., 2021)

Predicting genetic interactions, cell line dependencies and drug sensitivities with variational graph auto-encoder. - Asia Gervits; Roded Sharan (Frontiers Bioinform., 2022)

ScalpelSig Designs Targeted Genomic Panels from Data to Detect Activity of Mutational Signatures. - Nicholas Franzese; Jason Fan; Roded Sharan; Mark D. M. Leiserson (J. Comput. Biol., 2022)

Deep Unfolding for Non-Negative Matrix Factorization with Application to Mutational Signature Analysis. - Rami Nasser; Yonina C. Eldar; Roded Sharan (J. Comput. Biol., 2022)

A mutation-level covariate model for mutational signatures. - Itay Kahane; Mark D. M. Leiserson; Roded Sharan (PLoS Comput. Biol., 2023)

Integer Programming Based Algorithms for Overlapping Correlation Clustering. - Barel I. Mashiach; Roded Sharan (From Computational Logic to Computational Biology, 2024)

An Integer Programming Framework for Identifying Stable Components in Asynchronous Boolean Networks. - Shani Jacobson; Roded Sharan (RECOMB, 2024)

Multi-modal contrastive learning of subcellular organization using DICE. - Rami Nasser; Leah V. Schaffer; Trey Ideker; Roded Sharan (Bioinform., 2024)

A network-based method for associating genes with autism spectrum disorder. - Neta Zadok; Gil Ast; Roded Sharan (Frontiers Bioinform., 2024)

An Adversarial Scheme for Integrating Multi-modal Data on Protein Function. - Rami Nasser; Leah V. Schaffer; Trey Ideker; Roded Sharan (RECOMB, 2025)

Mutational Signature Refitting on Sparse Pan-Cancer Data. - Gal Gilad; Teresa M. Przytycka; Roded Sharan (WABI, 2025)