Roded Sharan

According to our database, Roded Sharan authored at least 121 papers between 1996 and 2023.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of three.

2023

A mutation-level covariate model for mutational signatures.

Itay Kahane, Mark D. M. Leiserson, Roded Sharan

PLoS Comput. Biol., 2023

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

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

Predicting genetic interactions, cell line dependencies and drug sensitivities with variational graph auto-encoder.

Asia Gervits, Roded Sharan

Frontiers Bioinform., 2022

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

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

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

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

2020

A Robustness Analysis of Dynamic Boolean Models of Cellular Circuits.

Ariel Bruner, Roded Sharan

J. Comput. Biol., 2020

A Mixture Model for Signature Discovery from Sparse Mutation Data.

Itay Sason, Yuexi Chen, Mark D. M. Leiserson, Roded Sharan

Proceedings of the Research in Computational Molecular Biology, 2020

DNA Repair Footprint Uncovers Contribution of DNA Repair Mechanism to MutationalSignatures.

Damian Wójtowicz, Mark D. M. Leiserson, Roded Sharan, Teresa M. Przytycka

Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

Session Introduction.

Mark D. M. Leiserson, Teresa M. Przytycka, Roded Sharan

Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

2019

Modeling clinical and molecular covariates of mutational process activity in cancer.

Welles Robinson, Roded Sharan, Mark D. M. Leiserson

Bioinform., 2019

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

Proceedings of the Research in Computational Molecular Biology, 2019

2018

Genome Rearrangement with ILP.

Tom Hartmann, Nicolas Wieseke, Roded Sharan, Martin Middendorf, Matthias Bernt

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

An optimization framework for network annotation.

Sushant Patkar, Roded Sharan

Bioinform., 2018

A Dynamic Algorithm for Network Propagation.

Barak Sternberg, Roded Sharan

Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules.

Dana Silverbush, Simona Cristea, Gali Yanovich, Tamar Geiger, Niko Beerenwinkel, Roded Sharan

Proceedings of the Research in Computational Molecular Biology, 2018

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

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

ANAT 2.0: reconstructing functional protein subnetworks.

Yomtov Almozlino, Nir Atias, Dana Silverbush, Roded Sharan

BMC Bioinform., 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

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

Proceedings of the Research in Computational Molecular Biology, 2017

2016

Functional Alignment of Metabolic Networks.

Arnon Mazza, Allon Wagner, Eytan Ruppin, Roded Sharan

J. Comput. Biol., 2016

An integer programming framework for inferring disease complexes from network data.

Arnon Mazza, Konrad Klockmeier, Erich E. Wanker, Roded Sharan

Bioinform., 2016

Copy-Number Evolution Problems: Complexity and Algorithms.

Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira

Proceedings of the Algorithms in Bioinformatics - 16th International Workshop, 2016

Inference of Personalized Drug Targets via Network Propagation.

Ortal Shnaps, Eyal Perry, Dana Silverbush, Roded Sharan

Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

2015

Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer.

Matthew Ruffalo, Mehmet Koyutürk, Roded Sharan

PLoS Comput. Biol., 2015

Preface.

Roded Sharan

J. Comput. Biol., 2015

2014

Elucidating Influenza Inhibition Pathways via Network Reconstruction.

Arnon Mazza, Irit Gat-Viks, Roded Sharan

J. Comput. Biol., 2014

Network orientation via shortest paths.

Dana Silverbush, Roded Sharan

Bioinform., 2014

Experimental design schemes for learning Boolean network models.

Nir Atias, Michal Gershenzon, Katia Labazin, Roded Sharan

Bioinform., 2014

A minimum-labeling approach for reconstructing protein networks across multiple conditions.

Arnon Mazza, Irit Gat-Viks, Hesso Farhan, Roded Sharan

Algorithms Mol. Biol., 2014

2013

Approximation algorithms for orienting mixed graphs.

Michael Elberfeld, Danny Segev, Colin R. Davidson, Dana Silverbush, Roded Sharan

Theor. Comput. Sci., 2013

Simultaneous Identification of Multiple Driver Pathways in Cancer.

Mark D. M. Leiserson, Dima Blokh, Roded Sharan, Benjamin J. Raphael

PLoS Comput. Biol., 2013

Reconstructing Boolean Models of Signaling.

Roded Sharan, Richard M. Karp

J. Comput. 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

Estimating population size via line graph reconstruction.

Bjarni V. Halldórsson, Dima Blokh, Roded Sharan

Algorithms Mol. Biol., 2013

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

A Linearized Constraint-Based Approach for Modeling Signaling Networks.

Liram Vardi, Eytan Ruppin, Roded Sharan

J. Comput. Biol., 2012

Large-Scale Elucidation of Drug Response Pathways in Humans.

Yael Silberberg, Assaf Gottlieb, Martin Kupiec, Eytan Ruppin, Roded Sharan

J. Comput. Biol., 2012

Comparative analysis of protein networks: hard problems, practical solutions.

Nir Atias, Roded Sharan

Commun. ACM, 2012

Sign Assignment Problems on Protein Networks.

Shay Houri, Roded Sharan

Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

Invited: From protein networks to disease mechanisms.

Roded Sharan

Proceedings of the IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, 2012

Approximation Algorithms and Hardness Results for Shortest Path Based Graph Orientations.

Dima Blokh, Danny Segev, Roded Sharan

Proceedings of the Combinatorial Pattern Matching - 23rd Annual Symposium, 2012

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

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

Optimally Orienting Physical Networks.

Dana Silverbush, Michael Elberfeld, 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

An Algorithmic Framework for Predicting Side Effects of Drugs.

Nir Atias, Roded Sharan

J. Comput. Biol., 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

PRINCIPLE: a tool for associating genes with diseases via network propagation.

Assaf Gottlieb, Oded Magger, Igor Berman, Eytan Ruppin, Roded Sharan

Bioinform., 2011

Identification of protein complexes from co-immunoprecipitation data.

Guy Geva, Roded Sharan

Bioinform., 2011

Similarity-based methods to predict drug targets, indications and side-effects.

Roded Sharan

Proceedings of the Fourth International Conference on Similarity Search and Applications, 2011

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

Network-Free Inference of Knockout Effects in Yeast.

Tal Peleg, Nir Yosef, Eytan Ruppin, Roded Sharan

PLoS 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

Topology-Free Querying of Protein Interaction Networks.

Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan

J. Comput. Biol., 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

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

Improved Orientations of Physical Networks.

Iftah Gamzu, Danny Segev, Roded Sharan

Proceedings of the Algorithms in Bioinformatics, 10th International Workshop, 2010

2009

Torque: topology-free querying of protein interaction networks.

Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan

Nucleic Acids Res., 2009

A Network-Based Method for Predicting Disease-Causing Genes.

Shaul Karni, Hermona Soreq, Roded Sharan

J. Comput. Biol., 2009

Fast and Accurate Alignment of Multiple Protein Networks.

Maxim Kalaev, Vineet Bafna, Roded Sharan

J. Comput. Biol., 2009

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

2008

QNet: A Tool for Querying Protein Interaction Networks.

Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan

J. Comput. Biol., 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

NetworkBLAST: comparative analysis of protein networks.

Maxim Kalaev, Michael E. Smoot, Trey Ideker, Roded Sharan

Bioinform., 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

Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

A Propagation-based Algorithm for Inferring Gene-Disease Assocations.

Oron Vanunu, Roded Sharan

Proceedings of the German Conference on Bioinformatics, 2008

Improved network-based identification of protein orthologs.

Nir Yosef, Roded Sharan, William Stafford Noble

Proceedings of the ECCB'08 Proceedings, 2008

Cross-Species Analysis of Protein-protein Interaction Networks.

Nir Yosef, Eytan Ruppin, Roded Sharan

Proceedings of the Protein-protein Interactions and Networks: Identification, 2008

2007

Bayesian Haplotype Inference via the Dirichlet Process.

Eric P. Xing, Michael I. Jordan, Roded Sharan

J. Comput. Biol., 2007

Haplotyping with missing data via perfect path phylogenies.

Jens Gramm, Till Nierhoff, Roded Sharan, Till Tantau

Discret. Appl. Math., 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

Constraint-based functional similarity of metabolic genes: going beyond network topology.

Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin, Ron Y. Pinter

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

Identification of conserved protein complexes based on a model of protein network evolution.

Eitan Hirsh, Roded Sharan

Bioinform., 2007

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments.

Oved Ourfali, Tomer Shlomi, Trey Ideker, Eytan Ruppin, Roded Sharan

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006

Islands of Tractability for Parsimony Haplotyping.

Roded Sharan, Bjarni V. Halldórsson, Sorin Istrail

IEEE ACM Trans. Comput. Biol. Bioinform., 2006

Reconstructing Chain Functions in Genetic Networks.

Irit Gat-Viks, Richard M. Karp, Ron Shamir, Roded Sharan

SIAM J. Discret. Math., 2006

Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks.

Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan

J. 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

A Note on Phasing Long Genomic Regions Using Local Haplotype Predictions.

Eleazar Eskin, Roded Sharan, Eran Halperin

J. Bioinform. Comput. Biol., 2006

A direct comparison of protein interaction confidence assignment schemes.

Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker

BMC Bioinform., 2006

QPath: a method for querying pathways in a protein-protein interaction network.

Tomer Shlomi, Daniel Segal, Eytan Ruppin, Roded Sharan

BMC Bioinform., 2006

Flux-Based <i>vs.</i> Topology-Based Similarity of Metabolic Genes.

Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin, Ron Y. Pinter

Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements.

Shaojie Zhang, Ilya Borovok, Yair Aharonowitz, Roded Sharan, Vineet Bafna

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005

A 1.5-approximation algorithm for sorting by transpositions and transreversals.

Tzvika Hartman, Roded Sharan

J. Comput. Syst. Sci., 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

Multiplexing Schemes for Generic SNP Genotyping Assays.

Roded Sharan, Jens Gramm, Zohar Yakhini, Amir Ben-Dor

J. Comput. Biol., 2005

A Discriminative Model for Identifying Spatial cis-Regulatory Modules.

Eran Segal, Roded Sharan

J. Comput. Biol., 2005

<i>EXPANDER </i>- 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

Comparison of Protein-Protein Interaction Confidence Assignment Schemes.

Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker

Proceedings of the Systems Biology and Regulatory Genomics, 2005

A motif-based framework for recognizing sequence families.

Roded Sharan, Eugene W. Myers

Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

2004

Incomplete Directed Perfect Phylogeny.

Itsik Pe'er, Tal Pupko, Ron Shamir, Roded Sharan

SIAM J. Comput., 2004

CREME: Cis-Regulatory Module Explorer for the human genome.

Roded Sharan, Asa Ben-Hur, Gabriela G. Loots, Ivan Ovcharenko

Nucleic Acids Res., 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

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

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

Cluster graph modification problems.

Ron Shamir, Roded Sharan, Dekel Tsur

Discret. Appl. Math., 2004

A fully dynamic algorithm for modular decomposition and recognition of cographs.

Ron Shamir, Roded Sharan

Discret. Appl. Math., 2004

Multiplexing Schemes for Generic SNP Genotyping Assays.

Roded Sharan, Amir Ben-Dor, Zohar Yakhini

Proceedings of the Biocomputing 2004, 2004

Bayesian haplo-type inference via the dirichlet process.

Eric P. Xing, Roded Sharan, Michael I. Jordan

Proceedings of the Machine Learning, 2004

2003

CLICK and EXPANDER: a system for clustering and visualizing gene expression data.

Roded Sharan, Adi Maron-Katz, Ron Shamir

Bioinform., 2003

Scoring clustering solutions by their biological relevance.

Irit Gat-Viks, Roded Sharan, Ron Shamir

Bioinform., 2003

Identifying Blocks and Sub-populations in Noisy SNP Data.

Gad Kimmel, Roded Sharan, Ron Shamir

Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003

Towards optimally multiplexed applications of universal DNA tag systems.

Amir Ben-Dor, Tzvika Hartman, Benno Schwikowski, Roded Sharan, Zohar Yakhini

Proceedings of the Sventh Annual International Conference on Computational Biology, 2003

CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments.

Roded Sharan, Ivan Ovcharenko, Asa Ben-Hur, Richard M. Karp

Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2002

Graph modification problems and their applications to genomic research

Roded Sharan

PhD thesis, 2002

On the Complexity of Positional Sequencing by Hybridization.

Amir Ben-Dor, Itsik Pe'er, Ron Shamir, Roded Sharan

J. Comput. Biol., 2002

On the Generality of Phylogenies from Incomplete Directed Characters.

Itsik Pe'er, Ron Shamir, Roded Sharan

Proceedings of the Algorithm Theory, 2002

Discovering statistically significant biclusters in gene expression data.

Amos Tanay, Roded Sharan, Ron Shamir

Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

2001

A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs.

Pavol Hell, Ron Shamir, Roded Sharan

SIAM J. Comput., 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

Complexity classification of some edge modification problems.

Assaf Natanzon, Ron Shamir, Roded Sharan

Discret. Appl. Math., 2001

A Chemical-Distance-Based Test for Positive Darwinian Selection.

Tal Pupko, Roded Sharan, Masami Hasegawa, Ron Shamir, Dan Graur

Proceedings of the Algorithms in Bioinformatics, First International Workshop, 2001

2000

A Polynomial Approximation Algorithm for the Minimum Fill-In Problem.

Assaf Natanzon, Ron Shamir, Roded Sharan

SIAM J. Comput., 2000

Center CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis.

Roded Sharan, Ron Shamir

Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

Incomplete Directed Perfect Phylogeny.

Itsik Pe'er, Ron Shamir, Roded Sharan

Proceedings of the Combinatorial Pattern Matching, 11th Annual Symposium, 2000

1996

A New <i>NC</i>Algorithm for Perfect Matching in Bipartite Cubic Graphs.

Roded Sharan, Avi Wigderson

Proceedings of the Fourth Israel Symposium on Theory of Computing and Systems, 1996