Roded Sharan

ORCID

Publication Activity (10 Years)

Years Active: 1996-2024
Publications (10 Years): 33

Top Venues

Publications

Shani Jacobson, Roded Sharan
An Integer Programming Framework for Identifying Stable Components in Asynchronous Boolean Networks. RECOMB (2024)
Neta Zadok, Gil Ast, Roded Sharan
A network-based method for associating genes with autism spectrum disorder. Frontiers Bioinform. 4 (2024)
Barel I. Mashiach, Roded Sharan
Integer Programming Based Algorithms for Overlapping Correlation Clustering. From Computational Logic to Computational Biology (2024)
Itay Kahane, Mark D. M. Leiserson, Roded Sharan
A mutation-level covariate model for mutational signatures. PLoS Comput. Biol. 19 (6) (2023)
Rami Nasser, Yonina C. Eldar, Roded Sharan
Deep Unfolding for Non-Negative Matrix Factorization with Application to Mutational Signature Analysis. J. Comput. Biol. 29 (1) (2022)
Nicholas Franzese, Jason Fan, Roded Sharan, Mark D. M. Leiserson
ScalpelSig Designs Targeted Genomic Panels from Data to Detect Activity of Mutational Signatures. J. Comput. Biol. 29 (1) (2022)
Asia Gervits, Roded Sharan
Predicting genetic interactions, cell line dependencies and drug sensitivities with variational graph auto-encoder. Frontiers Bioinform. 2 (2022)
Gal Gilad, Itay Sason, Roded Sharan
An automated approach for determining the number of components in non-negative matrix factorization with application to mutational signature learning. Mach. Learn. Sci. Technol. 2 (1) (2021)
Rami Nasser, Yonina C. Eldar, Roded Sharan
deep unfolding for non-negative matrix factorization with application to mutational signature analysis. CoRR (2021)
Gal Gilad, Mark D. M. Leiserson, Roded Sharan
A data-driven approach for constructing mutation categories for mutational signature analysis. PLoS Comput. Biol. 17 (10) (2021)
Sapir Margalit, Yotam Abramson, Hila Sharim, Zohar Manber, Surajit Bhattacharya, Yi-Wen Chen, Eric Vilain, Hayk Barseghyan, Ran Elkon, Roded Sharan, Yuval Ebenstein
Long reads capture simultaneous enhancer-promoter methylation status for cell-type deconvolution. Bioinform. 37 (Supplement) (2021)
L. F. Signorini, T. Almozlino, Roded Sharan
ANAT 3.0: a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches. BMC Bioinform. 22 (3) (2021)
Damian Wójtowicz, Mark D. M. Leiserson, Roded Sharan, Teresa M. Przytycka
DNA Repair Footprint Uncovers Contribution of DNA Repair Mechanism to MutationalSignatures. PSB (2020)
Mark D. M. Leiserson, Teresa M. Przytycka, Roded Sharan
Session Introduction. PSB (2020)
Itay Sason, Yuexi Chen, Mark D. M. Leiserson, Roded Sharan
A Mixture Model for Signature Discovery from Sparse Mutation Data. RECOMB (2020)
Ariel Bruner, Roded Sharan
A Robustness Analysis of Dynamic Boolean Models of Cellular Circuits. J. Comput. Biol. 27 (2) (2020)
Itay Sason, Damian Wójtowicz, Welles Robinson, Mark D. M. Leiserson, Teresa M. Przytycka, Roded Sharan
A Sticky Multinomial Mixture Model of Strand-Coordinated Mutational Processes in Cancer. RECOMB (2019)
Ariel Bruner, Roded Sharan
A Robustness Analysis of Dynamic Boolean Models of Cellular Circuits. ISBRA (2019)
Welles Robinson, Roded Sharan, Mark D. M. Leiserson
Modeling clinical and molecular covariates of mutational process activity in cancer. Bioinform. 35 (14) (2019)
Dana Silverbush, Simona Cristea, Gali Yanovich, Tamar Geiger, Niko Beerenwinkel, Roded Sharan
ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules. RECOMB (2018)
Sushant Patkar, Roded Sharan
An optimization framework for network annotation. Bioinform. 34 (13) (2018)
Tom Hartmann, Nicolas Wieseke, Roded Sharan, Martin Middendorf, Matthias Bernt
Genome Rearrangement with ILP. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (5) (2018)
Barak Sternberg, Roded Sharan
A Dynamic Algorithm for Network Propagation. WABI (2018)
Yomtov Almozlino, Nir Atias, Dana Silverbush, Roded Sharan
ANAT 2.0: reconstructing functional protein subnetworks. BMC Bioinform. 18 (1) (2017)
Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira
Complexity and algorithms for copy-number evolution problems. Algorithms Mol. Biol. 12 (1) (2017)
Phuong Dao, Yoo-Ah Kim, Damian Wójtowicz, Sanna Madan, Roded Sharan, Teresa M. Przytycka
BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions. PLoS Comput. Biol. 13 (10) (2017)
Sushant Patkar, Assaf Magen, Roded Sharan, Sridhar Hannenhalli
A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer. PLoS Comput. Biol. 13 (11) (2017)
Phuong Dao, Yoo-Ah Kim, Sanna Madan, Roded Sharan, Teresa M. Przytycka
BeWith: A Between-Within Method for Module Discovery in Cancer using Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions (Extended Abstract). RECOMB (2017)
Arnon Mazza, Konrad Klockmeier, Erich E. Wanker, Roded Sharan
An integer programming framework for inferring disease complexes from network data. Bioinform. 32 (24) (2016)
Arnon Mazza, Konrad Klockmeier, Erich E. Wanker, Roded Sharan
An integer programming framework for inferring disease complexes from network data. Bioinform. 32 (12) (2016)
Ortal Shnaps, Eyal Perry, Dana Silverbush, Roded Sharan
Inference of Personalized Drug Targets via Network Propagation. PSB (2016)
Arnon Mazza, Allon Wagner, Eytan Ruppin, Roded Sharan
Functional Alignment of Metabolic Networks. J. Comput. Biol. 23 (5) (2016)
Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira
Copy-Number Evolution Problems: Complexity and Algorithms. WABI (2016)
Arnon Mazza, Allon Wagner, Eytan Ruppin, Roded Sharan
Functional Alignment of Metabolic Networks. RECOMB (2015)
Matthew Ruffalo, Mehmet Koyutürk, Roded Sharan
Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer. PLoS Comput. Biol. 11 (12) (2015)
Roded Sharan
Preface. J. Comput. Biol. 22 (5) (2015)
Nir Atias, Michal Gershenzon, Katia Labazin, Roded Sharan
Experimental design schemes for learning Boolean network models. Bioinform. 30 (17) (2014)
Dana Silverbush, Roded Sharan
Network orientation via shortest paths. Bioinform. 30 (10) (2014)
Arnon Mazza, Irit Gat-Viks, Roded Sharan
Elucidating Influenza Inhibition Pathways via Network Reconstruction. J. Comput. Biol. 21 (5) (2014)
Arnon Mazza, Irit Gat-Viks, Hesso Farhan, Roded Sharan
A minimum-labeling approach for reconstructing protein networks across multiple conditions. Algorithms Mol. Biol. 9 (2014)
Arnon Mazza, Irit Gat-Viks, Hesso Farhan, Roded Sharan
A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions. WABI (2013)
Michael Elberfeld, Danny Segev, Colin R. Davidson, Dana Silverbush, Roded Sharan
Approximation algorithms for orienting mixed graphs. Theor. Comput. Sci. 483 (2013)
Bjarni V. Halldórsson, Dima Blokh, Roded Sharan
Estimating population size via line graph reconstruction. Algorithms Mol. Biol. 8 (2013)
Roded Sharan, Richard M. Karp
Reconstructing Boolean Models of Signaling. J. Comput. Biol. 20 (3) (2013)
Mark D. M. Leiserson, Dima Blokh, Roded Sharan, Benjamin J. Raphael
Simultaneous Identification of Multiple Driver Pathways in Cancer. PLoS Comput. Biol. 9 (5) (2013)
Dima Blokh, Danny Segev, Roded Sharan
The Approximability of Shortest Path-Based Graph Orientations of Protein-Protein Interaction Networks. J. Comput. Biol. 20 (12) (2013)
Roded Sharan, Richard M. Karp
Reconstructing Boolean Models of Signaling. RECOMB (2012)
Liram Vardi, Eytan Ruppin, Roded Sharan
A Linearized Constraint-Based Approach for Modeling Signaling Networks. J. Comput. Biol. 19 (2) (2012)
Bjarni V. Halldórsson, Dima Blokh, Roded Sharan
Estimating Population Size via Line Graph Reconstruction. WABI (2012)
Nir Atias, Roded Sharan
Comparative analysis of protein networks: hard problems, practical solutions. Commun. ACM 55 (5) (2012)
Shay Houri, Roded Sharan
Sign Assignment Problems on Protein Networks. WABI (2012)
Dima Blokh, Danny Segev, Roded Sharan
Approximation Algorithms and Hardness Results for Shortest Path Based Graph Orientations. CPM (2012)
Oded Magger, Yedael Y. Waldman, Eytan Ruppin, Roded Sharan
Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks. PLoS Comput. Biol. 8 (9) (2012)
Roded Sharan
Invited: From protein networks to disease mechanisms. ICCABS (2012)
Yael Silberberg, Assaf Gottlieb, Martin Kupiec, Eytan Ruppin, Roded Sharan
Large-Scale Elucidation of Drug Response Pathways in Humans. J. Comput. Biol. 19 (2) (2012)
Assaf Gottlieb, Oded Magger, Igor Berman, Eytan Ruppin, Roded Sharan
PRINCIPLE: a tool for associating genes with diseases via network propagation. Bioinform. 27 (23) (2011)
Dana Silverbush, Michael Elberfeld, Roded Sharan
Optimally Orienting Physical Networks. J. Comput. Biol. 18 (11) (2011)
Roded Sharan
Similarity-based methods to predict drug targets, indications and side-effects. SISAP (2011)
Michael Elberfeld, Vineet Bafna, Iftah Gamzu, Alexander Medvedovsky, Danny Segev, Dana Silverbush, Uri Zwick, Roded Sharan
On the Approximability of Reachability-Preserving Network Orientations. Internet Math. 7 (4) (2011)
Lior Wolf, Chen Goldberg, Nathan Manor, Roded Sharan, Eytan Ruppin
Gene Expression in the Rodent Brain is Associated with Its Regional Connectivity. PLoS Comput. Biol. 7 (5) (2011)
Liat Perlman, Assaf Gottlieb, Nir Atias, Eytan Ruppin, Roded Sharan
Combining Drug and Gene Similarity Measures for Drug-Target Elucidation. J. Comput. Biol. 18 (2) (2011)
Dana Silverbush, Michael Elberfeld, Roded Sharan
Optimally Orienting Physical Networks. RECOMB (2011)
Tomer Shlomi, Tomer Benyamini, Eyal Gottlieb, Roded Sharan, Eytan Ruppin
Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect. PLoS Comput. Biol. 7 (3) (2011)
Guy Geva, Roded Sharan
Identification of protein complexes from co-immunoprecipitation data. Bioinform. 27 (1) (2011)
Nir Atias, Roded Sharan
An Algorithmic Framework for Predicting Side Effects of Drugs. J. Comput. Biol. 18 (3) (2011)
Michael Elberfeld, Danny Segev, Colin R. Davidson, Dana Silverbush, Roded Sharan
Approximation Algorithms for Orienting Mixed Graphs. CPM (2011)
Jens Gramm, Richard M. Karp, William S. Noble, Roded Sharan, Qianfei Wang, Nir Yosef
Prediction of Phenotype Information from Genotype Data. Commun. Inf. Syst. 10 (2) (2010)
Iftah Gamzu, Danny Segev, Roded Sharan
Improved Orientations of Physical Networks. WABI (2010)
Misael Mongiovì, Raffaele Di Natale, Rosalba Giugno, Alfredo Pulvirenti, Alfredo Ferro, Roded Sharan
Sigma: a Set-Cover-Based Inexact Graph Matching Algorithm. J. Bioinform. Comput. Biol. 8 (2) (2010)
Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Uri Gophna, Roded Sharan, Eytan Ruppin
Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species. PLoS Comput. Biol. 6 (2) (2010)
Oron Vanunu, Oded Magger, Eytan Ruppin, Tomer Shlomi, Roded Sharan
Associating Genes and Protein Complexes with Disease via Network Propagation. PLoS Comput. Biol. 6 (1) (2010)
Tal Peleg, Nir Yosef, Eytan Ruppin, Roded Sharan
Network-Free Inference of Knockout Effects in Yeast. PLoS Comput. Biol. 6 (1) (2010)
Nir Atias, Roded Sharan
An Algorithmic Framework for Predicting Side-Effects of Drugs. RECOMB (2010)
Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan
Topology-Free Querying of Protein Interaction Networks. J. Comput. Biol. 17 (3) (2010)
Jens Gramm, Tzvika Hartman, Till Nierhoff, Roded Sharan, Till Tantau
On the complexity of SNP block partitioning under the perfect phylogeny model. Discret. Math. 309 (18) (2009)
Shaul Karni, Hermona Soreq, Roded Sharan
A Network-Based Method for Predicting Disease-Causing Genes. J. Comput. Biol. 16 (2) (2009)
Maxim Kalaev, Vineet Bafna, Roded Sharan
Fast and Accurate Alignment of Multiple Protein Networks. J. Comput. Biol. 16 (8) (2009)
Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan
Topology-Free Querying of Protein Interaction Networks. RECOMB (2009)
Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan
Torque: topology-free querying of protein interaction networks. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Maxim Kalaev, Vineet Bafna, Roded Sharan
Fast and Accurate Alignment of Multiple Protein Networks. RECOMB (2008)
Alexander Medvedovsky, Vineet Bafna, Uri Zwick, Roded Sharan
An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks. WABI (2008)
Oron Vanunu, Roded Sharan
A Propagation-based Algorithm for Inferring Gene-Disease Assocations. German Conference on Bioinformatics (2008)
Maxim Kalaev, Michael E. Smoot, Trey Ideker, Roded Sharan
NetworkBLAST: comparative analysis of protein networks. Bioinform. 24 (4) (2008)
Nir Yosef, Roded Sharan, William Stafford Noble
Improved network-based identification of protein orthologs. ECCB (2008)
Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan
QNet: A Tool for Querying Protein Interaction Networks. J. Comput. Biol. 15 (7) (2008)
Oranit Dror, Dina Schneidman-Duhovny, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson, Roded Sharan
Structural similarity of genetically interacting proteins. BMC Syst. Biol. 2 (2008)
Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin, Ron Y. Pinter
Constraint-based functional similarity of metabolic genes: going beyond network topology. Bioinform. 23 (16) (2007)
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
Pepitope: epitope mapping from affinity-selected peptides. Bioinform. 23 (23) (2007)
Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan
QNet: A Tool for Querying Protein Interaction Networks. RECOMB (2007)
Jens Gramm, Till Nierhoff, Roded Sharan, Till Tantau
Haplotyping with missing data via perfect path phylogenies. Discret. Appl. Math. 155 (6-7) (2007)
Eric P. Xing, Michael I. Jordan, Roded Sharan
Bayesian Haplotype Inference via the Dirichlet Process. J. Comput. Biol. 14 (3) (2007)
Eitan Hirsh, Roded Sharan
Identification of conserved protein complexes based on a model of protein network evolution. Bioinform. 23 (2) (2007)
Oved Ourfali, Tomer Shlomi, Trey Ideker, Eytan Ruppin, Roded Sharan
SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Nir Yosef, Zohar Yakhini, Anya Tsalenko, Vessela N. Kristensen, Anne-Lise Børresen-Dale, Eytan Ruppin, Roded Sharan
A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data. Bioinform. 23 (2) (2007)
Shaojie Zhang, Ilya Borovok, Yair Aharonowitz, Roded Sharan, Vineet Bafna
A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. ISMB (Supplement of Bioinformatics) (2006)
Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin, Ron Y. Pinter
Topology-Based Similarity of Metabolic Genes. WABI (2006)
Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker
A direct comparison of protein interaction confidence assignment schemes. BMC Bioinform. 7 (2006)
Anya Tsalenko, Roded Sharan, Vessela N. Kristensen, Hege Edvardsen, Anne-Lise Børresen-Dale, Amir Ben-Dor, Zohar Yakhini
Analysis of Snp-expression Association Matrices. J. Bioinform. Comput. Biol. 4 (2) (2006)
Jens Gramm, Tzvika Hartman, Till Nierhoff, Roded Sharan, Till Tantau
On the Complexity of SNP Block Partitioning Under the Perfect Phylogeny Model. WABI (2006)
Roded Sharan, Bjarni V. Halldórsson, Sorin Istrail
Islands of Tractability for Parsimony Haplotyping. IEEE ACM Trans. Comput. Biol. Bioinform. 3 (3) (2006)

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Publication Activity (10 Years)

Top Topics

Top Venues

Roded Sharan