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ORCIDRon Shamir
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- affiliation: Tel Aviv University, Blavatnik School of Computer Science, Israel
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2020 – today
- 2023
[i5]Omer Noy, Ron Shamir:
Time-dependent Iterative Imputation for Multivariate Longitudinal Clinical Data. CoRR abs/2304.07821 (2023)- 2022
- [j130]Hagai Levi
, Nima Rahmanian, Ran Elkon, Ron Shamir:
The DOMINO web-server for active module identification analysis. Bioinform. 38(8): 2364-2366 (2022) - [j129]Dan Flomin, David Pellow, Ron Shamir:
Data Set-Adaptive Minimizer Order Reduces Memory Usage in k-Mer Counting. J. Comput. Biol. 29(8): 825-838 (2022) - [j128]Abhinav Dutta, David Pellow, Ron Shamir:
Parameterized syncmer schemes improve long-read mapping. PLoS Comput. Biol. 18(10): 1010638 (2022) - 2021
- [j127]Ron Zeira, Ron Shamir:
Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions. Bioinform. 37(11): 1489-1496 (2021) - [j126]Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2020 ISCB Overton Prize: Jian Peng. Bioinform. 37(11): 1630-1631 (2021) - [j125]Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2020 ISCB Innovatory Award: Xiaole Shirley Liu. Bioinform. 37(21): 3697-3698 (2021) - [j124]Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2020 ISCB accomplishments by a Senior Scientist Award: Steven Salzberg. Bioinform. 37(21): 3699-3700 (2021) - [j123]Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2020 Outstanding contributions to ISCB award: Judith Blake. Bioinform. 37(21): 3701 (2021) - [c61]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: 4:1-4:9 - 2020
- [j122]Gal Dinstag, Ron Shamir:
PRODIGY: personalized prioritization of driver genes. Bioinform. 36(6): 1831-1839 (2020) - [j121]Christiana N. Fogg, Ron Shamir, Diane E. Kovats:
Bonnie Berger named ISCB 2019 ISCB Accomplishments by a Senior Scientist Award recipient. Bioinform. 36(20): 5122-5123 (2020) - [j120]Christiana N. Fogg, Ron Shamir, Diane E. Kovats:
2019 ISCB Overton Prize: Christophe Dessimoz. Bioinform. 36(20): 5124-5125 (2020) - [j119]Christiana N. Fogg, Ron Shamir, Diane E. Kovats:
2019 Outstanding Contributions to ISCB Awarded to Barb Bryant. Bioinform. 36(20): 5126 (2020) - [j118]Christiana N. Fogg, Ron Shamir, Diane E. Kovats:
2019 ISCB Innovator Award Recognizes William Stafford Noble. Bioinform. 36(20): 5127-5128 (2020) - [j117]David Pellow, Itzik Mizrahi, Ron Shamir:
PlasClass improves plasmid sequence classification. PLoS Comput. Biol. 16(4) (2020) - [j116]Nimrod Rappoport, Roy Safra, Ron Shamir:
MONET: Multi-omic module discovery by omic selection. PLoS Comput. Biol. 16(9) (2020)
2010 – 2019
- 2019
- [j115]Nimrod Rappoport, Ron Shamir:
NEMO: cancer subtyping by integration of partial multi-omic data. Bioinform. 35(18): 3348-3356 (2019) - [j114]Dvir Netanely, Neta Stern, Itay Laufer, Ron Shamir:
PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets. BMC Bioinform. 20(1): 732 (2019) - [i4]Diane E. Kovats, Ron Shamir, Christiana N. Fogg:
2019 ISCB Overton Prize: Christophe Dessimoz. F1000Research 8: 722 (2019) - [i3]Diane E. Kovats, Ron Shamir, Christiana N. Fogg:
2019 ISCB Innovator Award recognizes William Stafford Noble. F1000Research 8: 723 (2019) - 2018
- [j113]Roye Rozov, Gil Goldshlager, Eran Halperin, Ron Shamir:
Faucet: streaming de novo assembly graph construction. Bioinform. 34(1): 147-154 (2018) - [j112]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): 1959-1961 (2018) - [j111]Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2018 ISCB Overton Prize awarded to Cole Trapnell. Bioinform. 34(13): 2330-2331 (2018) - [j110]Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
Message from the ISCB: 2018 ISCB Accomplishments by a Senior Scientist Award. Bioinform. 34(13): 2332-2333 (2018) - [j109]Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
Message from the ISCB: 2018 Outstanding Contributions to ISCB Award: Russ Altman. Bioinform. 34(13): 2334-2335 (2018) - [j108]Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2018 ISCB Innovator Award recognizes M. Madan Babu. Bioinform. 34(13): 2336-2337 (2018) - [j107]Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2018 outstanding contributions to ISCB award: Russ Altman. PLoS Comput. Biol. 14(5) (2018) - [j106]Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2018 ISCB accomplishments by a senior scientist award. PLoS Comput. Biol. 14(5) (2018) - [j105]Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2018 ISCB Innovator Award recognizes M. Madan Babu. PLoS Comput. Biol. 14(6) (2018) - [j104]Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2018 ISCB Overton Prize awarded to Cole Trapnell. PLoS Comput. Biol. 14(6) (2018) - 2017
- [j103]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): 13:1-13:11 (2017) - [j102]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): 475-482 (2017) - [j101]Guillaume Marçais, David Pellow, Daniel Bork, Yaron Orenstein, Ron Shamir, Carl Kingsford:
Improving the performance of minimizers and winnowing schemes. Bioinform. 33(14): i110-i117 (2017) - [j100]Rami Eitan, Ron Shamir:
Reconstructing cancer karyotypes from short read data: the half empty and half full glass. BMC Bioinform. 18(1): 488 (2017) - [j99]Ron Zeira, Ron Shamir:
Sorting by Cuts, Joins, and Whole Chromosome Duplications. J. Comput. Biol. 24(2): 127-137 (2017) - [j98]Ron Zeira, Meirav Zehavi, Ron Shamir:
A Linear-Time Algorithm for the Copy Number Transformation Problem. J. Comput. Biol. 24(12): 1179-1194 (2017) - [j97]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) - [j96]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) - 2016
- [c60]Ron Shamir, Meirav Zehavi, Ron Zeira:
A Linear-Time Algorithm for the Copy Number Transformation Problem. CPM 2016: 16:1-16:13 - [c59]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: 137-149 - [c58]Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford:
Compact Universal k-mer Hitting Sets. WABI 2016: 257-268 - 2015
- [j95]Yaron Orenstein, Ron Shamir:
Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers. Bioinform. 31(8): 1340 (2015) - [j94]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): 17-26 (2015) - [c57]Ron Zeira, Ron Shamir:
Sorting by Cuts, Joins and Whole Chromosome Duplications. CPM 2015: 396-409 - 2014
- [j93]Roye Rozov, Ron Shamir, Eran Halperin:
Fast lossless compression via cascading Bloom filters. BMC Bioinform. 15(S-9): S7 (2014) - 2013
- [j92]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): 571-579 (2013) - [j91]Yaron Orenstein, Ron Shamir:
Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers. Bioinform. 29(13): 71-79 (2013) - [j90]Yaron Orenstein, Eran Mick, Ron Shamir:
RAP: Accurate and Fast Motif Finding Based on Protein-Binding Microarray Data. J. Comput. Biol. 20(5): 375-382 (2013) - [j89]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) - 2012
- [j88]Roye Rozov, Eran Halperin, Ron Shamir:
MGMR: leveraging RNA-Seq population data to optimize expression estimation. BMC Bioinform. 13(S-6): S2 (2012) - [j87]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): 30-41 (2012) - [j86]Ofer Lavi, Gideon Dror, Ron Shamir:
Network-Induced Classification Kernels for Gene Expression Profile Analysis. J. Comput. Biol. 19(6): 694-709 (2012) - [c56]Ron Shamir:
Gene Regulation, Protein Networks and Disease: A Computational Perspective. CPM 2012: 1 - 2011
- [j85]Pavel A. Pevzner, Ron Shamir:
Preface: 2nd Satellite Meeting on Bioinformatics Education, Research in Computational Molecular Biology (RECOMB-BE 2010). J. Comput. Biol. 18(7): 865 (2011) - [j84]Mukul S. Bansal, Guy Banay, J. Peter Gogarten, Ron Shamir:
Detecting Highways of Horizontal Gene Transfer. J. Comput. Biol. 18(9): 1087-1114 (2011) - [j83]Michal Ozery-Flato, Ron Shamir:
An O(n3/2sqrt(log(n))) algorithm for sorting by reciprocal translocations. J. Discrete Algorithms 9(4): 344-357 (2011) - [j82]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): 793-799 (2011) - [j81]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): 848-850 (2011) - [c55]Ron Zeira, Dmitry Korchemny, Ron Shamir:
Using Computational Biology Methods to Improve Post-silicon Microprocessor Testing. Haifa Verification Conference 2011: 261-262 - [c54]Irit Gat-Viks, Renana Meller, Martin Kupiec, Ron Shamir:
Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast. RECOMB 2011: 69 - 2010
- [j80]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: 15 (2010) - [j79]Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan:
Topology-Free Querying of Protein Interaction Networks. J. Comput. Biol. 17(3): 237-252 (2010) - [j78]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): 1051-1065 (2010) - [c53]Mukul S. Bansal, J. Peter Gogarten, Ron Shamir:
Detecting Highways of Horizontal Gene Transfer. RECOMB-CG 2010: 109-120 - [c52]Yonit Halperin, Chaim Linhart, Igor Ulitsky, Ron Shamir:
Discovering Transcriptional Modules by Combined Analysis of Expression Profiles and Regulatory Sequences. RECOMB 2010: 578-579
2000 – 2009
- 2009
- [j77]Firas Swidan, Ron Shamir:
Assessing the Quality of Whole Genome Alignments in Bacteria. Adv. Bioinformatics 2009: 749027:1-749027:8 (2009) - [j76]Igor Ulitsky, Ron Shamir:
Identifying functional modules using expression profiles and confidence-scored protein interactions. Bioinform. 25(9): 1158-1164 (2009) - [j75]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): 269-282 (2009) - [j74]Chaim Linhart, Ron Shamir:
Matching with don't-cares and a small number of mismatches. Inf. Process. Lett. 109(5): 273-277 (2009) - [j73]Michal Ozery-Flato, Ron Shamir:
Sorting Cancer Karyotypes by Elementary Operations. J. Comput. Biol. 16(10): 1445-1460 (2009) - [j72]Chaim Linhart, Ron Shamir:
Faster pattern matching with character classes using prime number encoding. J. Comput. Syst. Sci. 75(3): 155-162 (2009) - [j71]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): 106-108 (2009) - [c51]Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan:
Topology-Free Querying of Protein Interaction Networks. RECOMB 2009: 74-89 - 2008
- [j70]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) - [j69]Michal Ozery-Flato, Ron Shamir:
Sorting Genomes with Centromeres by Translocations. J. Comput. Biol. 15(7): 793-812 (2008) - [j68]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) - [j67]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): 101-109 (2008) - [c50]Michal Ozery-Flato, Ron Shamir:
Sorting Cancer Karyotypes by Elementary Operations. RECOMB-CG 2008: 211-225 - [c49]Igor Ulitsky, Richard M. Karp, Ron Shamir:
Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles. RECOMB 2008: 347-359 - [c48]Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir:
A Faster Algorithm for RNA Co-folding. WABI 2008: 174-185 - 2007
- [j66]Ofir Davidovich, Gad Kimmel, Ron Shamir:
GEVALT: An integrated software tool for genotype analysis. BMC Bioinform. 8 (2007) - [j65]Igor Ulitsky, Ron Shamir:
Identification of functional modules using network topology and high-throughput data. BMC Syst. Biol. 1: 8 (2007) - [j64]Sorin Istrail, Pavel A. Pevzner, Ron Shamir:
Preface. Discret. Appl. Math. 155(6-7): 673-674 (2007) - [j63]Michal Ozery-Flato, Ron Shamir:
Sorting by Reciprocal Translocations via Reversals Theory. J. Comput. Biol. 14(4): 408-422 (2007) - [j62]Richard M. Karp, Ming Li, Pavel A. Pevzner, Ron Shamir:
Special issue on computational molecular biology. J. Comput. Syst. Sci. 73(7): 1023 (2007) - [j61]Ron Shamir, Dekel Tsur:
Improved algorithms for the random cluster graph model. Random Struct. Algorithms 31(4): 418-449 (2007) - [c47]Michal Ozery-Flato, Ron Shamir:
Rearrangements in Genomes with Centromeres Part I: Translocations. RECOMB 2007: 339-353 - 2006
- [j60]Tzvika Hartman, Ron Shamir:
A simpler and faster 1.5-approximation algorithm for sorting by transpositions. Inf. Comput. 204(2): 275-290 (2006) - [j59]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): 165-181 (2006) - [j58]Irit Gat-Viks, Richard M. Karp, Ron Shamir, Roded Sharan:
Reconstructing Chain Functions in Genetic Networks. SIAM J. Discret. Math. 20(3): 727-740 (2006) - [c46]Michal Ozery-Flato, Ron Shamir:
An O(n3/2sqrt(log n)) Algorithm for Sorting by Reciprocal Translocations. CPM 2006: 258-269 - [c45]Ron Shamir:
Some Computational Challenges in Today's Bio-medicine. ESA 2006: 3 - [c44]Michal Ozery-Flato, Ron Shamir:
Sorting by Translocations Via Reversals Theory. Comparative Genomics 2006: 87-98 - 2005
- [j57]Gideon Dror, Rotem Sorek, Ron Shamir:
Accurate identification of alternatively spliced exons using support vector machine. Bioinform. 21(7): 897-901 (2005) - [j56]Ron Shamir, Adi Maron-Katz, Amos Tanay, Chaim Linhart, Israel Steinfeld, Roded Sharan, Yosef Shiloh, Ran Elkon:
EXPANDER - an integrative program suite for microarray data analysis. BMC Bioinform. 6: 232 (2005) - [j55]Gad Kimmel, Ron Shamir:
The Incomplete Perfect Phylogeny Haplotype Problem. J. Bioinform. Comput. Biol. 3(2): 359-384 (2005) - [j54]Chaim Linhart, Ron Shamir:
The Degenerate Primer Design Problem: Theory and Applications. J. Comput. Biol. 12(4): 431-456 (2005) - [j53]Roded Sharan, Trey Ideker, Brian P. Kelley, Ron Shamir, Richard M. Karp:
Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data. J. Comput. Biol. 12(6): 835-846 (2005) - [j52]Gad Kimmel, Ron Shamir:
A Block-Free Hidden Markov Model for Genotypes and Its Application to Disease Association. J. Comput. Biol. 12(10): 1243-1260 (2005) - [j51]Richard M. Karp, Ming Li, Pavel A. Pevzner, Ron Shamir:
Guest Editors' foreword. J. Comput. Syst. Sci. 70(3): 283- (2005) - [c43]Eran Halperin, Gad Kimmel, Ron Shamir:
Tag SNP selection in genotype data for maximizing SNP prediction accuracy. ISMB (Supplement of Bioinformatics) 2005: 195-203 - [c42]Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir:
The Factor Graph Network Model for Biological Systems. RECOMB 2005: 31-47 - 2004
- [j50]Nir Orlev, Ron Shamir, Yosef Shiloh:
PIVOT: Protein Interacions VisualizatiOn Tool. Bioinform. 20(3): 424-425 (2004) - [j49]Ron Shamir, Roded Sharan:
A fully dynamic algorithm for modular decomposition and recognition of cographs. Discret. Appl. Math. 136(2-3): 329-340 (2004) - [j48]Ryan B. Hayward, Ron Shamir:
A note on tolerance graph recognition. Discret. Appl. Math. 143(1-3): 307-311 (2004) - [j47]Ron Shamir, Roded Sharan, Dekel Tsur:
Cluster graph modification problems. Discret. Appl. Math. 144(1-2): 173-182 (2004) - [j46]Gad Kimmel, Roded Sharan, Ron Shamir:
Computational Problems in Noisy SNP and Haplotype Analysis: Block Scores, Block Identification, and Population Stratification. INFORMS J. Comput. 16(4): 360-370 (2004) - [j45]Amos Tanay, Ron Shamir:
Multilevel Modeling and Inference of Transcription Regulation. J. Comput. Biol. 11(2/3): 357-375 (2004) - [j44]Irit Gat-Viks, Amos Tanay, Ron Shamir:
Modeling and Analysis of Heterogeneous Regulation in Biological Networks. J. Comput. Biol. 11(6): 1034-1049 (2004) - [j43]Itsik Pe'er, Tal Pupko, Ron Shamir, Roded Sharan:
Incomplete Directed Perfect Phylogeny. SIAM J. Comput. 33(3): 590-607 (2004) - [c41]Tamar Barzuza, Jacques S. Beckmann, Ron Shamir, Itsik Pe'er:
Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPs. CPM 2004: 14-31 - [c40]Ron Shamir:
Computational Dissection of Regulatory Networks Using Diverse High-Throughput Data. CSB 2004: 2-3 - [c39]Irit Gat-Viks, Ron Shamir, Richard M. Karp, Roded Sharan:
Reconstructing Chain Functions in Genetic Networks. Pacific Symposium on Biocomputing 2004: 498-509 - [c38]Gad Kimmel, Ron Shamir:
Maximum likelihood resolution of multi-block genotypes. RECOMB 2004: 2-9 - [c37]Irit Gat-Viks, Amos Tanay, Ron Shamir:
Modeling and Analysis of Heterogeneous Regulation in Biological Networks. Regulatory Genomics 2004: 98-113 - [c36]Roded Sharan, Trey Ideker, Brian P. Kelley, Ron Shamir, Richard M. Karp:
Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. RECOMB 2004: 282-289 - 2003
- [j42]Roded Sharan, Adi Maron-Katz, Ron Shamir:
CLICK and EXPANDER: a system for clustering and visualizing gene expression data. Bioinform. 19(14): 1787-1799 (2003) - [j41]