A Family of Simplex Variants Solving an m × d Linear Program in Expected Number of Pivot Steps Depending on d Only. - Ilan Adler; Richard M. Karp; Ron Shamir (Math. Oper. Res., 1986)

A simplex variant solving an m times d linear program in O(min(m2, d2) expected number of pivot steps. - Ilan Adler; Richard M. Karp; Ron Shamir (J. Complex., 1987)

An O(n log2 n) Algorithm for the Maximum Weighted Tardiness Problem. - Dorit S. Hochbaum; Ron Shamir (Inf. Process. Lett., 1989)

Characterization and Algorithms for Greedily Solvable Transportation Problems. - Ron Shamir; Brenda L. Dietrich (SODA, 1990)

Minimizing the number of tardy job units under release time constraints. - Dorit S. Hochbaum; Ron Shamir (Discret. Appl. Math., 1990)

Strongly Polynomial Algorithms for the High Multiplicity Scheduling Problem. - Dorit S. Hochbaum; Ron Shamir (Oper. Res., 1991)

Algorithms and Complexity for Reasoning about Time. - Martin Charles Golumbic; Ron Shamir (AAAI, 1992)

Interval Graphs, Interval Orders and the Consistency of Temporal Events. - Martin Charles Golumbic; Ron Shamir (ISTCS, 1992)

A polynomial algorithm for an integer quadratic non-separable transportation problem. - Dorit S. Hochbaum; Ron Shamir; J. George Shanthikumar (Math. Program., 1992)

A Polynomial Algorithm for Balancing Acyclic Data Flow Graphs. - Endre Boros; Peter L. Hammer; Ron Shamir (IEEE Trans. Computers, 1992)

Algorithms and Complexity of Sandwich Problems in Graphs (Extended Abstract). - Martin Charles Golumbic; Haim Kaplan; Ron Shamir (WG, 1993)

Monge and Feasibility Sequences in General Flow Problems. - Ilan Adler; Alan J. Hoffman; Ron Shamir (Discret. Appl. Math., 1993)

A fast algorithm for constructing monge sequences in transportation problems with forbidden arcs. - Ron Shamir (Discret. Math., 1993)

Complexity and Algorithms for Reasoning about Time: A Graph-Theoretic Approach. - Martin Charles Golumbic; Ron Shamir (J. ACM, 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)

Tractability of parameterized completion problems on chordal and interval graphs: Minimum Fill-in and Physical Mapping - Haim Kaplan; Ron Shamir; Robert Endre Tarjan (FOCS, 1994)

Efficient Algorithms for Minimum-Cost Flow Problems with Piecewise-Linear Convex Costs. - Yaron Pinto; Ron Shamir (Algorithmica, 1994)

Balancing Problems in Acyclic Networks. - Endre Boros; Peter L. Hammer; Mark E. Hartmann; Ron Shamir (Discret. Appl. Math., 1994)

The Domatic Number Problem on Some Perfect Graph Families. - Haim Kaplan; Ron Shamir (Inf. Process. Lett., 1994)

Interval Graphs with Side (and Size) Constraints. - Itsik Pe'er; Ron Shamir (ESA, 1995)

Graph Sandwich Problems. - Martin Charles Golumbic; Haim Kaplan; Ron Shamir (J. Algorithms, 1995)

Four Strikes Against Physical Mapping of DNA. - Paul W. Goldberg; Martin Charles Golumbic; Haim Kaplan; Ron Shamir (J. Comput. Biol., 1995)

Physical Maps and Interval Sandwich Problems: Bounded Degrees Help. - Haim Kaplan; Ron Shamir (ISTCS, 1996)

Pathwidth, Bandwidth, and Completion Problems to Proper Interval Graphs with Small Cliques. - Haim Kaplan; Ron Shamir (SIAM J. Comput., 1996)

Realizing Interval Graphs with Size and Distance Constraints. - Itsik Pe'er; Ron Shamir (SIAM J. Discret. Math., 1997)

Satisfiability Problems on Intervals and Unit Intervals. - Itsik Pe'er; Ron Shamir (Theor. Comput. Sci., 1997)

The Maximum Subforest Problem: Approximation and Exact Algorithms (Extended Abstract). - Ron Shamir; Dekel Tsur (SODA, 1998)

The median problems for breakpoints are NP-complete - Itsik Pe'er; Ron Shamir (Electron. Colloquium Comput. Complex., 1998)

An algorithm for clustering cDNAs for gene expression analysis. - Erez Hartuv; Armin O. Schmitt; Jörg Lange; Sebastian Meier-Ewert; Hans Lehrach; Ron Shamir (RECOMB, 1999)

Bounded Degree Interval Sandwich Problems. - Haim Kaplan; Ron Shamir (Algorithmica, 1999)

Faster Subtree Isomorphism. - Ron Shamir; Dekel Tsur (J. Algorithms, 1999)

Clustering Gene Expression Patterns. - Amir Ben-Dor; Ron Shamir; Zohar Yakhini (J. Comput. Biol., 1999)

Construction of Physical Maps from Oligonucleotide Fingerprints Data. - Guy Mayraz; Ron Shamir (J. Comput. Biol., 1999)

A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals. - Haim Kaplan; Ron Shamir; Robert Endre Tarjan (SIAM J. Comput., 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)

Incomplete Directed Perfect Phylogeny. - Itsik Pe'er; Ron Shamir; Roded Sharan (CPM, 2000)

Spectrum Alignment: Efficient Resequencing by Hybridization. - Itsik Pe'er; Ron Shamir (ISMB, 2000)

Center CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis. - Roded Sharan; Ron Shamir (ISMB, 2000)

Foreword. - Sorin Istrail; Pavel A. Pevzner; Ron Shamir (Discret. Appl. Math., 2000)

A clustering algorithm based on graph connectivity. - Erez Hartuv; Ron Shamir (Inf. Process. Lett., 2000)

An Algorithm Combining Discrete and Continuous Methods for Optical Mapping. - Richard M. Karp; Itsik Pe'er; Ron Shamir (J. Comput. Biol., 2000)

Algorithms for Optical Mapping. - Richard M. Karp; Ron Shamir (J. Comput. Biol., 2000)

Preface: Special RECOMB 2000 Issue. - Ron Shamir (J. Comput. Biol., 2000)

A Polynomial Approximation Algorithm for the Minimum Fill-In Problem. - Assaf Natanzon; Ron Shamir; Roded Sharan (SIAM J. Comput., 2000)

Computational expansion of genetic networks. - Amos Tanay; Ron Shamir (ISMB (Supplement of Bioinformatics), 2001)

A Chemical-Distance-Based Test for Positive Darwinian Selection. - Tal Pupko; Roded Sharan; Masami Hasegawa; Ron Shamir; Dan Graur (WABI, 2001)

Complexity classification of some edge modification problems. - Assaf Natanzon; Ron Shamir; Roded Sharan (Discret. Appl. Math., 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)

A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs. - Pavol Hell; Ron Shamir; Roded Sharan (SIAM J. Comput., 2001)

The degenerate primer design problem. - Chaim Linhart; Ron Shamir (ISMB, 2002)

Discovering statistically significant biclusters in gene expression data. - Amos Tanay; Roded Sharan; Ron Shamir (ISMB, 2002)

On the Generality of Phylogenies from Incomplete Directed Characters. - Itsik Pe'er; Ron Shamir; Roded Sharan (SWAT, 2002)

On the Complexity of Positional Sequencing by Hybridization. - Amir Ben-Dor; Itsik Pe'er; Ron Shamir; Roded Sharan (J. Comput. Biol., 2002)

Large Scale Sequencing by Hybridization. - Ron Shamir; Dekel Tsur (J. Comput. Biol., 2002)

Foreword. - Ming Li; Pavel A. Pevzner; Ron Shamir (J. Comput. Syst. Sci., 2002)

Chain functions and scoring functions in genetic networks. - Irit Gat-Viks; Ron Shamir (ISMB (Supplement of Bioinformatics), 2003)

Modeling transcription programs: inferring binding site activity and dose-response model optimization. - Amos Tanay; Ron Shamir (RECOMB, 2003)

Identifying Blocks and Sub-populations in Noisy SNP Data. - Gad Kimmel; Roded Sharan; Ron Shamir (WABI, 2003)

Scoring clustering solutions by their biological relevance. - Irit Gat-Viks; Roded Sharan; Ron Shamir (Bioinform., 2003)

CLICK and EXPANDER: a system for clustering and visualizing gene expression data. - Roded Sharan; Adi Maron-Katz; Ron Shamir (Bioinform., 2003)

Two Notes on Genome Rearrangement. - Michal Ozery-Flato; Ron Shamir (J. Bioinform. Comput. Biol., 2003)

The Restriction Scaffold Problem. - Amir Ben-Dor; Richard M. Karp; Benno Schwikowski; Ron Shamir (J. Comput. Biol., 2003)

Handling Long Targets and Errors in Sequencing by Hybridization. - Eran Halperin; Shay Halperin; Tzvika Hartman; Ron Shamir (J. Comput. Biol., 2003)

Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPs. - Tamar Barzuza; Jacques S. Beckmann; Ron Shamir; Itsik Pe'er (CPM, 2004)

Computational Dissection of Regulatory Networks Using Diverse High-Throughput Data. - Ron Shamir (CSB, 2004)

Maximum likelihood resolution of multi-block genotypes. - Gad Kimmel; Ron Shamir (RECOMB, 2004)

PIVOT: Protein Interacions VisualizatiOn Tool. - Nir Orlev; Ron Shamir; Yosef Shiloh (Bioinform., 2004)

A note on tolerance graph recognition. - Ryan B. Hayward; Ron Shamir (Discret. Appl. Math., 2004)

A fully dynamic algorithm for modular decomposition and recognition of cographs. - Ron Shamir; Roded Sharan (Discret. Appl. Math., 2004)

Cluster graph modification problems. - Ron Shamir; Roded Sharan; Dekel Tsur (Discret. Appl. Math., 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)

Modeling and Analysis of Heterogeneous Regulation in Biological Networks. - Irit Gat-Viks; Amos Tanay; Ron Shamir (J. Comput. Biol., 2004)

Multilevel Modeling and Inference of Transcription Regulation. - Amos Tanay; Ron Shamir (J. Comput. Biol., 2004)

Incomplete Directed Perfect Phylogeny. - Itsik Pe'er; Tal Pupko; Ron Shamir; Roded Sharan (SIAM J. Comput., 2004)

Tag SNP selection in genotype data for maximizing SNP prediction accuracy. - Eran Halperin; Gad Kimmel; Ron Shamir (ISMB (Supplement of Bioinformatics), 2005)

The Factor Graph Network Model for Biological Systems. - Irit Gat-Viks; Amos Tanay; Daniela Raijman; Ron Shamir (RECOMB, 2005)

Accurate identification of alternatively spliced exons using support vector machine. - Gideon Dror; Rotem Sorek; Ron Shamir (Bioinform., 2005)

EXPANDER - 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)

The Incomplete Perfect Phylogeny Haplotype Problem. - Gad Kimmel; Ron Shamir (J. Bioinform. 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 Degenerate Primer Design Problem: Theory and Applications. - Chaim Linhart; Ron Shamir (J. Comput. Biol., 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)

Guest Editors' foreword. - Richard M. Karp; Ming Li; Pavel A. Pevzner; Ron Shamir (J. Comput. Syst. Sci., 2005)

Some Computational Challenges in Today's Bio-medicine. - Ron Shamir (ESA, 2006)

Sorting by Translocations Via Reversals Theory. - Michal Ozery-Flato; Ron Shamir (Comparative Genomics, 2006)

A simpler and faster 1.5-approximation algorithm for sorting by transpositions. - Tzvika Hartman; Ron Shamir (Inf. Comput., 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)

Reconstructing Chain Functions in Genetic Networks. - Irit Gat-Viks; Richard M. Karp; Ron Shamir; Roded Sharan (SIAM J. Discret. Math., 2006)

Rearrangements in Genomes with Centromeres Part I: Translocations. - Michal Ozery-Flato; Ron Shamir (RECOMB, 2007)

GEVALT: An integrated software tool for genotype analysis. - Ofir Davidovich; Gad Kimmel; Ron Shamir (BMC Bioinform., 2007)

Identification of functional modules using network topology and high-throughput data. - Igor Ulitsky; Ron Shamir (BMC Syst. Biol., 2007)

Preface. - Sorin Istrail; Pavel A. Pevzner; Ron Shamir (Discret. Appl. Math., 2007)

Sorting by Reciprocal Translocations via Reversals Theory. - Michal Ozery-Flato; Ron Shamir (J. Comput. Biol., 2007)

Special issue on computational molecular biology. - Richard M. Karp; Ming Li; Pavel A. Pevzner; Ron Shamir (J. Comput. Syst. Sci., 2007)

Improved algorithms for the random cluster graph model. - Ron Shamir; Dekel Tsur (Random Struct. Algorithms, 2007)

Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles. - Igor Ulitsky; Richard M. Karp; Ron Shamir (RECOMB, 2008)

A Faster Algorithm for RNA Co-folding. - Michal Ziv-Ukelson; Irit Gat-Viks; Ydo Wexler; Ron Shamir (WABI, 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; et al. (BMC Bioinform., 2008)

Sorting Genomes with Centromeres by Translocations. - Michal Ozery-Flato; Ron Shamir (J. Comput. Biol., 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)

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)

Assessing the Quality of Whole Genome Alignments in Bacteria. - Firas Swidan; Ron Shamir (Adv. Bioinformatics, 2009)

Identifying functional modules using expression profiles and confidence-scored protein interactions. - Igor Ulitsky; Ron Shamir (Bioinform., 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)

Matching with don't-cares and a small number of mismatches. - Chaim Linhart; Ron Shamir (Inf. Process. Lett., 2009)

Sorting Cancer Karyotypes by Elementary Operations. - Michal Ozery-Flato; Ron Shamir (J. Comput. Biol., 2009)

Faster pattern matching with character classes using prime number encoding. - Chaim Linhart; Ron Shamir (J. Comput. Syst. Sci., 2009)

Torque: topology-free querying of protein interaction networks. - Sharon Bruckner; Falk Hüffner; Richard M. Karp; Ron Shamir; Roded Sharan (Nucleic Acids Res., 2009)

Detecting Highways of Horizontal Gene Transfer. - Mukul S. Bansal; J. Peter Gogarten; Ron Shamir (RECOMB-CG, 2010)

Discovering Transcriptional Modules by Combined Analysis of Expression Profiles and Regulatory Sequences. - Yonit Halperin; Chaim Linhart; Igor Ulitsky; Ron Shamir (RECOMB, 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)

Topology-Free Querying of Protein Interaction Networks. - Sharon Bruckner; Falk Hüffner; Richard M. Karp; Ron Shamir; Roded Sharan (J. Comput. Biol., 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)

Using Computational Biology Methods to Improve Post-silicon Microprocessor Testing. - Ron Zeira; Dmitry Korchemny; Ron Shamir (Haifa Verification Conference, 2011)

Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast. - Irit Gat-Viks; Renana Meller; Martin Kupiec; Ron Shamir (RECOMB, 2011)

Detecting Highways of Horizontal Gene Transfer. - Mukul S. Bansal; Guy Banay; J. Peter Gogarten; Ron Shamir (J. Comput. Biol., 2011)

Preface: 2nd Satellite Meeting on Bioinformatics Education, Research in Computational Molecular Biology (RECOMB-BE 2010). - Pavel A. Pevzner; Ron Shamir (J. Comput. Biol., 2011)

An O(n3/2sqrt(log(n))) algorithm for sorting by reciprocal translocations. - Michal Ozery-Flato; Ron Shamir (J. Discrete Algorithms, 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)

A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem. - Mukul S. Bansal; Ron Shamir (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Gene Regulation, Protein Networks and Disease: A Computational Perspective. - Ron Shamir (CPM, 2012)

MGMR: leveraging RNA-Seq population data to optimize expression estimation. - Roye Rozov; Eran Halperin; Ron Shamir (BMC Bioinform., 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)

Network-Induced Classification Kernels for Gene Expression Profile Analysis. - Ofer Lavi; Gideon Dror; Ron Shamir (J. Comput. Biol., 2012)

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)

RAP: Accurate and Fast Motif Finding Based on Protein-Binding Microarray Data. - Yaron Orenstein; Eran Mick; Ron Shamir (J. Comput. Biol., 2013)

Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression. - David Amar; Hershel Safer; Ron Shamir (PLoS Comput. Biol., 2013)

Fast lossless compression via cascading Bloom filters. - Roye Rozov; Ron Shamir; Eran Halperin (BMC Bioinform., 2014)

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)

Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers. - Yaron Orenstein; Ron Shamir (Bioinform., 2015)

Copy-Number Evolution Problems: Complexity and Algorithms. - Mohammed El-Kebir; Benjamin J. Raphael; Ron Shamir; Roded Sharan; Simone Zaccaria; Meirav Zehavi; Ron Zeira (WABI, 2016)

Compact Universal k-mer Hitting Sets. - Yaron Orenstein; David Pellow; Guillaume Marçais; Ron Shamir; Carl Kingsford (WABI, 2016)

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)

Improving the performance of minimizers and winnowing schemes. - Guillaume Marçais; David Pellow; Daniel Bork; Yaron Orenstein; Ron Shamir; Carl Kingsford (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)

Reconstructing cancer karyotypes from short read data: the half empty and half full glass. - Rami Eitan; Ron Shamir (BMC Bioinform., 2017)

Sorting by Cuts, Joins, and Whole Chromosome Duplications. - Ron Zeira; Ron Shamir (J. Comput. Biol., 2017)

A Linear-Time Algorithm for the Copy Number Transformation Problem. - Ron Zeira; Meirav Zehavi; Ron Shamir (J. 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)

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)

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)

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

Faucet: streaming de novo assembly graph construction. - Roye Rozov; Gil Goldshlager; Eran Halperin; Ron Shamir (Bioinform., 2018)

2018 outstanding contributions to ISCB award: Russ Altman. - Christiana N. Fogg; Diane E. Kovats; Ron Shamir (PLoS Comput. Biol., 2018)

2018 ISCB accomplishments by a senior scientist award. - Christiana N. Fogg; Diane E. Kovats; Ron Shamir (PLoS Comput. Biol., 2018)

2018 ISCB Innovator Award recognizes M. Madan Babu. - Christiana N. Fogg; Diane E. Kovats; Ron Shamir (PLoS Comput. Biol., 2018)

2018 ISCB Overton Prize awarded to Cole Trapnell. - Christiana N. Fogg; Diane E. Kovats; Ron Shamir (PLoS Comput. Biol., 2018)

NEMO: cancer subtyping by integration of partial multi-omic data. - Nimrod Rappoport; Ron Shamir (Bioinform., 2019)

PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets. - Dvir Netanely; Neta Stern; Itay Laufer; Ron Shamir (BMC Bioinform., 2019)

PRODIGY: personalized prioritization of driver genes. - Gal Dinstag; Ron Shamir (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)

2019 ISCB Overton Prize: Christophe Dessimoz. - Christiana N. Fogg; Ron Shamir; Diane E. Kovats (Bioinform., 2020)

2019 Outstanding Contributions to ISCB Awarded to Barb Bryant. - Christiana N. Fogg; Ron Shamir; Diane E. Kovats (Bioinform., 2020)

2019 ISCB Innovator Award Recognizes William Stafford Noble. - Christiana N. Fogg; Ron Shamir; Diane E. Kovats (Bioinform., 2020)

PlasClass improves plasmid sequence classification. - David Pellow; Itzik Mizrahi; Ron Shamir (PLoS Comput. Biol., 2020)

MONET: Multi-omic module discovery by omic selection. - Nimrod Rappoport; Roy Safra; Ron Shamir (PLoS Comput. Biol., 2020)

Improving the efficiency of de Bruijn graph construction using compact universal hitting sets. - Yael Ben-Ari; Dan Flomin; Lianrong Pu; Yaron Orenstein; Ron Shamir (BCB, 2021)

2020 ISCB Overton Prize: Jian Peng. - 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 accomplishments by a Senior Scientist Award: Steven Salzberg. - Christiana N. Fogg; Diane E. Kovats; Ron Shamir (Bioinform., 2021)

2020 Outstanding contributions to ISCB award: Judith Blake. - Christiana N. Fogg; Diane E. Kovats; Ron Shamir (Bioinform., 2021)

Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions. - Ron Zeira; Ron Shamir (Bioinform., 2021)

The DOMINO web-server for active module identification analysis. - Hagai Levi; Nima Rahmanian; Ran Elkon; Ron Shamir (Bioinform., 2022)

3CAC: improving the classification of phages and plasmids in metagenomic assemblies using assembly graphs. - Lianrong Pu; Ron Shamir (Bioinform., 2022)

Data Set-Adaptive Minimizer Order Reduces Memory Usage in k-Mer Counting. - Dan Flomin; David Pellow; Ron Shamir (J. Comput. Biol., 2022)

Parameterized syncmer schemes improve long-read mapping. - Abhinav Dutta; David Pellow; Ron Shamir (PLoS Comput. Biol., 2022)

Time-dependent Iterative Imputation for Multivariate Longitudinal Clinical Data. - Omer Noy; Ron Shamir (CoRR, 2023)

Towards Regulatory-Confirmed Adaptive Clinical Trials: Machine Learning Opportunities and Solutions. - Omer Noy Klein; Alihan Hüyük; Ron Shamir; Uri Shalit; Mihaela van der Schaar (AISTATS, 2025)

Predicting appropriateness of antibiotic treatment among ICU patients with hospital-acquired infection. - Ella Goldschmidt; Ella Rannon; Daniel Bernstein; Asaf Wasserman; Michael Roimi; Anat Shrot; Dan Coster; Ron Shamir (npj Digit. Medicine, 2025)