Roded Sharan

Orcid: 0000-0001-8363-4882

Affiliations:
  • Tel Aviv University, Blavatnik School of Computer Science, Israel


According to our database1, Roded Sharan authored at least 124 papers between 1996 and 2024.

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Bibliography

2024
A network-based method for associating genes with autism spectrum disorder.
Frontiers Bioinform., 2024

An Integer Programming Framework for Identifying Stable Components in Asynchronous Boolean Networks.
Proceedings of the Research in Computational Molecular Biology, 2024

Integer Programming Based Algorithms for Overlapping Correlation Clustering.
Proceedings of the From Computational Logic to Computational Biology, 2024

2023
A mutation-level covariate model for mutational signatures.
PLoS Comput. Biol., 2023

2022
Deep Unfolding for Non-Negative Matrix Factorization with Application to Mutational Signature Analysis.
J. Comput. Biol., 2022

ScalpelSig Designs Targeted Genomic Panels from Data to Detect Activity of Mutational Signatures.
J. Comput. Biol., 2022

Predicting genetic interactions, cell line dependencies and drug sensitivities with variational graph auto-encoder.
Frontiers Bioinform., 2022

2021
A data-driven approach for constructing mutation categories for mutational signature analysis.
PLoS Comput. Biol., 2021

An automated approach for determining the number of components in non-negative matrix factorization with application to mutational signature learning.
Mach. Learn. Sci. Technol., 2021

ANAT 3.0: a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches.
BMC Bioinform., 2021

Long reads capture simultaneous enhancer-promoter methylation status for cell-type deconvolution.
Bioinform., 2021

2020
A Robustness Analysis of Dynamic Boolean Models of Cellular Circuits.
J. Comput. Biol., 2020

A Mixture Model for Signature Discovery from Sparse Mutation Data.
Proceedings of the Research in Computational Molecular Biology, 2020

DNA Repair Footprint Uncovers Contribution of DNA Repair Mechanism to MutationalSignatures.
Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

Session Introduction.
Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

2019
Modeling clinical and molecular covariates of mutational process activity in cancer.
Bioinform., 2019

A Sticky Multinomial Mixture Model of Strand-Coordinated Mutational Processes in Cancer.
Proceedings of the Research in Computational Molecular Biology, 2019

2018
Genome Rearrangement with ILP.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

An optimization framework for network annotation.
Bioinform., 2018

A Dynamic Algorithm for Network Propagation.
Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules.
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.
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.
PLoS Comput. Biol., 2017

ANAT 2.0: reconstructing functional protein subnetworks.
BMC Bioinform., 2017

Complexity and algorithms for copy-number evolution problems.
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).
Proceedings of the Research in Computational Molecular Biology, 2017

2016
Functional Alignment of Metabolic Networks.
J. Comput. Biol., 2016

An integer programming framework for inferring disease complexes from network data.
Bioinform., 2016

Copy-Number Evolution Problems: Complexity and Algorithms.
Proceedings of the Algorithms in Bioinformatics - 16th International Workshop, 2016

Inference of Personalized Drug Targets via Network Propagation.
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.
PLoS Comput. Biol., 2015

Preface.
J. Comput. Biol., 2015

2014
Elucidating Influenza Inhibition Pathways via Network Reconstruction.
J. Comput. Biol., 2014

Network orientation via shortest paths.
Bioinform., 2014

Experimental design schemes for learning Boolean network models.
Bioinform., 2014

A minimum-labeling approach for reconstructing protein networks across multiple conditions.
Algorithms Mol. Biol., 2014

2013
Approximation algorithms for orienting mixed graphs.
Theor. Comput. Sci., 2013

Simultaneous Identification of Multiple Driver Pathways in Cancer.
PLoS Comput. Biol., 2013

Reconstructing Boolean Models of Signaling.
J. Comput. Biol., 2013

The Approximability of Shortest Path-Based Graph Orientations of Protein-Protein Interaction Networks.
J. Comput. Biol., 2013

Estimating population size via line graph reconstruction.
Algorithms Mol. Biol., 2013

2012
Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks.
PLoS Comput. Biol., 2012

A Linearized Constraint-Based Approach for Modeling Signaling Networks.
J. Comput. Biol., 2012

Large-Scale Elucidation of Drug Response Pathways in Humans.
J. Comput. Biol., 2012

Comparative analysis of protein networks: hard problems, practical solutions.
Commun. ACM, 2012

Sign Assignment Problems on Protein Networks.
Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

Invited: From protein networks to disease mechanisms.
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.
Proceedings of the Combinatorial Pattern Matching - 23rd Annual Symposium, 2012

2011
Gene Expression in the Rodent Brain is Associated with Its Regional Connectivity.
PLoS Comput. Biol., 2011

Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect.
PLoS Comput. Biol., 2011

Optimally Orienting Physical Networks.
J. Comput. Biol., 2011

Combining Drug and Gene Similarity Measures for Drug-Target Elucidation.
J. Comput. Biol., 2011

An Algorithmic Framework for Predicting Side Effects of Drugs.
J. Comput. Biol., 2011

On the Approximability of Reachability-Preserving Network Orientations.
Internet Math., 2011

PRINCIPLE: a tool for associating genes with diseases via network propagation.
Bioinform., 2011

Identification of protein complexes from co-immunoprecipitation data.
Bioinform., 2011

Similarity-based methods to predict drug targets, indications and side-effects.
Proceedings of the Fourth International Conference on Similarity Search and Applications, 2011

2010
Associating Genes and Protein Complexes with Disease via Network Propagation.
PLoS Comput. Biol., 2010

Network-Free Inference of Knockout Effects in Yeast.
PLoS Comput. Biol., 2010

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species.
PLoS Comput. Biol., 2010

Topology-Free Querying of Protein Interaction Networks.
J. Comput. Biol., 2010

Sigma: a Set-Cover-Based Inexact Graph Matching Algorithm.
J. Bioinform. Comput. Biol., 2010

Prediction of Phenotype Information from Genotype Data.
Commun. Inf. Syst., 2010

Improved Orientations of Physical Networks.
Proceedings of the Algorithms in Bioinformatics, 10th International Workshop, 2010

2009
Torque: topology-free querying of protein interaction networks.
Nucleic Acids Res., 2009

A Network-Based Method for Predicting Disease-Causing Genes.
J. Comput. Biol., 2009

Fast and Accurate Alignment of Multiple Protein Networks.
J. Comput. Biol., 2009

On the complexity of SNP block partitioning under the perfect phylogeny model.
Discret. Math., 2009

2008
QNet: A Tool for Querying Protein Interaction Networks.
J. Comput. Biol., 2008

Structural similarity of genetically interacting proteins.
BMC Syst. Biol., 2008

NetworkBLAST: comparative analysis of protein networks.
Bioinform., 2008

An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks.
Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

A Propagation-based Algorithm for Inferring Gene-Disease Assocations.
Proceedings of the German Conference on Bioinformatics, 2008

Improved network-based identification of protein orthologs.
Proceedings of the ECCB'08 Proceedings, 2008

Cross-Species Analysis of Protein-protein Interaction Networks.
Proceedings of the Protein-protein Interactions and Networks: Identification, 2008

2007
Bayesian Haplotype Inference via the Dirichlet Process.
J. Comput. Biol., 2007

Haplotyping with missing data via perfect path phylogenies.
Discret. Appl. Math., 2007

A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data.
Bioinform., 2007

Constraint-based functional similarity of metabolic genes: going beyond network topology.
Bioinform., 2007

Pepitope: epitope mapping from affinity-selected peptides.
Bioinform., 2007

Identification of conserved protein complexes based on a model of protein network evolution.
Bioinform., 2007

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments.
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.
IEEE ACM Trans. Comput. Biol. Bioinform., 2006

Reconstructing Chain Functions in Genetic Networks.
SIAM J. Discret. Math., 2006

Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks.
J. Comput. Biol., 2006

Analysis of Snp-expression Association Matrices.
J. Bioinform. Comput. Biol., 2006

A Note on Phasing Long Genomic Regions Using Local Haplotype Predictions.
J. Bioinform. Comput. Biol., 2006

A direct comparison of protein interaction confidence assignment schemes.
BMC Bioinform., 2006

QPath: a method for querying pathways in a protein-protein interaction network.
BMC Bioinform., 2006

Flux-Based <i>vs.</i> Topology-Based Similarity of Metabolic Genes.
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.
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.
J. Comput. Syst. Sci., 2005

Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data.
J. Comput. Biol., 2005

Multiplexing Schemes for Generic SNP Genotyping Assays.
J. Comput. Biol., 2005

A Discriminative Model for Identifying Spatial cis-Regulatory Modules.
J. Comput. Biol., 2005

<i>EXPANDER </i>- an integrative program suite for microarray data analysis.
BMC Bioinform., 2005

Comparison of Protein-Protein Interaction Confidence Assignment Schemes.
Proceedings of the Systems Biology and Regulatory Genomics, 2005

A motif-based framework for recognizing sequence families.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

2004
Incomplete Directed Perfect Phylogeny.
SIAM J. Comput., 2004

CREME: Cis-Regulatory Module Explorer for the human genome.
Nucleic Acids Res., 2004

PathBLAST: a tool for alignment of protein interaction networks.
Nucleic Acids Res., 2004

Towards Optimally Multiplexed Applications of Universal Arrays.
J. Comput. Biol., 2004

Computational Problems in Noisy SNP and Haplotype Analysis: Block Scores, Block Identification, and Population Stratification.
INFORMS J. Comput., 2004

Cluster graph modification problems.
Discret. Appl. Math., 2004

A fully dynamic algorithm for modular decomposition and recognition of cographs.
Discret. Appl. Math., 2004

Multiplexing Schemes for Generic SNP Genotyping Assays.
Proceedings of the Biocomputing 2004, 2004

Bayesian haplo-type inference via the dirichlet process.
Proceedings of the Machine Learning, 2004

2003
CLICK and EXPANDER: a system for clustering and visualizing gene expression data.
Bioinform., 2003

Scoring clustering solutions by their biological relevance.
Bioinform., 2003

Identifying Blocks and Sub-populations in Noisy SNP Data.
Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003

Towards optimally multiplexed applications of universal DNA tag systems.
Proceedings of the Sventh Annual International Conference on Computational Biology, 2003

CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments.
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
PhD thesis, 2002

On the Complexity of Positional Sequencing by Hybridization.
J. Comput. Biol., 2002

On the Generality of Phylogenies from Incomplete Directed Characters.
Proceedings of the Algorithm Theory, 2002

Discovering statistically significant biclusters in gene expression data.
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.
SIAM J. Comput., 2001

On the Complexity of Positional Sequencing by Hybridization
Electron. Colloquium Comput. Complex., 2001

Complexity classification of some edge modification problems.
Discret. Appl. Math., 2001

A Chemical-Distance-Based Test for Positive Darwinian Selection.
Proceedings of the Algorithms in Bioinformatics, First International Workshop, 2001

2000
A Polynomial Approximation Algorithm for the Minimum Fill-In Problem.
SIAM J. Comput., 2000

Center CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis.
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

Incomplete Directed Perfect Phylogeny.
Proceedings of the Combinatorial Pattern Matching, 11th Annual Symposium, 2000

1996
A New <i>NC</i>Algorithm for Perfect Matching in Bipartite Cubic Graphs.
Proceedings of the Fourth Israel Symposium on Theory of Computing and Systems, 1996


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