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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]Irit Gat-Viks, Roded Sharan, Ron Shamir:
Scoring clustering solutions by their biological relevance. Bioinform. 19(18): 2381-2389 (2003) - [j40]Michal Ozery-Flato, Ron Shamir:
Two Notes on Genome Rearrangement. J. Bioinform. Comput. Biol. 1(1): 71-94 (2003) - [j39]Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Ron Shamir:
The Restriction Scaffold Problem. J. Comput. Biol. 10(3/4): 385-398 (2003) - [j38]Eran Halperin, Shay Halperin, Tzvika Hartman, Ron Shamir:
Handling Long Targets and Errors in Sequencing by Hybridization. J. Comput. Biol. 10(3/4): 483-497 (2003) - [c35]Irit Gat-Viks, Ron Shamir:
Chain functions and scoring functions in genetic networks. ISMB (Supplement of Bioinformatics) 2003: 108-117 - [c34]Amos Tanay, Ron Shamir:
Modeling transcription programs: inferring binding site activity and dose-response model optimization. RECOMB 2003: 301-310 - [c33]Gad Kimmel, Roded Sharan, Ron Shamir:
Identifying Blocks and Sub-populations in Noisy SNP Data. WABI 2003: 303-319 - 2002
- [j37]Amir Ben-Dor, Itsik Pe'er, Ron Shamir, Roded Sharan:
On the Complexity of Positional Sequencing by Hybridization. J. Comput. Biol. 8(4): 361-371 (2002) - [j36]Ron Shamir, Dekel Tsur:
Large Scale Sequencing by Hybridization. J. Comput. Biol. 9(2): 413-428 (2002) - [j35]Ming Li, Pavel A. Pevzner, Ron Shamir:
Foreword. J. Comput. Syst. Sci. 65(3): 441 (2002) - [c32]Amos Tanay, Roded Sharan, Ron Shamir:
Discovering statistically significant biclusters in gene expression data. ISMB 2002: 136-144 - [c31]Chaim Linhart, Ron Shamir:
The degenerate primer design problem. ISMB 2002: 172-181 - [c30]Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Ron Shamir:
The restriction scaffold problem. RECOMB 2002: 58-66 - [c29]Eran Halperin, Shay Halperin, Tzvika Hartman, Ron Shamir:
Handling long targets and errors in sequencing by hybridization. RECOMB 2002: 176-185 - [c28]Ron Shamir, Dekel Tsur:
Improved Algorithms for the Random Cluster Graph Model. SWAT 2002: 230-239 - [c27]Itsik Pe'er, Ron Shamir, Roded Sharan:
On the Generality of Phylogenies from Incomplete Directed Characters. SWAT 2002: 358-367 - [c26]Ron Shamir, Roded Sharan, Dekel Tsur:
Cluster Graph Modification Problems. WG 2002: 379-390 - 2001
- [j34]Assaf Natanzon, Ron Shamir, Roded Sharan:
Complexity classification of some edge modification problems. Discret. Appl. Math. 113(1): 109-128 (2001) - [j33]Pavol Hell, Ron Shamir, Roded Sharan:
A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs. SIAM J. Comput. 31(1): 289-305 (2001) - [c25]Amos Tanay, Ron Shamir:
Computational expansion of genetic networks. ISMB (Supplement of Bioinformatics) 2001: 270-278 - [c24]Ron Shamir, Dekel Tsur:
Large scale sequencing by hybridization. RECOMB 2001: 269-277 - [c23]Tal Pupko, Roded Sharan, Masami Hasegawa, Ron Shamir, Dan Graur:
A Chemical-Distance-Based Test for Positive Darwinian Selection. WABI 2001: 142-155 - [i2]Piotr Berman, Amir Ben-Dor, Itsik Pe'er, Roded Sharan, Ron Shamir:
On the Complexity of Positional Sequencing by Hybridization. Electron. Colloquium Comput. Complex. TR01 (2001) - 2000
- [j32]Sorin Istrail, Pavel A. Pevzner, Ron Shamir:
Foreword. Discret. Appl. Math. 104(1-3): 1-2 (2000) - [j31]Erez Hartuv, Ron Shamir:
A clustering algorithm based on graph connectivity. Inf. Process. Lett. 76(4-6): 175-181 (2000) - [j30]Richard M. Karp, Ron Shamir:
Algorithms for Optical Mapping. J. Comput. Biol. 7(1-2): 303-316 (2000) - [j29]Ron Shamir:
Preface: Special RECOMB 2000 Issue. J. Comput. Biol. 7(3-4): 329-330 (2000) - [j28]Richard M. Karp, Itsik Pe'er, Ron Shamir:
An Algorithm Combining Discrete and Continuous Methods for Optical Mapping. J. Comput. Biol. 7(5): 745-760 (2000) - [j27]Assaf Natanzon, Ron Shamir, Roded Sharan:
A Polynomial Approximation Algorithm for the Minimum Fill-In Problem. SIAM J. Comput. 30(4): 1067-1079 (2000) - [c22]Itsik Pe'er, Ron Shamir, Roded Sharan:
Incomplete Directed Perfect Phylogeny. CPM 2000: 143-153 - [c21]Itsik Pe'er, Ron Shamir:
Spectrum Alignment: Efficient Resequencing by Hybridization. ISMB 2000: 260-268 - [c20]Roded Sharan, Ron Shamir:
Center CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis. ISMB 2000: 307-316 - [e1]Ron Shamir, Satoru Miyano, Sorin Istrail, Pavel A. Pevzner, Michael S. Waterman:
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, RECOMB 2000, Tokyo, Japan, April 8-11, 2000. ACM 2000, ISBN 1-58113-186-0 [contents]
1990 – 1999
- 1999
- [j26]Haim Kaplan, Ron Shamir:
Bounded Degree Interval Sandwich Problems. Algorithmica 24(2): 96-104 (1999) - [j25]Ron Shamir, Dekel Tsur:
Faster Subtree Isomorphism. J. Algorithms 33(2): 267-280 (1999) - [j24]Guy Mayraz, Ron Shamir:
Construction of Physical Maps from Oligonucleotide Fingerprints Data. J. Comput. Biol. 6(2): 237-252 (1999) - [j23]Amir Ben-Dor, Ron Shamir, Zohar Yakhini:
Clustering Gene Expression Patterns. J. Comput. Biol. 6(3/4): 281-297 (1999) - [j22]Haim Kaplan, Ron Shamir, Robert Endre Tarjan:
Tractability of Parameterized Completion Problems on Chordal, Strongly Chordal, and Proper Interval Graphs. SIAM J. Comput. 28(5): 1906-1922 (1999) - [j21]Haim Kaplan, Ron Shamir, Robert Endre Tarjan:
A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals. SIAM J. Comput. 29(3): 880-892 (1999) - [c19]Amir Ben-Dor, Itsik Pe'er, Ron Shamir, Roded Sharan:
On the Complexity of Positional Sequencing by Hybridization. CPM 1999: 88-100 - [c18]Pavol Hell, Ron Shamir, Roded Sharan:
A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs. ESA 1999: 527-539 - [c17]Richard M. Karp, Itsik Pe'er, Ron Shamir:
An Algorithm Combining Discrete and Continuous Methods for Optical Mapping. ISMB 1999: 159-168 - [c16]Erez Hartuv, Armin O. Schmitt, Jörg Lange, Sebastian Meier-Ewert, Hans Lehrach, Ron Shamir:
An algorithm for clustering cDNAs for gene expression analysis. RECOMB 1999: 188-197 - [c15]Guy Mayraz, Ron Shamir:
Construction of physical maps from oligonucleotide fingerprints data. RECOMB 1999: 268-277 - [c14]Assaf Natanzon, Ron Shamir, Roded Sharan:
Complexity Classification of Some Edge Modification Problems. WG 1999: 65-77 - 1998
- [j20]Sorin Istrail, Pavel A. Pevzner, Ron Shamir:
Foreword. Discret. Appl. Math. 88(1-3): 3-6 (1998) - [c13]Richard M. Karp, Ron Shamir:
Algorithms for optical mapping. RECOMB 1998: 117-124 - [c12]Ron Shamir, Dekel Tsur:
The Maximum Subforest Problem: Approximation and Exact Algorithms (Extended Abstract). SODA 1998: 394-399 - [c11]Assaf Natanzon, Ron Shamir, Roded Sharan:
A Polynomial Approximation Algorithm for the Minimum Fill-In Problem. STOC 1998: 41-47 - [i1]Itsik Pe'er, Ron Shamir:
The median problems for breakpoints are NP-complete. Electron. Colloquium Comput. Complex. TR98 (1998) - 1997
- [j19]Itsik Pe'er, Ron Shamir:
Realizing Interval Graphs with Size and Distance Constraints. SIAM J. Discret. Math. 10(4): 662-687 (1997) - [j18]Itsik Pe'er, Ron Shamir:
Satisfiability Problems on Intervals and Unit Intervals. Theor. Comput. Sci. 175(2): 349-372 (1997) - [c10]Ron Shamir, Dekel Tsur:
Faster subtree isomorphism. ISTCS 1997: 126-131 - [c9]Haim Kaplan, Ron Shamir, Robert Endre Tarjan:
Faster and simpler algorithm for sorting signed permutations by reversals. RECOMB 1997: 163 - [c8]Haim Kaplan, Ron Shamir, Robert Endre Tarjan:
Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals. SODA 1997: 344-351 - 1996
- [j17]Haim Kaplan, Ron Shamir:
Pathwidth, Bandwidth, and Completion Problems to Proper Interval Graphs with Small Cliques. SIAM J. Comput. 25(3): 540-561 (1996) - [c7]Haim Kaplan, Ron Shamir:
Physical Maps and Interval Sandwich Problems: Bounded Degrees Help. ISTCS 1996: 195-201 - 1995
- [j16]Martin Charles Golumbic, Haim Kaplan, Ron Shamir:
Graph Sandwich Problems. J. Algorithms 19(3): 449-473 (1995) - [j15]Paul W. Goldberg, Martin Charles Golumbic, Haim Kaplan, Ron Shamir:
Four Strikes Against Physical Mapping of DNA. J. Comput. Biol. 2(1): 139-152 (1995) - [c6]Itsik Pe'er, Ron Shamir:
Interval Graphs with Side (and Size) Constraints. ESA 1995: 142-154 - 1994
- [j14]Yaron Pinto, Ron Shamir:
Efficient Algorithms for Minimum-Cost Flow Problems with Piecewise-Linear Convex Costs. Algorithmica 11(3): 256-276 (1994) - [j13]Endre Boros, Peter L. Hammer, Mark E. Hartmann, Ron Shamir:
Balancing Problems in Acyclic Networks. Discret. Appl. Math. 49(1-3): 77-93 (1994) - [j12]Haim Kaplan, Ron Shamir:
The Domatic Number Problem on Some Perfect Graph Families. Inf. Process. Lett. 49(1): 51-56 (1994) - [c5]Haim Kaplan, Ron Shamir, Robert Endre Tarjan:
Tractability of parameterized completion problems on chordal and interval graphs: Minimum Fill-in and Physical Mapping. FOCS 1994: 780-791 - 1993
- [j11]Ilan Adler, Alan J. Hoffman, Ron Shamir:
Monge and Feasibility Sequences in General Flow Problems. Discret. Appl. Math. 44(1-3): 21-38 (1993) - [j10]Ron Shamir:
A fast algorithm for constructing monge sequences in transportation problems with forbidden arcs. Discret. Math. 114(1-3): 435-444 (1993) - [j9]Martin Charles Golumbic, Ron Shamir:
Complexity and Algorithms for Reasoning about Time: A Graph-Theoretic Approach. J. ACM 40(5): 1108-1133 (1993) - [j8]Ilan Adler, Ron Shamir:
A randomized scheme for speeding up algorithms for linear and convex programming problems with high constraints-to-variables ratio. Math. Program. 61: 39-52 (1993) - [c4]Martin Charles Golumbic, Haim Kaplan, Ron Shamir:
Algorithms and Complexity of Sandwich Problems in Graphs (Extended Abstract). WG 1993: 57-69 - 1992
- [j7]Dorit S. Hochbaum, Ron Shamir, J. George Shanthikumar:
A polynomial algorithm for an integer quadratic non-separable transportation problem. Math. Program. 55: 359-371 (1992) - [j6]Endre Boros, Peter L. Hammer, Ron Shamir:
A Polynomial Algorithm for Balancing Acyclic Data Flow Graphs. IEEE Trans. Computers 41(11): 1380-1385 (1992) - [c3]Martin Charles Golumbic, Ron Shamir:
Algorithms and Complexity for Reasoning about Time. AAAI 1992: 741-747 - [c2]Martin Charles Golumbic, Ron Shamir:
Interval Graphs, Interval Orders and the Consistency of Temporal Events. ISTCS 1992: 32-42 - 1991
- [j5]Dorit S. Hochbaum, Ron Shamir:
Strongly Polynomial Algorithms for the High Multiplicity Scheduling Problem. Oper. Res. 39(4): 648-653 (1991) - 1990
- [j4]Dorit S. Hochbaum, Ron Shamir:
Minimizing the number of tardy job units under release time constraints. Discret. Appl. Math. 28(1): 45-57 (1990) - [c1]Ron Shamir, Brenda L. Dietrich:
Characterization and Algorithms for Greedily Solvable Transportation Problems. SODA 1990: 358-366
1980 – 1989
- 1989
- [j3]Dorit S. Hochbaum, Ron Shamir:
An O(n log2 n) Algorithm for the Maximum Weighted Tardiness Problem. Inf. Process. Lett. 31(4): 215-219 (1989) - 1987
- [j2]Ilan Adler, Richard M. Karp, Ron Shamir:
A simplex variant solving an m times d linear program in O(min(m2, d2) expected number of pivot steps. J. Complex. 3(4): 372-387 (1987) - 1986
- [j1]Ilan Adler, Richard M. Karp, Ron Shamir:
A Family of Simplex Variants Solving an m × d Linear Program in Expected Number of Pivot Steps Depending on d Only. Math. Oper. Res. 11(4): 570-590 (1986)
Coauthor Index
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