Ron Shamir

ORCID

Publication Activity (10 Years)

Years Active: 1986-2023
Publications (10 Years): 42

Top Venues

Publications

Omer Noy, Ron Shamir
Time-dependent Iterative Imputation for Multivariate Longitudinal Clinical Data. CoRR (2023)
Hagai Levi, Nima Rahmanian, Ran Elkon, Ron Shamir
The DOMINO web-server for active module identification analysis. Bioinform. 38 (8) (2022)
Abhinav Dutta, David Pellow, Ron Shamir
Parameterized syncmer schemes improve long-read mapping. PLoS Comput. Biol. 18 (10) (2022)
Dan Flomin, David Pellow, Ron Shamir
-Mer Counting. J. Comput. Biol. 29 (8) (2022)
Christiana N. Fogg, Diane E. Kovats, Ron Shamir
2020 ISCB Overton Prize: Jian Peng. Bioinform. 37 (11) (2021)
Christiana N. Fogg, Diane E. Kovats, Ron Shamir
2020 ISCB accomplishments by a Senior Scientist Award: Steven Salzberg. Bioinform. 37 (21) (2021)
Yael Ben-Ari, Dan Flomin, Lianrong Pu, Yaron Orenstein, Ron Shamir
Improving the efficiency of de Bruijn graph construction using compact universal hitting sets. BCB (2021)
Christiana N. Fogg, Diane E. Kovats, Ron Shamir
2020 Outstanding contributions to ISCB award: Judith Blake. Bioinform. 37 (21) (2021)
Ron Zeira, Ron Shamir
Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions. Bioinform. 37 (11) (2021)
Christiana N. Fogg, Diane E. Kovats, Ron Shamir
2020 ISCB Innovatory Award: Xiaole Shirley Liu. Bioinform. 37 (21) (2021)
Nimrod Rappoport, Roy Safra, Ron Shamir
MONET: Multi-omic module discovery by omic selection. PLoS Comput. Biol. 16 (9) (2020)
Christiana N. Fogg, Ron Shamir, Diane E. Kovats
Bonnie Berger named ISCB 2019 ISCB Accomplishments by a Senior Scientist Award recipient. Bioinform. 36 (20) (2020)
Christiana N. Fogg, Ron Shamir, Diane E. Kovats
2019 ISCB Overton Prize: Christophe Dessimoz. Bioinform. 36 (20) (2020)
Christiana N. Fogg, Ron Shamir, Diane E. Kovats
2019 Outstanding Contributions to ISCB Awarded to Barb Bryant. Bioinform. 36 (20) (2020)
Christiana N. Fogg, Ron Shamir, Diane E. Kovats
2019 ISCB Innovator Award Recognizes William Stafford Noble. Bioinform. 36 (20) (2020)
David Pellow, Itzik Mizrahi, Ron Shamir
PlasClass improves plasmid sequence classification. PLoS Comput. Biol. 16 (4) (2020)
Gal Dinstag, Ron Shamir
PRODIGY: personalized prioritization of driver genes. Bioinform. 36 (6) (2020)
Diane E. Kovats, Ron Shamir, Christiana N. Fogg
2019 ISCB Innovator Award recognizes William Stafford Noble. F1000Research 8 (2019)
Nimrod Rappoport, Ron Shamir
NEMO: cancer subtyping by integration of partial multi-omic data. Bioinform. 35 (18) (2019)
Dvir Netanely, Neta Stern, Itay Laufer, Ron Shamir
PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets. BMC Bioinform. 20 (1) (2019)
Diane E. Kovats, Ron Shamir, Christiana N. Fogg
2019 ISCB Overton Prize: Christophe Dessimoz. F1000Research 8 (2019)
David Amar, Amir Vizel, Carmit Levy, Ron Shamir
ADEPTUS: a discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases. Bioinform. 34 (11) (2018)
Christiana N. Fogg, Diane E. Kovats, Ron Shamir
2018 ISCB Overton Prize awarded to Cole Trapnell. PLoS Comput. Biol. 14 (6) (2018)
Christiana N. Fogg, Diane E. Kovats, Ron Shamir
2018 outstanding contributions to ISCB award: Russ Altman. PLoS Comput. Biol. 14 (5) (2018)
Christiana N. Fogg, Diane E. Kovats, Ron Shamir
2018 ISCB Overton Prize awarded to Cole Trapnell. Bioinform. 34 (13) (2018)
Roye Rozov, Gil Goldshlager, Eran Halperin, Ron Shamir
Faucet: streaming de novo assembly graph construction. Bioinform. 34 (1) (2018)
Christiana N. Fogg, Diane E. Kovats, Ron Shamir
Message from the ISCB: 2018 ISCB Accomplishments by a Senior Scientist Award. Bioinform. 34 (13) (2018)
Christiana N. Fogg, Diane E. Kovats, Ron Shamir
Message from the ISCB: 2018 Outstanding Contributions to ISCB Award: Russ Altman. Bioinform. 34 (13) (2018)
Christiana N. Fogg, Diane E. Kovats, Ron Shamir
2018 ISCB Innovator Award recognizes M. Madan Babu. PLoS Comput. Biol. 14 (6) (2018)
Christiana N. Fogg, Diane E. Kovats, Ron Shamir
2018 ISCB accomplishments by a senior scientist award. PLoS Comput. Biol. 14 (5) (2018)
Christiana N. Fogg, Diane E. Kovats, Ron Shamir
2018 ISCB Innovator Award recognizes M. Madan Babu. Bioinform. 34 (13) (2018)
David Amar, Ron Shamir, Daniel Yekutieli
Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate. PLoS Comput. Biol. 13 (8) (2017)
Guillaume Marçais, David Pellow, Daniel Bork, Yaron Orenstein, Ron Shamir, Carl Kingsford
Improving the performance of minimizers and winnowing schemes. Bioinform. 33 (14) (2017)
Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira
Complexity and algorithms for copy-number evolution problems. Algorithms Mol. Biol. 12 (1) (2017)
Rami Eitan, Ron Shamir
Reconstructing cancer karyotypes from short read data: the half empty and half full glass. BMC Bioinform. 18 (1) (2017)
Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, Ron Shamir
Recycler: an algorithm for detecting plasmids from de novo assembly graphs. Bioinform. 33 (4) (2017)
Ron Zeira, Meirav Zehavi, Ron Shamir
A Linear-Time Algorithm for the Copy Number Transformation Problem. J. Comput. Biol. 24 (12) (2017)
Ron Zeira, Ron Shamir
Sorting by Cuts, Joins, and Whole Chromosome Duplications. J. Comput. Biol. 24 (2) (2017)
Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford
Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing. PLoS Comput. Biol. 13 (10) (2017)
Ron Shamir, Meirav Zehavi, Ron Zeira
A Linear-Time Algorithm for the Copy Number Transformation Problem. CPM (2016)
Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira
Copy-Number Evolution Problems: Complexity and Algorithms. WABI (2016)
Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford
Compact Universal k-mer Hitting Sets. WABI (2016)
Ron Zeira, Ron Shamir
Sorting by Cuts, Joins and Whole Chromosome Duplications. CPM (2015)
Yaron Orenstein, Ron Shamir
-mers with applications to protein-binding microarrays and synthetic enhancers. Bioinform. 31 (8) (2015)
David Amar, Daniel Yekutieli, Adi Maron-Katz, Talma Hendler, Ron Shamir
A hierarchical Bayesian model for flexible module discovery in three-way time-series data. Bioinform. 31 (12) (2015)
Roye Rozov, Ron Shamir, Eran Halperin
Fast lossless compression via cascading Bloom filters. BMC Bioinform. 15 (S-9) (2014)
Mukul S. Bansal, Guy Banay, Timothy J. Harlow, J. Peter Gogarten, Ron Shamir
Systematic inference of highways of horizontal gene transfer in prokaryotes. Bioinform. 29 (5) (2013)
David Amar, Hershel Safer, Ron Shamir
Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression. PLoS Comput. Biol. 9 (3) (2013)
Yaron Orenstein, Eran Mick, Ron Shamir
RAP: Accurate and Fast Motif Finding Based on Protein-Binding Microarray Data. J. Comput. Biol. 20 (5) (2013)
Yaron Orenstein, Ron Shamir
-mers with applications to protein-binding microarrays and synthetic enhancers. Bioinform. 29 (13) (2013)
Ron Shamir
Gene Regulation, Protein Networks and Disease: A Computational Perspective. CPM (2012)
Ofer Lavi, Gideon Dror, Ron Shamir
Network-Induced Classification Kernels for Gene Expression Profile Analysis. J. Comput. Biol. 19 (6) (2012)
Roye Rozov, Eran Halperin, Ron Shamir
MGMR: leveraging RNA-Seq population data to optimize expression estimation. BMC Bioinform. 13 (S-6) (2012)
Guy Karlebach, Ron Shamir
Constructing Logical Models of Gene Regulatory Networks by Integrating Transcription Factor-DNA Interactions with Expression Data: An Entropy-Based Approach. J. Comput. Biol. 19 (1) (2012)
Pavel A. Pevzner, Ron Shamir
Satellite Meeting on Bioinformatics Education, Research in Computational Molecular Biology (RECOMB-BE 2010). J. Comput. Biol. 18 (7) (2011)
Michal Ozery-Flato, Ron Shamir
sqrt(log(n))) algorithm for sorting by reciprocal translocations. J. Discrete Algorithms 9 (4) (2011)
Mukul S. Bansal, Ron Shamir
A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (3) (2011)
Ron Zeira, Dmitry Korchemny, Ron Shamir
Using Computational Biology Methods to Improve Post-silicon Microprocessor Testing. Haifa Verification Conference (2011)
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
SPIKE: a database of highly curated human signaling pathways. Nucleic Acids Res. 39 (Database-Issue) (2011)
Irit Gat-Viks, Renana Meller, Martin Kupiec, Ron Shamir
Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast. RECOMB (2011)
Mukul S. Bansal, Guy Banay, J. Peter Gogarten, Ron Shamir
Detecting Highways of Horizontal Gene Transfer. J. Comput. Biol. 18 (9) (2011)
Guy Karlebach, Ron Shamir
Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case. BMC Syst. Biol. 4 (2010)
Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir
A Faster Algorithm for Simultaneous Alignment and Folding of RNA. J. Comput. Biol. 17 (8) (2010)
Mukul S. Bansal, J. Peter Gogarten, Ron Shamir
Detecting Highways of Horizontal Gene Transfer. RECOMB-CG (2010)
Yonit Halperin, Chaim Linhart, Igor Ulitsky, Ron Shamir
Discovering Transcriptional Modules by Combined Analysis of Expression Profiles and Regulatory Sequences. RECOMB (2010)
Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan
Topology-Free Querying of Protein Interaction Networks. J. Comput. Biol. 17 (3) (2010)
Igor Ulitsky, Ron Shamir
Identifying functional modules using expression profiles and confidence-scored protein interactions. Bioinform. 25 (9) (2009)
Chaim Linhart, Ron Shamir
Faster pattern matching with character classes using prime number encoding. J. Comput. Syst. Sci. 75 (3) (2009)
Chaim Linhart, Ron Shamir
Matching with don't-cares and a small number of mismatches. Inf. Process. Lett. 109 (5) (2009)
Firas Swidan, Ron Shamir
Assessing the Quality of Whole Genome Alignments in Bacteria. Adv. Bioinformatics 2009 (2009)
Michal Ozery-Flato, Ron Shamir
Sorting Cancer Karyotypes by Elementary Operations. J. Comput. Biol. 16 (10) (2009)
Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan
Topology-Free Querying of Protein Interaction Networks. RECOMB (2009)
Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan
Torque: topology-free querying of protein interaction networks. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Ofir Davidovich, Eran Halperin, Gad Kimmel, Ron Shamir
Increasing the Power of Association Studies by Imputation-based Sparse Tag SNP Selection. Commun. Inf. Syst. 9 (3) (2009)
Igor Ulitsky, Richard M. Karp, Ron Shamir
Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles. RECOMB (2008)
Tamar Barzuza, Jacques S. Beckmann, Ron Shamir, Itsik Pe'er
Computational Problems in Perfect Phylogeny Haplotyping: Typing without Calling the Allele. IEEE ACM Trans. Comput. Biol. Bioinform. 5 (1) (2008)
Michal Ozery-Flato, Ron Shamir
Sorting Genomes with Centromeres by Translocations. J. Comput. Biol. 15 (7) (2008)
Michal Ozery-Flato, Ron Shamir
Sorting Cancer Karyotypes by Elementary Operations. RECOMB-CG (2008)
Daniela Raijman, Ron Shamir, Amos Tanay
Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites. PLoS Comput. Biol. 4 (1) (2008)
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
SPIKE - a database, visualization and analysis tool of cellular signaling pathways. BMC Bioinform. 9 (2008)
Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir
A Faster Algorithm for RNA Co-folding. WABI (2008)
Ron Shamir, Dekel Tsur
Improved algorithms for the random cluster graph model. Random Struct. Algorithms 31 (4) (2007)
Michal Ozery-Flato, Ron Shamir
Rearrangements in Genomes with Centromeres Part I: Translocations. RECOMB (2007)
Richard M. Karp, Ming Li, Pavel A. Pevzner, Ron Shamir
Special issue on computational molecular biology. J. Comput. Syst. Sci. 73 (7) (2007)
Igor Ulitsky, Ron Shamir
Identification of functional modules using network topology and high-throughput data. BMC Syst. Biol. 1 (2007)
Ofir Davidovich, Gad Kimmel, Ron Shamir
GEVALT: An integrated software tool for genotype analysis. BMC Bioinform. 8 (2007)
Michal Ozery-Flato, Ron Shamir
Sorting by Reciprocal Translocations via Reversals Theory. J. Comput. Biol. 14 (4) (2007)
Sorin Istrail, Pavel A. Pevzner, Ron Shamir
Preface. Discret. Appl. Math. 155 (6-7) (2007)
Ron Shamir
Some Computational Challenges in Today's Bio-medicine. ESA (2006)
Michal Ozery-Flato, Ron Shamir
Sorting by Translocations Via Reversals Theory. Comparative Genomics (2006)
Michal Ozery-Flato, Ron Shamir
sqrt(log n)) Algorithm for Sorting by Reciprocal Translocations. CPM (2006)
Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir
A Probabilistic Methodology for Integrating Knowledge and Experiments on Biological Networks. J. Comput. Biol. 13 (2) (2006)
Tzvika Hartman, Ron Shamir
A simpler and faster 1.5-approximation algorithm for sorting by transpositions. Inf. Comput. 204 (2) (2006)
Irit Gat-Viks, Richard M. Karp, Ron Shamir, Roded Sharan
Reconstructing Chain Functions in Genetic Networks. SIAM J. Discret. Math. 20 (3) (2006)
Chaim Linhart, Ron Shamir
The Degenerate Primer Design Problem: Theory and Applications. J. Comput. Biol. 12 (4) (2005)
Gad Kimmel, Ron Shamir
A Block-Free Hidden Markov Model for Genotypes and Its Application to Disease Association. J. Comput. Biol. 12 (10) (2005)
Richard M. Karp, Ming Li, Pavel A. Pevzner, Ron Shamir
Guest Editors' foreword. J. Comput. Syst. Sci. 70 (3) (2005)
Gad Kimmel, Ron Shamir
The Incomplete Perfect Phylogeny Haplotype Problem. J. Bioinform. Comput. Biol. 3 (2) (2005)
Gideon Dror, Rotem Sorek, Ron Shamir
Accurate identification of alternatively spliced exons using support vector machine. Bioinform. 21 (7) (2005)
Ron Shamir, Adi Maron-Katz, Amos Tanay, Chaim Linhart, Israel Steinfeld, Roded Sharan, Yosef Shiloh, Ran Elkon
- an integrative program suite for microarray data analysis. BMC Bioinform. 6 (2005)

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Publication Activity (10 Years)

Top Topics

Top Venues

Ron Shamir