Ron Shamir

发表

Construction of physical maps from oligonucleotide fingerprints data

Guy Mayraz, Ron Shamir, 1999, RECOMB.

Complexity and algorithms for reasoning about time: a graph-theoretic approach

Ron Shamir, Martin Charles Golumbic, M. Golumbic, 1993, JACM.

Algorithms for Molecular Biology 4.1 Multiple Alignment

Ron Shamir, R. Shamir, 2002 .

Faucet: streaming de novo assembly graph construction

Eran Halperin, Ron Shamir, Roye Rozov, 2017, bioRxiv.

Bioinformatics for Biologists: Preface

Ron Shamir, Pavel Pevzner, P. Pevzner, 2011 .

Discovering statistically significant biclusters in gene expression data

Roded Sharan, Ron Shamir, Amos Tanay, 2002, ISMB.

Fast lossless compression via cascading Bloom filters

Eran Halperin, Ron Shamir, Roye Rozov, 2014, BMC Bioinformatics.

A randomized scheme for speeding up algorithms for linear and convex programming problems with high constraints-to-variables ratio

Ron Shamir, Ilan Adler, I. Adler, 1993, Math. Program..

MGMR: leveraging RNA-Seq population data to optimize expression estimation

Eran Halperin, Ron Shamir, Roye Rozov, 2012, BMC Bioinformatics.

A Chemical-Distance-Based Test for Positive Darwinian Selection

Roded Sharan, Ron Shamir, Tal Pupko, 2001, WABI.

DOMINO: a novel network-based module detection algorithm with reduced rate of false calls

Ron Shamir, Ran Elkon, Hagai Levi, 2020 .

Message from the ISCB: 2018 ISCB Accomplishments by a Senior Scientist Award

Ron Shamir, Diane E. Kovats, Christiana N. Fogg, 2018, Bioinform..

Algorithms for optical mapping

Richard M. Karp, Ron Shamir, 1998, RECOMB '98.

Preface

Ron Shamir, Sorin Istrail, Pavel A. Pevzner, 2007, Discret. Appl. Math..

Compact Universal k-mer Hitting Sets

Ron Shamir, Carl Kingsford, Guillaume Marçais, 2016, WABI.

A Probabilistic Methodology for Integrating Knowledge and Experiments on Biological Networks

Ron Shamir, Amos Tanay, Irit Gat-Viks, 2006, J. Comput. Biol..

Accurate identification of alternatively spliced exons using support vector machine

Ron Shamir, Gideon Dror, Rotem Sorek, 2005, Bioinform..

Faster and simpler algorithm for sorting signed permutations by reversals

Haim Kaplan, Robert E. Tarjan, Ron Shamir, 1997, SODA '97.

Faster pattern matching with character classes using prime number encoding

Ron Shamir, Chaim Linhart, R. Shamir, 2009, J. Comput. Syst. Sci..

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

Ron Shamir, Roded Sharan, Adi Maron-Katz, 2003, Bioinform..

Clustering Gene Expression Patterns

Ron Shamir, Zohar Yakhini, Amir Ben-Dor, 1999, J. Comput. Biol..

Bounded Degree Interval Sandwich Problems

Haim Kaplan, Ron Shamir, 1999, Algorithmica.

Improved algorithms for the random cluster graph model

Ron Shamir, Dekel Tsur, R. Shamir, 2002, Random Struct. Algorithms.

2018 ISCB Innovator Award recognizes M. Madan Babu

Ron Shamir, Diane E. Kovats, Christiana N. Fogg, 2018, PLoS computational biology.

Modeling and Analysis of Heterogeneous Regulation in Biological Networks

Ron Shamir, Amos Tanay, Irit Gat-Viks, 2004, Regulatory Genomics.

A hierarchical Bayesian model for flexible module discovery in three-way time-series data

Ron Shamir, Talma Hendler, David Amar, 2015, Bioinform..

Sorting Cancer Karyotypes by Elementary Operations

Ron Shamir, Michal Ozery-Flato, 2008, RECOMB-CG.

Sorting by Reciprocal Translocations via Reversals Theory

Ron Shamir, Michal Ozery-Flato, R. Shamir, 2007, J. Comput. Biol..

A note on tolerance graph recognition

Ron Shamir, Ryan B. Hayward, R. Hayward, 2004, Discret. Appl. Math..

Physical Maps and Interval Sandwich Problems: Bounded Degrees Help

Haim Kaplan, Ron Shamir, 1996, ISTCS.

Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast

Ron Shamir, Irit Gat-Viks, Martin Kupiec, 2011, RECOMB.

A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem

Ron Shamir, Mukul S. Bansal, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

A Family of Simplex Variants Solving for An mxd Linear Program in

Richard M. Karp, Ron Shamir, Ilan Adler, 1983 .

Torque: topology-free querying of protein interaction networks

Roded Sharan, Richard M. Karp, Ron Shamir, 2009, Nucleic Acids Res..

Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites

Ron Shamir, Amos Tanay, Daniela Raijman, 2008, PLoS Comput. Biol..

Two Notes on Genome Rearrangement

Ron Shamir, Michal Ozery-Flato, R. Shamir, 2003, J. Bioinform. Comput. Biol..

Sorting Cancer Karyotypes by Elementary Operations

Ron Shamir, Michal Ozery-Flato, R. Shamir, 2008, RECOMB-CG.

A Linear-Time Algorithm for the Copy Number Transformation Problem

Ron Shamir, Meirav Zehavi, Ron Zeira, 2017, J. Comput. Biol..

Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles

Richard M. Karp, Ron Shamir, Igor Ulitsky, 2008, RECOMB.

Theory and applications

Ron Shamir, Chaim Linhart, R. Shamir, 2004 .

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

Roded Sharan, Ron Shamir, R. Sharan, 2000, ISMB.

Balancing Problems in Acyclic Networks

Endre Boros, Ron Shamir, Peter L. Hammer, 1994, Discret. Appl. Math..

Large Scale Sequencing by Hybridization

Ron Shamir, Dekel Tsur, 2002, J. Comput. Biol..

Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPs

Ron Shamir, Jacques S. Beckmann, Tamar Barzuza, 2004, CPM.

Algorithms and Complexity of Sandwich Problems in Graphs (Extended Abstract)

Haim Kaplan, Ron Shamir, Martin Charles Golumbic, 1993, WG.

ABLE: an Activity-Based Level Set Segmentation Algorithm for Two-Photon Calcium Imaging Data

Ron Shamir, Ran Elkon, David Amar, 2017 .

A fast algorithm for constructing monge sequences in transportation problems with forbidden arcs

Ron Shamir, 1993, Discret. Math..

Computational Problems in Noisy SNP and Haplotype Analysis: Block Scores, Block Identification, and Population Stratification

Roded Sharan, Ron Shamir, Gad Kimmel, 2004, INFORMS J. Comput..

The restriction scaffold problem

Richard M. Karp, Ron Shamir, Benno Schwikowski, 2002, RECOMB '02.

Complexity classification of some edge modification problems

Roded Sharan, Ron Shamir, Assaf Natanzon, 1999, Discret. Appl. Math..

Spectrum Alignment: Efficient Resequencing by Hybridization

Ron Shamir, Itsik Pe'er, R. Shamir, 2000, ISMB.

Identifying functional modules using expression profiles and confidence-scored protein interactions

Ron Shamir, Igor Ulitsky, R. Shamir, 2009, Bioinform..

CLICK: A Clustering Algorithm for Gene Expression Analysis

Roded Sharan, Ron Shamir, 2000, ISMB 2000.

Artificial Intelligence and Heuristic Methods in Bioinformatics

Ron Shamir, Paolo Frasconi, Heuristic Methods in Bioinformatics, 2003 .

Reconstructing Chain Functions in Genetic Networks

Richard M. Karp, Ron Shamir, Irit Gat-Viks, 2004, Pacific Symposium on Biocomputing.

A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs

Roded Sharan, Ron Shamir, Pavol Hell, 2001, SIAM J. Comput..

Improving the efficiency of de Bruijn graph construction using compact universal hitting sets

Ron Shamir, Yaron Orenstein, Lianrong Pu, 2020, bioRxiv.

Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers

Ron Shamir, Yaron Orenstein, R. Shamir, 2013, Bioinform..

Topology-Free Querying of Protein Interaction Networks

Roded Sharan, Richard M. Karp, Ron Shamir, 2009, RECOMB.

Copy-Number Evolution Problems: Complexity and Algorithms

Ron Shamir, Benjamin J. Raphael, Meirav Zehavi, 2016, WABI.

A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals

Haim Kaplan, Robert E. Tarjan, Ron Shamir, 1999, SIAM J. Comput..

PO-351 Promo: an interactive tool for analysing large multi-omic cancer datasets

Ron Shamir, Dvir Netanely, N Stern, 2018 .

PIVOT: Protein Interacions VisualizatiOn Tool

Ron Shamir, Nir Orlev, Yosef Shiloh, 2004, Bioinform..

An O(n3/2sqrt(log n)) Algorithm for Sorting by Reciprocal Translocations

Ron Shamir, Michal Ozery-Flato, 2006, CPM.

Guest Editors' foreword

Ron Shamir, Pavel Pevzner, Richard Karp, 2001, J. Comput. Syst. Sci..

Constructing Logical Models of Gene Regulatory Networks by Integrating Transcription Factor-DNA Interactions with Expression Data: An Entropy-Based Approach

Ron Shamir, Guy Karlebach, Guy Karlebach, 2012, J. Comput. Biol..

Sorting by Translocations Via Reversals Theory

Ron Shamir, Michal Ozery-Flato, 2006, Comparative Genomics.

Monge and Feasibility Sequences in General Flow Problems

Ron Shamir, Ilan Adler, Alan J. Hoffman, 1993, Discret. Appl. Math..

RichMind: A Tool for Improved Inference from Large-Scale Neuroimaging Results

Ron Shamir, Talma Hendler, David Amar, 2016, PloS one.

Dynamic programming: one algorithmic key for many biological locks

Ron Shamir, Mikhail S. Gelfand, Pavel Pevzner, 2011 .

Bioinformatics for Biologists: REFERENCES

Ron Shamir, Pavel Pevzner, P. Pevzner, 2011 .

Foreword

Ron Shamir, Sorin Istrail, Pavel A. Pevzner, 1998, Discret. Appl. Math..

Modeling and Analysis of Heterogeneous Regulation in Biological Networks

Ron Shamir, Amos Tanay, Irit Gat-Viks, 2004, Regulatory Genomics.

2018 ISCB Overton Prize awarded to Cole Trapnell

Ron Shamir, Diane E. Kovats, Christiana N. Fogg, 2018, Bioinform..

Modeling transcription programs: inferring binding site activity and dose-response model optimization

Ron Shamir, Amos Tanay, 2003, RECOMB '03.

Network-induced Classification Kernels for Gene Expression Profile Analysis

Ron Shamir, Gideon Dror, Ofer Lavi, 2012 .

NEMO: Cancer subtyping by integration of partial multi-omic data

Ron Shamir, Nimrod Rappoport, 2018 .

Increasing the Power of Association Studies by Imputation-based Sparse Tag SNP Selection

Eran Halperin, Ron Shamir, Gad Kimmel, 2009, Commun. Inf. Syst..

Identification of functional modules using network topology and high-throughput data

Ron Shamir, Igor Ulitsky, R. Shamir, 2007, BMC Systems Biology.

EXPANDER – an integrative program suite for microarray data analysis

Ron Shamir, Ran Elkon, Amos Tanay, 2005, BMC Bioinformatics.

MONET: Multi-omic module discovery by omic selection

Ron Shamir, Nimrod Rappoport, Roy Safra, 2020, PLoS Comput. Biol..

Algorithms for Optical Mapping

Richard M. Karp, Ron Shamir, 2000, J. Comput. Biol..

Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data.

Roded Sharan, Ron Shamir, Amos Tanay, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Foreword

Ming Li, Ron Shamir, Pavel A. Pevzner, 2002, Journal of computer and system sciences (Print).

A Polynomial Approximation Algorithm for the Minimum Fill-In Problem

Roded Sharan, Ron Shamir, Assaf Natanzon, 2000, SIAM J. Comput..

On the Generality of Phylogenies from Incomplete Directed Characters

Ron Shamir, Roded Sharan, Itsik Pe'er, 2002, SWAT.

2018 ISCB Innovator Award recognizes M. Madan Babu

Ron Shamir, Diane E. Kovats, Christiana N. Fogg, 2018, Bioinform..

Multilevel Modeling and Inference of Transcription Regulation

Ron Shamir, Amos Tanay, 2004, J. Comput. Biol..

Reconstructing chain functions in genetic networks.

Roded Sharan, Richard M. Karp, Ron Shamir, 2003 .

Recycler: an algorithm for detecting plasmids from de novo assembly graphs

Eran Halperin, Ron Shamir, Roye Rozov, 2016, bioRxiv.

Rearrangements in Genomes with Centromeres Part I: Translocations

Ron Shamir, Michal Ozery-Flato, R. Shamir, 2007, RECOMB.

Handling Long Targets and Errors in Sequencing by Hybridization

Eran Halperin, Ron Shamir, Tzvika Hartman, 2003, J. Comput. Biol..

Tractability of parameterized completion problems on chordal and interval graphs: minimum fill-in and physical mapping

Haim Kaplan, Robert E. Tarjan, Ron Shamir, 1994, Proceedings 35th Annual Symposium on Foundations of Computer Science.

MorphDB: Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants

Ron Shamir, David Amar, Arthur Zwaenepoel, 2018, Front. Plant Sci..

Algorithmic approaches to clustering gene expression data

Roded Sharan, Ron Shamir, R. Sharan, 2001 .

Interval Graphs, Interval Orders and the Consistency of Temporal Events

Ron Shamir, Martin Charles Golumbic, M. Golumbic, 1992, ISTCS.

Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers

Ron Shamir, Yaron Orenstein, 2015, Bioinform..

Strongly Polynomial Algorithms for the High Multiplicity Scheduling Problem

Ron Shamir, Dorit S. Hochbaum, R. Shamir, 1991, Oper. Res..

An algorithm for clustering cDNAs for gene expression analysis

Ron Shamir, Hans Lehrach, Jörg Lange, 1999, RECOMB.

An Algorithm Combining Discrete and Continuous Methods for Optical Mapping

Richard M. Karp, Ron Shamir, Itsik Pe'er, 1999, ISMB.

Improved algorithms for the random cluster graph model

Ron Shamir, Dekel Tsur, R. Shamir, 2002, Random Struct. Algorithms.

A Faster Algorithm for RNA Co-folding

Ron Shamir, Michal Ziv-Ukelson, Irit Gat-Viks, 2008, WABI.

Identifying Blocks and Sub-populations in Noisy SNP Data

Roded Sharan, Ron Shamir, Gad Kimmel, 2003, WABI.

Preface: Special RECOMB 2000 Issue

Ron Shamir, 2000, J. Comput. Biol..

Topology-Free Querying of Protein Interaction Networks

Roded Sharan, Richard M. Karp, Ron Shamir, 2009, RECOMB.

The Degenerate Primer Design Problem

Ron Shamir, Chaim Linhart, R. Shamir, 2002, ISMB.

Faster subtree isomorphism

Ron Shamir, Dekel Tsur, R. Shamir, 1997, Proceedings of the Fifth Israeli Symposium on Theory of Computing and Systems.

Incomplete Directed Perfect Phylogeny

Ron Shamir, Tal Pupko, Roded Sharan, 2000, CPM.

Faster Subtree Isomorphism

Ron Shamir, Dekel Tsur, 1999, J. Algorithms.

Computational Problems in Perfect Phylogeny Haplotyping: Typing without Calling the Allele

Ron Shamir, Itsik Pe'er, Jacques S. Beckmann, 2008, IEEE ACM Trans. Comput. Biol. Bioinform..

Tractability of Parameterized Completion Problems on Chordal, Strongly Chordal, and Proper Interval Graphs

Haim Kaplan, Robert E. Tarjan, Ron Shamir, 1999, SIAM J. Comput..

Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate

Ron Shamir, David Amar, Daniel Yekutieli, 2016, PLoS Comput. Biol..

Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case

Ron Shamir, Guy Karlebach, Guy Karlebach, 2010, BMC Systems Biology.

Algorithms and Complexity for Reasoning about Time

Ron Shamir, Martin Charles Golumbic, M. Golumbic, 1992, AAAI.

Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing

Ron Shamir, Carl Kingsford, Guillaume Marçais, 2017, PLoS Comput. Biol..

2018 outstanding contributions to ISCB award: Russ Altman

Ron Shamir, Diane E. Kovats, Christiana N. Fogg, 2018, PLoS Comput. Biol..

Sorting by Cuts, Joins, and Whole Chromosome Duplications

Ron Shamir, Ron Zeira, R. Shamir, 2017, J. Comput. Biol..

Computational dissection of regulatory networks using diverse high-throughput data

Ron Shamir, 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..

Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression

Ron Shamir, David Amar, Hershel Safer, 2013, PLoS Comput. Biol..

Advanced topics in Graph Algorithms

Ron Shamir, R. Shamir, 1994 .

On the Complexity of Positional Sequencing by Hybridization

Ron Shamir, Amir Ben-Dor, Roded Sharan, 2002, J. Comput. Biol..

PlasClass improves plasmid sequence classification

Ron Shamir, David Pellow, Itzik Mizrahi, 2019, bioRxiv.

RECOMB 2000 : proceedings of the Fourth annual international conference on computational molecular biology : April 8-11, 2000, Tokyo, Japan

Satoru Miyano, Ron Shamir, Sorin Istrail, 2000 .

Satisfiability Problems on Intervals and Unit Intervals

Ron Shamir, Itsik Pe'er, R. Shamir, 1997, Theor. Comput. Sci..

NEMO: cancer subtyping by integration of partial multi-omic data

Ron Shamir, Nimrod Rappoport, R. Shamir, 2018, bioRxiv.

Faucet: streaming de novo assembly graph construction

Ron Shamir, Roye Rozov, Gil Goldshlager, 2017 .

The Factor Graph Network Model for Biological Systems

Ron Shamir, Amos Tanay, Irit Gat-Viks, 2005, RECOMB.

Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions

Ron Shamir, Ron Zeira, R. Shamir, 2018, Bioinform..

2018 ISCB Overton Prize awarded to Cole Trapnell

Ron Shamir, Diane E. Kovats, Christiana N. Fogg, 2018, PLoS computational biology.

The maximum subforest problem: approximation and exact algorithms

Ron Shamir, Dekel Tsur, R. Shamir, 1998, SODA '98.

A fully dynamic algorithm for modular decomposition and recognition of cographs

Roded Sharan, Ron Shamir, R. Sharan, 2004, Discret. Appl. Math..

Pathwidth, Bandwidth, and Completion Problems to Proper Interval Graphs with Small Cliques

Haim Kaplan, Ron Shamir, R. Shamir, 1996, SIAM J. Comput..

Complexity and algorithms for copy-number evolution problems

Ron Shamir, Benjamin J. Raphael, Meirav Zehavi, 2017, Algorithms for Molecular Biology.

PRODIGY: personalized prioritization of driver genes

Ron Shamir, Gal Dinstag, 2020, Bioinform..

PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets

Ron Shamir, Dvir Netanely, Neta Stern, 2019, bioRxiv.

Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data

Roded Sharan, Richard M. Karp, Ron Shamir, 2004, J. Comput. Biol..

MONET: Multi-omic patient module detection by omic selection

Ron Shamir, Nimrod Rappoport, Roy Safra, 2020, bioRxiv.

ADEPTUS: a discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases

Ron Shamir, David Amar, Amir Vizel, 2018, Bioinform..

PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets

Ron Shamir, Dvir Netanely, Neta Stern, 2019, BMC Bioinformatics.

Improving the performance of minimizers and winnowing schemes

Ron Shamir, Carl Kingsford, Guillaume Marçais, 2017, bioRxiv.

A Polynomial Algorithm for Balancing Acyclic Data Flow Graphs

Endre Boros, Ron Shamir, Peter L. Hammer, 1992, IEEE Trans. Computers.

Foreword

Ron Shamir, Sorin Istrail, Pavel A. Pevzner, 2000, Discrete Applied Mathematics.

The Restriction Scaffold Problem

Richard M. Karp, Ron Shamir, Benno Schwikowski, 2003, J. Comput. Biol..

The median problems for breakpoints are NP-complete

Ron Shamir, Itsik Pe'er, R. Shamir, 1998, Electron. Colloquium Comput. Complex..

The Incomplete Perfect Phylogeny Haplotype Problem

Ron Shamir, Gad Kimmel, R. Shamir, 2005, J. Bioinform. Comput. Biol..

Four Strikes Against Physical Mapping of DNA

Haim Kaplan, Paul W. Goldberg, Ron Shamir, 1995, J. Comput. Biol..

Incomplete Directed Perfect Phylogeny

Ron Shamir, Roded Sharan, Itsik Pe'er, 2000, CPM.

Sorting by Cuts, Joins and Whole Chromosome Duplications

Ron Shamir, Ron Zeira, R. Shamir, 2017, CPM.

Efficient algorithms for minimum-cost flow problems with piecewise-linear convex costs

Ron Shamir, Yaron Pinto, 2005, Algorithmica.

A polynomial algorithm for an integer quadratic non-separable transportation problem

Ron Shamir, J. George Shanthikumar, Dorit S. Hochbaum, 1992, Math. Program..

An O(n log2 n) Algorithm for the Maximum Weighted Tardiness Problem

Ron Shamir, Dorit S. Hochbaum, 1989, Inf. Process. Lett..

Message from the ISCB: 2018 Outstanding Contributions to ISCB Award: Russ Altman

Ron Shamir, Diane E. Kovats, Christiana N. Fogg, 2018, Bioinform..

An O(n3/2sqrt(log(n))) algorithm for sorting by reciprocal translocations

Ron Shamir, Michal Ozery-Flato, 2011, J. Discrete Algorithms.

A clustering algorithm based on graph connectivity

Ron Shamir, Erez Hartuv, R. Shamir, 2000, Inf. Process. Lett..

Minimizing the number of tardy job units under release time constraints

Ron Shamir, Dorit S. Hochbaum, 1990, Discret. Appl. Math..

Detecting Highways of Horizontal Gene Transfer

Ron Shamir, J. Peter Gogarten, Mukul S. Bansal, 2011, J. Comput. Biol..

Large scale sequencing by hybridization

Ron Shamir, Dekel Tsur, R. Shamir, 2001, J. Comput. Biol..

Cluster Graph Modification Problems

Roded Sharan, Ron Shamir, Dekel Tsur, 2002, WG.

Systematic inference of highways of horizontal gene transfer in prokaryotes

Ron Shamir, Timothy J. Harlow, J. Peter Gogarten, 2013, Bioinform..

A Block-Free Hidden Markov Model for Genotypes and Its Application to Disease Association

Ron Shamir, Gad Kimmel, R. Shamir, 2005, J. Comput. Biol..

Detecting Highways of Horizontal Gene Transfer

Ron Shamir, J. Peter Gogarten, Mukul S. Bansal, 2010, RECOMB-CG.

RAP: Accurate and Fast Motif Finding Based on Protein-Binding Microarray Data

Ron Shamir, Yaron Orenstein, Eran Mick, 2013, J. Comput. Biol..

A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs

Roded Sharan, Ron Shamir, Pavol Hell, 1999, SIAM J. Comput..

Modularity, evolution and regulation in bionetworks

Ron Shamir, Amos Tanay, Aviv Regev, 2005 .

Assessing the Quality of Whole Genome Alignments in Bacteria

Ron Shamir, Firas Swidan, R. Shamir, 2009, Adv. Bioinformatics.

Biclustering Algorithms: A Survey

Roded Sharan, Ron Shamir, Amos Tanay, 2007 .

Special issue on computational molecular biology

Ming Li, Richard M. Karp, Ron Shamir, 2007, J. Comput. Syst. Sci..

Bioinformatics for Biologists: Glossary

Ron Shamir, Pavel Pevzner, P. Pevzner, 2011 .

Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, RECOMB 2000, Tokyo, Japan, April 8-11, 2000

Satoru Miyano, Ron Shamir, Sorin Istrail, 1997, Annual International Conference on Research in Computational Molecular Biology.

Some Computational Challenges in Today's Bio-medicine

Ron Shamir, 2006, ESA.

Characterization and algorithms for greedily solvable transportation problems

Ron Shamir, Brenda L. Dietrich, 1990, SODA '90.

On the efficiency of the simplex method (linear programming, complexity, algorithms)

Ron Shamir, R. Shamir, 1984 .

Scoring clustering solutions by their biological relevance

Ron Shamir, Irit Gat-Viks, Roded Sharan, 2003, Bioinform..

Using Computational Biology Methods to Improve Post-silicon Microprocessor Testing

Ron Shamir, Dmitry Korchemny, Ron Zeira, 2011, Haifa Verification Conference.

A Linear-Time Algorithm for the Copy Number Transformation Problem

Ron Shamir, Meirav Zehavi, Ron Zeira, 2017, J. Comput. Biol..

Gene Regulation, Protein Networks and Disease: A Computational Perspective

Ron Shamir, 2012, CPM.

Discovering Transcriptional Modules by Combined Analysis of Expression Profiles and Regulatory Sequences

Ron Shamir, Chaim Linhart, Igor Ulitsky, 2010, RECOMB.

Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data

Roded Sharan, Richard M. Karp, Ron Shamir, 2005, J. Comput. Biol..

Construction of Physical Maps from Oligonucleotide Fingerprints Data

Guy Mayraz, Ron Shamir, 1999, J. Comput. Biol..

A polynomial approximation algorithm for the minimum fill-in problem

Roded Sharan, Ron Shamir, Assaf Natanzon, 1998, STOC '98.

Maximum likelihood resolution of multi-block genotypes

Ron Shamir, Gad Kimmel, R. Shamir, 2004, RECOMB.

Bioinformatics for Biologists

Ron Shamir, Pavel Pevzner, 2011 .

A Faster Algorithm for Simultaneous Alignment and Folding of RNA

Ron Shamir, Michal Ziv-Ukelson, Irit Gat-Viks, 2010, J. Comput. Biol..

Preface: 2nd Satellite Meeting on Bioinformatics Education, Research in Computational Molecular Biology (RECOMB-BE 2010)

Ron Shamir, Pavel A. Pevzner, P. Pevzner, 2011, J. Comput. Biol..

Computational expansion of genetic networks

Ron Shamir, Amos Tanay, 2001, ISMB.

Chain functions and scoring functions in genetic networks

Ron Shamir, Irit Gat-Viks, R. Shamir, 2003, ISMB.

GEVALT: An integrated software tool for genotype analysis

Ron Shamir, Gad Kimmel, Ofir Davidovich, 2007, BMC Bioinformatics.

A simpler and faster 1.5-approximation algorithm for sorting by transpositions

Ron Shamir, Tzvika Hartman, R. Shamir, 2006, Inf. Comput..

Handling long targets and errors in sequencing by hybridization

Eran Halperin, Ron Shamir, Tzvika Hartman, 2002, RECOMB '02.

Complexity classification of some edge modification problems

Roded Sharan, Ron Shamir, Assaf Natanzon, 2001, Discret. Appl. Math..

Realizing Interval Graphs with Size and Distance Constraints

Ron Shamir, Itsik Pe'er, R. Shamir, 1997, SIAM J. Discret. Math..

The Domatic Number Problem on Some Perfect Graph Families

Haim Kaplan, Ron Shamir, 1994, Inf. Process. Lett..

2018 ISCB accomplishments by a senior scientist award

Ron Shamir, Diane E. Kovats, Christiana N. Fogg, 2018, PLoS Comput. Biol..

A Family of Simplex Variants Solving an m × d Linear Program in Expected Number of Pivot Steps Depending on d Only

Richard M. Karp, Ron Shamir, Ilan Adler, 1986, Math. Oper. Res..

The EXPANDER Integrated Platform for Transcriptome Analysis.

Roded Sharan, Ron Shamir, Ran Elkon, 2019, Journal of molecular biology.

Sorting Genomes with Centromeres by Translocations

Ron Shamir, Michal Ozery-Flato, R. Shamir, 2008, J. Comput. Biol..

SPIKE: a database of highly curated human signaling pathways

Ron Shamir, Ran Elkon, Eyal David, 2010, Nucleic Acids Res..

A computational micro primer

Ron Shamir, Pavel Pevzner, Pavel A. Pevzner, 2011 .

Matching with don't-cares and a small number of mismatches

Ron Shamir, Chaim Linhart, 2009, Inf. Process. Lett..

Greedily Solvable Transportation Networks and Edge-Guided Vertex Elimination

Ron Shamir, Ilan Adler, 1993 .

Interval Graphs with Side (and Size) Constraints

Ron Shamir, Itsik Pe'er, R. Shamir, 1995, ESA.

Tag SNP selection in genotype data for maximizing SNP prediction accuracy

Eran Halperin, Ron Shamir, Gad Kimmel, 2005, ISMB.

Multi-omic and multi-view clustering algorithms: review and cancer benchmark

Ron Shamir, Nimrod Rappoport, 2018 .

A simplex variant solving an m times d linear program in O(min(m2, d2) expected number of pivot steps

Richard M. Karp, Ron Shamir, Ilan Adler, 1987, J. Complex..

On the Complexity of Positional Sequencing by Hybridization

Roded Sharan, Ron Shamir, Itsik Pe'er, 1999, CPM.

Cluster graph modification problems

Roded Sharan, Ron Shamir, Dekel Tsur, 2002, Discret. Appl. Math..

SPIKE – a database, visualization and analysis tool of cellular signaling pathways

Ron Shamir, Ran Elkon, Jackie Assa, 2008, BMC Bioinformatics.

2020 ISCB Overton Prize: Jian Peng

Ron Shamir, Diane E. Kovats, Christiana N. Fogg, 2021, Bioinform..

2020 Outstanding contributions to ISCB award: Judith Blake

Ron Shamir, Diane E. Kovats, Christiana N. Fogg, 2021, Bioinform..

2020 ISCB accomplishments by a Senior Scientist Award: Steven Salzberg

Ron Shamir, Diane E. Kovats, Christiana N. Fogg, 2021, Bioinform..

Improving the efficiency of de Bruijn graph construction using compact universal hitting sets

Ron Shamir, Yaron Orenstein, Lianrong Pu, 2021, BCB.

2020 ISCB Innovatory Award: Xiaole Shirley Liu

Ron Shamir, Diane E. Kovats, Christiana N. Fogg, 2021, Bioinform..

BARCODE: fast lossless compression via cascading bloom filters

Eran Halperin, Ron Shamir, Roye Rozov, 2014 .

Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome

Ron Shamir, Annelyse Thévenin, Liat Ein-Dor, 2014, Nucleic acids research.

Parallel Profiling of the Transcriptome, Cistrome, and Epigenome in the Cellular Response to Ionizing Radiation

Ron Shamir, Ran Elkon, Hans Lehrach, 2014, Science Signaling.

On the frequency of genome rearrangement events in cancer karyotypes

Ron Shamir, Michal Ozery-Flato, R. Shamir, 2007 .

A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs

Ron Shamir, Yitzhak Pilpel, Michal Lapidot, 2005, Genome Biology.

PIVOT : Protein Interactions VisualizatiOn Tool

Ron Shamir, Nir Orlev, Yosef Shiloh, 2003 .

MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data

Ron Shamir, Irit Gat-Viks, Igor Ulitsky, 2008, Genome Biology.

Integration of Transcriptomics, Proteomics, and MicroRNA Analyses Reveals Novel MicroRNA Regulation of Targets in the Mammalian Inner Ear

Ron Shamir, Ran Elkon, Amiel A. Dror, 2011, PloS one.

Detecting pathways transcriptionally correlated with clinical parameters.

Ron Shamir, Igor Ulitsky, R. Shamir, 2008, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.

Functional genomic delineation of TLR-induced transcriptional networks

Ron Shamir, Ran Elkon, Chaim Linhart, 2007, BMC Genomics.

HTS-IBIS: fast and accurate inference of binding site motifs from HT-SELEX data

Ron Shamir, Yaron Orenstein, R. Shamir, 2015, bioRxiv.

DEGAS: De Novo Discovery of Dysregulated Pathways in Human Diseases

Richard M. Karp, Ron Shamir, Igor Ulitsky, 2010, PloS one.

DEFOG: a practical scheme for deciphering families of genes.

Roded Sharan, Ron Shamir, Miriam Khen, 2002, Genomics.

Erratum to: Expression and methylation patterns partition luminal-A breast tumors into distinct prognostic subgroups

Ron Shamir, Dvir Netanely, R. Shamir, 2016, Breast Cancer Research.

Genome Rearrangement Problems with Single and Multiple Gene Copies: A Review

Ron Shamir, Ron Zeira, R. Shamir, 2019, Bioinformatics and Phylogenetics.

Different sets of QTLs influence fitness variation in yeast

Ron Shamir, Martin Kupiec, Ofer Lavi, 2010, Molecular systems biology.

Degenerate Primer Design

Ron Shamir, Chaim Linhart, R. Shamir, 2007 .

Constructing module maps for integrated analysis of heterogeneous biological networks

Ron Shamir, David Amar, R. Shamir, 2014, Nucleic acids research.

Assessment of Algorithms for Inferring Positional Weight Matrix Motifs of Transcription Factor Binding Sites Using Protein Binding Microarray Data

Ron Shamir, Yaron Orenstein, Chaim Linhart, 2012, PloS one.

Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets

Ron Shamir, David Amar, Shai Izraeli, 2015, Nucleic acids research.

Allegro: Analyzing expression and sequence in concert to discover regulatory programs

Ron Shamir, Chaim Linhart, Igor Ulitsky, 2009, Nucleic acids research.

Convex separable minimization over partial order constraints

Endre Boros, Ron Shamir, R. Shamir, 1991 .

Deciphering Transcriptional Regulatory Elements That Encode Specific Cell-Cycle Phasing by Comparative Genomics Analysis

Ron Shamir, Ran Elkon, Chaim Linhart, 2005, Cell cycle.

A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription

Ron Shamir, Israel Steinfeld, Martin Kupiec, 2007, Nature Genetics.

Comprehensive MicroRNA Profiling Reveals a Unique Human Embryonic Stem Cell Signature Dominated by a Single Seed Sequence

Ron Shamir, Jing Chen, Igor Ulitsky, 2008, Stem cells.

A non-EST-based method for exon-skipping prediction.

Ron Shamir, Rotem Sorek, Gil Ast, 2004, Genome research.

Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium

Ron Shamir, Amos Tanay, Israel Steinfeld, 2005, Molecular systems biology.

SlimPLS: A Method for Feature Selection in Gene Expression-Based Disease Classification

Ron Shamir, Gideon Dror, R. Shamir, 2009, PloS one.

A randomization test for controlling population stratification in whole-genome association studies.

Michael I. Jordan, Eran Halperin, Ron Shamir, 2007, American journal of human genetics.

Perfect Completion and Deletion in Random

Ron Shamir, GraphsAssaf Natanzon, 2007 .

A computational method for resequencing long DNA targets by universal oligonucleotide arrays

Ron Shamir, Itsik Pe'er, Naama Arbili, 2002, Proceedings of the National Academy of Sciences of the United States of America.

The canine olfactory subgenome.

Ron Shamir, Tsviya Olender, Miriam Khen, 2004, Genomics.

Assessing the capabilities of geospatial data to map built structures and evaluate their bushfire threat.

Ron Shamir, Kim Lowell, Andreia Siqueira, 2009 .

Evidence of TAF1 dysfunction in peripheral models of X-linked dystonia-parkinsonism

Ron Shamir, Christine Klein, Uwe Walter, 2016, Cellular and Molecular Life Sciences.

Dissection of a DNA-damage-induced transcriptional network using a combination of microarrays, RNA interference and computational promoter analysis

Ron Shamir, Ran Elkon, Gideon Rechavi, 2005, Genome Biology.

A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking

Ron Shamir, Nevan J Krogan, Matthias Mann, 2010, Nature Structural &Molecular Biology.

Recycler: an algorithm for detecting plasmids from de novo assembly graphs

Eran Halperin, Ron Shamir, Roye Rozov, 2016 .

GERBIL: Genotype resolution and block identification using likelihood.

Ron Shamir, Gad Kimmel, R. Shamir, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Probabilistic Analysis in Linear Programming

Ron Shamir, R. Shamir, 1993 .