Ron Shamir

According to our database, Ron Shamir authored at least 167 papers between 1986 and 2023.

Collaborative distances:

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

2023

Time-dependent Iterative Imputation for Multivariate Longitudinal Clinical Data.

Omer Noy, Ron Shamir

CoRR, 2023

2022

Parameterized syncmer schemes improve long-read mapping.

Abhinav Dutta, David Pellow, Ron Shamir

PLoS Comput. Biol., October, 2022

Data Set-Adaptive Minimizer Order Reduces Memory Usage in <i>k</i>-Mer Counting.

Dan Flomin, David Pellow, Ron Shamir

J. Comput. Biol., 2022

The DOMINO web-server for active module identification analysis.

Hagai Levi, Nima Rahmanian, Ran Elkon, Ron Shamir

Bioinform., 2022

2021

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

Ron Zeira, Ron Shamir

Bioinform., 2021

2020 Outstanding contributions to ISCB award: Judith Blake.

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

Bioinform., 2021

2020 ISCB accomplishments by a Senior Scientist Award: Steven Salzberg.

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

Bioinform., 2021

2020 ISCB Innovatory Award: Xiaole Shirley Liu.

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

Bioinform., 2021

2020 ISCB Overton Prize: Jian Peng.

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

Bioinform., 2021

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

Yael Ben-Ari, Dan Flomin, Lianrong Pu, Yaron Orenstein, Ron Shamir

Proceedings of the BCB '21: 12th ACM International Conference on Bioinformatics, 2021

2020

MONET: Multi-omic module discovery by omic selection.

Nimrod Rappoport, Roy Safra, Ron Shamir

PLoS Comput. Biol., 2020

PlasClass improves plasmid sequence classification.

David Pellow, Itzik Mizrahi, Ron Shamir

PLoS Comput. Biol., 2020

2019 Outstanding Contributions to ISCB Awarded to Barb Bryant.

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

Bioinform., 2020

Bonnie Berger named ISCB 2019 ISCB Accomplishments by a Senior Scientist Award recipient.

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

Bioinform., 2020

PRODIGY: personalized prioritization of driver genes.

Gal Dinstag, Ron Shamir

Bioinform., 2020

2019

2019 ISCB Innovator Award recognizes William Stafford Noble.

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

F1000Research, 2019

2019 ISCB Overton Prize: Christophe Dessimoz.

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

F1000Research, 2019

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

Dvir Netanely, Neta Stern, Itay Laufer, Ron Shamir

BMC Bioinform., 2019

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

Nimrod Rappoport, Ron Shamir

Bioinform., 2019

2018

2018 ISCB accomplishments by a senior scientist award.

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

PLoS Comput. Biol., 2018

2018 outstanding contributions to ISCB award: Russ Altman.

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

PLoS Comput. Biol., 2018

Faucet: streaming de novo assembly graph construction.

Roye Rozov, Gil Goldshlager, Eran Halperin, Ron Shamir

Bioinform., 2018

2018 ISCB Innovator Award recognizes M. Madan Babu.

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

Bioinform., 2018

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

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

Bioinform., 2018

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

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

Bioinform., 2018

2018 ISCB Overton Prize awarded to Cole Trapnell.

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

Bioinform., 2018

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

David Amar, Amir Vizel, Carmit Levy, Ron Shamir

Bioinform., 2018

2017

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

Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford

PLoS Comput. Biol., 2017

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

David Amar, Ron Shamir, Daniel Yekutieli

PLoS Comput. Biol., 2017

A Linear-Time Algorithm for the Copy Number Transformation Problem.

Ron Zeira, Meirav Zehavi, Ron Shamir

J. Comput. Biol., 2017

Sorting by Cuts, Joins, and Whole Chromosome Duplications.

Ron Zeira, Ron Shamir

J. Comput. Biol., 2017

Reconstructing cancer karyotypes from short read data: the half empty and half full glass.

Rami Eitan, Ron Shamir

BMC Bioinform., 2017

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

Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, Ron Shamir

Bioinform., 2017

Improving the performance of minimizers and winnowing schemes.

Guillaume Marçais, David Pellow, Daniel Bork, Yaron Orenstein, Ron Shamir, Carl Kingsford

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

2016

Compact Universal k-mer Hitting Sets.

Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford

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

2015

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

Yaron Orenstein, Ron Shamir

Bioinform., 2015

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

David Amar, Daniel Yekutieli, Adi Maron-Katz, Talma Hendler, Ron Shamir

Bioinform., 2015

2014

Fast lossless compression via cascading Bloom filters.

Roye Rozov, Ron Shamir, Eran Halperin

BMC Bioinform., 2014

2013

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

David Amar, Hershel Safer, Ron Shamir

PLoS Comput. Biol., 2013

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

Yaron Orenstein, Eran Mick, Ron Shamir

J. Comput. Biol., 2013

Systematic inference of highways of horizontal gene transfer in prokaryotes.

Mukul S. Bansal, Guy Banay, Timothy J. Harlow, J. Peter Gogarten, Ron Shamir

Bioinform., 2013

2012

Network-Induced Classification Kernels for Gene Expression Profile Analysis.

Ofer Lavi, Gideon Dror, Ron Shamir

J. Comput. Biol., 2012

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

Guy Karlebach, Ron Shamir

J. Comput. Biol., 2012

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

Roye Rozov, Eran Halperin, Ron Shamir

BMC Bioinform., 2012

Gene Regulation, Protein Networks and Disease: A Computational Perspective.

Ron Shamir

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

2011

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

Mukul S. Bansal, Ron Shamir

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

SPIKE: a database of highly curated human signaling pathways.

Arnon Paz, Zippora Brownstein, Yaara Ber, Shani Bialik, Eyal David, Dorit Sagir, Igor Ulitsky, Ran Elkon, Adi Kimchi, Karen B. Avraham, Yosef Shiloh, Ron Shamir

Nucleic Acids Res., 2011

An O(n^3/2sqrt(log(n))) algorithm for sorting by reciprocal translocations.

Michal Ozery-Flato, Ron Shamir

J. Discrete Algorithms, 2011

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

Pavel A. Pevzner, Ron Shamir

J. Comput. Biol., 2011

Detecting Highways of Horizontal Gene Transfer.

Mukul S. Bansal, Guy Banay, J. Peter Gogarten, Ron Shamir

J. Comput. Biol., 2011

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

Irit Gat-Viks, Renana Meller, Martin Kupiec, Ron Shamir

Proceedings of the Research in Computational Molecular Biology, 2011

Using Computational Biology Methods to Improve Post-silicon Microprocessor Testing.

Ron Zeira, Dmitry Korchemny, Ron Shamir

Proceedings of the Hardware and Software: Verification and Testing, 2011

2010

A Faster Algorithm for Simultaneous Alignment and Folding of RNA.

Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir

J. 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

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

Guy Karlebach, Ron Shamir

BMC Syst. Biol., 2010

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

Yonit Halperin, Chaim Linhart, Igor Ulitsky, Ron Shamir

Proceedings of the Research in Computational Molecular Biology, 2010

Detecting Highways of Horizontal Gene Transfer.

Mukul S. Bansal, J. Peter Gogarten, Ron Shamir

Proceedings of the Comparative Genomics - 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

Faster pattern matching with character classes using prime number encoding.

Chaim Linhart, Ron Shamir

J. Comput. Syst. Sci., 2009

Sorting Cancer Karyotypes by Elementary Operations.

Michal Ozery-Flato, Ron Shamir

J. Comput. Biol., 2009

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

Chaim Linhart, Ron Shamir

Inf. Process. Lett., 2009

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

Ofir Davidovich, Eran Halperin, Gad Kimmel, Ron Shamir

Commun. Inf. Syst., 2009

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

Igor Ulitsky, Ron Shamir

Bioinform., 2009

Assessing the Quality of Whole Genome Alignments in Bacteria.

Firas Swidan, Ron Shamir

Adv. Bioinformatics, 2009

2008

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

Tamar Barzuza, Jacques S. Beckmann, Ron Shamir, Itsik Pe'er

IEEE ACM Trans. Comput. Biol. Bioinform., 2008

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

Daniela Raijman, Ron Shamir, Amos Tanay

PLoS Comput. Biol., 2008

Sorting Genomes with Centromeres by Translocations.

Michal Ozery-Flato, Ron Shamir

J. Comput. Biol., 2008

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

Ran Elkon, Rita Vesterman, Nira Amit, Igor Ulitsky, Idan Zohar, Mali Weisz, Gilad Mass, Nir Orlev, Giora Sternberg, Ran Blekhman, Jackie Assa, Yosef Shiloh, Ron Shamir

BMC Bioinform., 2008

A Faster Algorithm for RNA Co-folding.

Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir

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

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

Igor Ulitsky, Richard M. Karp, Ron Shamir

Proceedings of the Research in Computational Molecular Biology, 2008

2007

Improved algorithms for the random cluster graph model.

Ron Shamir, Dekel Tsur

Random Struct. Algorithms, 2007

Special issue on computational molecular biology.

Richard M. Karp, Ming Li, Pavel A. Pevzner, Ron Shamir

J. Comput. Syst. Sci., 2007

Sorting by Reciprocal Translocations via Reversals Theory.

Michal Ozery-Flato, Ron Shamir

J. Comput. Biol., 2007

Preface.

Sorin Istrail, Pavel A. Pevzner, Ron Shamir

Discret. Appl. Math., 2007

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

Igor Ulitsky, Ron Shamir

BMC Syst. Biol., 2007

GEVALT: An integrated software tool for genotype analysis.

Ofir Davidovich, Gad Kimmel, Ron Shamir

BMC Bioinform., 2007

Rearrangements in Genomes with Centromeres Part I: Translocations.

Michal Ozery-Flato, Ron Shamir

Proceedings of the Research in Computational Molecular Biology, 2007

2006

Reconstructing Chain Functions in Genetic Networks.

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

SIAM J. Discret. Math., 2006

A Probabilistic Methodology for Integrating Knowledge and Experiments on Biological Networks.

Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir

J. Comput. Biol., 2006

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

Tzvika Hartman, Ron Shamir

Inf. Comput., 2006

Sorting by Translocations Via Reversals Theory.

Michal Ozery-Flato, Ron Shamir

Proceedings of the Comparative Genomics, 2006

Some Computational Challenges in Today's Bio-medicine.

Ron Shamir

Proceedings of the Algorithms, 2006

2005

Guest Editors' foreword.

Richard M. Karp, Ming Li, Pavel A. Pevzner, Ron Shamir

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

The Degenerate Primer Design Problem: Theory and Applications.

Chaim Linhart, Ron Shamir

J. Comput. Biol., 2005

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

Gad Kimmel, Ron Shamir

J. Comput. Biol., 2005

The Incomplete Perfect Phylogeny Haplotype Problem.

Gad Kimmel, Ron Shamir

J. Bioinform. 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

Accurate identification of alternatively spliced exons using support vector machine.

Gideon Dror, Rotem Sorek, Ron Shamir

Bioinform., 2005

The Factor Graph Network Model for Biological Systems.

Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir

Proceedings of the Research in Computational Molecular Biology, 2005

Tag SNP selection in genotype data for maximizing SNP prediction accuracy.

Eran Halperin, Gad Kimmel, Ron Shamir

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

Multilevel Modeling and Inference of Transcription Regulation.

Amos Tanay, Ron Shamir

J. Comput. Biol., 2004

Modeling and Analysis of Heterogeneous Regulation in Biological Networks.

Irit Gat-Viks, Amos Tanay, Ron Shamir

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

A note on tolerance graph recognition.

Ryan B. Hayward, Ron Shamir

Discret. Appl. Math., 2004

PIVOT: Protein Interacions VisualizatiOn Tool.

Nir Orlev, Ron Shamir, Yosef Shiloh

Bioinform., 2004

Maximum likelihood resolution of multi-block genotypes.

Gad Kimmel, Ron Shamir

Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004

Computational Dissection of Regulatory Networks Using Diverse High-Throughput Data.

Ron Shamir

Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

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

Tamar Barzuza, Jacques S. Beckmann, Ron Shamir, Itsik Pe'er

Proceedings of the Combinatorial Pattern Matching, 15th Annual Symposium, 2004

2003

Handling Long Targets and Errors in Sequencing by Hybridization.

Eran Halperin, Shay Halperin, Tzvika Hartman, Ron Shamir

J. Comput. Biol., 2003

The Restriction Scaffold Problem.

Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Ron Shamir

J. Comput. Biol., 2003

Two Notes on Genome Rearrangement.

Michal Ozery-Flato, Ron Shamir

J. Bioinform. Comput. Biol., 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

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

Amos Tanay, Ron Shamir

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

Chain functions and scoring functions in genetic networks.

Irit Gat-Viks, Ron Shamir

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

2002

Foreword.

Ming Li, Pavel A. Pevzner, Ron Shamir

J. Comput. Syst. Sci., 2002

Large Scale Sequencing by Hybridization.

Ron Shamir, Dekel Tsur

J. Comput. Biol., 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

The degenerate primer design problem.

Chaim Linhart, 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

Computational expansion of genetic networks.

Amos Tanay, Ron Shamir

Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

2000

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

Assaf Natanzon, Ron Shamir, Roded Sharan

SIAM J. Comput., 2000

Preface: Special RECOMB 2000 Issue.

Ron Shamir

J. Comput. Biol., 2000

Algorithms for Optical Mapping.

Richard M. Karp, Ron Shamir

J. Comput. Biol., 2000

An Algorithm Combining Discrete and Continuous Methods for Optical Mapping.

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

J. Comput. Biol., 2000

A clustering algorithm based on graph connectivity.

Erez Hartuv, Ron Shamir

Inf. Process. Lett., 2000

Foreword.

Sorin Istrail, Pavel A. Pevzner, Ron Shamir

Discret. Appl. Math., 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

Spectrum Alignment: Efficient Resequencing by Hybridization.

Itsik Pe'er, 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

1999

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

Haim Kaplan, Ron Shamir, Robert Endre Tarjan

SIAM J. Comput., 1999

A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals.

Haim Kaplan, Ron Shamir, Robert Endre Tarjan

SIAM J. Comput., 1999

Construction of Physical Maps from Oligonucleotide Fingerprints Data.

Guy Mayraz, Ron Shamir

J. Comput. Biol., 1999

Clustering Gene Expression Patterns.

Amir Ben-Dor, Ron Shamir, Zohar Yakhini

J. Comput. Biol., 1999

Faster Subtree Isomorphism.

Ron Shamir, Dekel Tsur

J. Algorithms, 1999

Bounded Degree Interval Sandwich Problems.

Haim Kaplan, Ron Shamir

Algorithmica, 1999

An algorithm for clustering cDNAs for gene expression analysis.

Erez Hartuv, Armin O. Schmitt, Jörg Lange, Sebastian Meier-Ewert, Hans Lehrach, Ron Shamir

Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999

1998

The median problems for breakpoints are NP-complete

Itsik Pe'er, Ron Shamir

Electron. Colloquium Comput. Complex., 1998

The Maximum Subforest Problem: Approximation and Exact Algorithms (Extended Abstract).

Ron Shamir, Dekel Tsur

Proceedings of the Ninth Annual ACM-SIAM Symposium on Discrete Algorithms, 1998

1997

Satisfiability Problems on Intervals and Unit Intervals.

Itsik Pe'er, Ron Shamir

Theor. Comput. Sci., 1997

Realizing Interval Graphs with Size and Distance Constraints.

Itsik Pe'er, Ron Shamir

SIAM J. Discret. Math., 1997

1996

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

Haim Kaplan, Ron Shamir

SIAM J. Comput., 1996

Physical Maps and Interval Sandwich Problems: Bounded Degrees Help.

Haim Kaplan, Ron Shamir

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

1995

Four Strikes Against Physical Mapping of DNA.

Paul W. Goldberg, Martin Charles Golumbic, Haim Kaplan, Ron Shamir

J. Comput. Biol., 1995

Graph Sandwich Problems.

Martin Charles Golumbic, Haim Kaplan, Ron Shamir

J. Algorithms, 1995

Interval Graphs with Side (and Size) Constraints.

Itsik Pe'er, Ron Shamir

Proceedings of the Algorithms, 1995

1994

The Domatic Number Problem on Some Perfect Graph Families.

Haim Kaplan, Ron Shamir

Inf. Process. Lett., 1994

Balancing Problems in Acyclic Networks.

Endre Boros, Peter L. Hammer, Mark E. Hartmann, Ron Shamir

Discret. Appl. Math., 1994

Efficient Algorithms for Minimum-Cost Flow Problems with Piecewise-Linear Convex Costs.

Yaron Pinto, Ron Shamir

Algorithmica, 1994

Tractability of parameterized completion problems on chordal and interval graphs: Minimum Fill-in and Physical Mapping

Haim Kaplan, Ron Shamir, Robert Endre Tarjan

Proceedings of the 35th Annual Symposium on Foundations of Computer Science, 1994

1993

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

Ilan Adler, Ron Shamir

Math. Program., 1993

Complexity and Algorithms for Reasoning about Time: A Graph-Theoretic Approach.

Martin Charles Golumbic, Ron Shamir

J. ACM, 1993

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

Ron Shamir

Discret. Math., 1993

Monge and Feasibility Sequences in General Flow Problems.

Ilan Adler, Alan J. Hoffman, Ron Shamir

Discret. Appl. Math., 1993

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

Martin Charles Golumbic, Haim Kaplan, Ron Shamir

Proceedings of the Graph-Theoretic Concepts in Computer Science, 1993

1992

A Polynomial Algorithm for Balancing Acyclic Data Flow Graphs.

Endre Boros, Peter L. Hammer, Ron Shamir

IEEE Trans. Computers, 1992

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

Dorit S. Hochbaum, Ron Shamir, J. George Shanthikumar

Math. Program., 1992

Interval Graphs, Interval Orders and the Consistency of Temporal Events.

Martin Charles Golumbic, Ron Shamir

Proceedings of the Theory of Computing and Systems, 1992

Algorithms and Complexity for Reasoning about Time.

Martin Charles Golumbic, Ron Shamir

Proceedings of the 10th National Conference on Artificial Intelligence, 1992

1991

Strongly Polynomial Algorithms for the High Multiplicity Scheduling Problem.

Dorit S. Hochbaum, Ron Shamir

Oper. Res., 1991

1990

Minimizing the number of tardy job units under release time constraints.

Dorit S. Hochbaum, Ron Shamir

Discret. Appl. Math., 1990

Characterization and Algorithms for Greedily Solvable Transportation Problems.

Ron Shamir, Brenda L. Dietrich

Proceedings of the First Annual ACM-SIAM Symposium on Discrete Algorithms, 1990

1989

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

Dorit S. Hochbaum, Ron Shamir

Inf. Process. Lett., 1989

1987

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

Ilan Adler, Richard M. Karp, Ron Shamir

J. Complex., 1987

1986

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

Ilan Adler, Richard M. Karp, Ron Shamir

Math. Oper. Res., 1986