| 2009 | ||
|---|---|---|
| 123 | Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan: Topology-Free Querying of Protein Interaction Networks. RECOMB 2009: 74-89 | |
| 122 | Igor Ulitsky, Ron Shamir: Identifying functional modules using expression profiles and confidence-scored protein interactions. Bioinformatics 25(9): 1158-1164 (2009) | |
| 121 | Chaim Linhart, Ron Shamir: Matching with don't-cares and a small number of mismatches. Inf. Process. Lett. 109(5): 273-277 (2009) | |
| 120 | Chaim Linhart, Ron Shamir: Faster pattern matching with character classes using prime number encoding. J. Comput. Syst. Sci. 75(3): 155-162 (2009) | |
| 119 | Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan: Torque: topology-free querying of protein interaction networks. Nucleic Acids Research 37(Web-Server-Issue): 106-108 (2009) | |
| 2008 | ||
| 118 | Igor Ulitsky, Richard M. Karp, Ron Shamir: Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles. RECOMB 2008: 347-359 | |
| 117 | Michal Ozery-Flato, Ron Shamir: Sorting Cancer Karyotypes by Elementary Operations. RECOMB-CG 2008: 211-225 | |
| 116 | Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir: A Faster Algorithm for RNA Co-folding. WABI 2008: 174-185 | |
| 115 | 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 Bioinformatics 9: (2008) | |
| 114 | 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. Biology Bioinform. 5(1): 101-109 (2008) | |
| 113 | Michal Ozery-Flato, Ron Shamir: Sorting Genomes with Centromeres by Translocations. Journal of Computational Biology 15(7): 793-812 (2008) | |
| 2007 | ||
| 112 | Michal Ozery-Flato, Ron Shamir: Rearrangements in Genomes with Centromeres Part I: Translocations. RECOMB 2007: 339-353 | |
| 111 | Ofir Davidovich, Gad Kimmel, Ron Shamir: GEVALT: An integrated software tool for genotype analysis. BMC Bioinformatics 8: (2007) | |
| 110 | Sorin Istrail, Pavel A. Pevzner, Ron Shamir: Preface. Discrete Applied Mathematics 155(6-7): 673-674 (2007) | |
| 109 | Richard M. Karp, Ming Li, Pavel A. Pevzner, Ron Shamir: Special issue on computational molecular biology. J. Comput. Syst. Sci. 73(7): 1023 (2007) | |
| 108 | Michal Ozery-Flato, Ron Shamir: Sorting by Reciprocal Translocations via Reversals Theory. Journal of Computational Biology 14(4): 408-422 (2007) | |
| 107 | Ron Shamir, Dekel Tsur: Improved algorithms for the random cluster graph model. Random Struct. Algorithms 31(4): 418-449 (2007) | |
| 2006 | ||
| 106 | Michal Ozery-Flato, Ron Shamir: An O(n3/2sqrt(log n)) Algorithm for Sorting by Reciprocal Translocations. CPM 2006: 258-269 | |
| 105 | Michal Ozery-Flato, Ron Shamir: Sorting by Translocations Via Reversals Theory. Comparative Genomics 2006: 87-98 | |
| 104 | Ron Shamir: Some Computational Challenges in Today's Bio-medicine. ESA 2006: 3 | |
| 103 | Tzvika Hartman, Ron Shamir: A simpler and faster 1.5-approximation algorithm for sorting by transpositions. Inf. Comput. 204(2): 275-290 (2006) | |
| 102 | Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir: A Probabilistic Methodology for Integrating Knowledge and Experiments on Biological Networks. Journal of Computational Biology 13(2): 165-181 (2006) | |
| 101 | Irit Gat-Viks, Richard M. Karp, Ron Shamir, Roded Sharan: Reconstructing Chain Functions in Genetic Networks. SIAM J. Discrete Math. 20(3): 727-740 (2006) | |
| 2005 | ||
| 100 | Eran Halperin, Gad Kimmel, Ron Shamir: Tag SNP selection in genotype data for maximizing SNP prediction accuracy. ISMB (Supplement of Bioinformatics) 2005: 195-203 | |
| 99 | Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir: The Factor Graph Network Model for Biological Systems. RECOMB 2005: 31-47 | |
| 98 | 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 Bioinformatics 6: 232 (2005) | |
| 97 | Gideon Dror, Rotem Sorek, Ron Shamir: Accurate identification of alternatively spliced exons using support vector machine. Bioinformatics 21(7): 897-901 (2005) | |
| 96 | Gad Kimmel, Ron Shamir: The Incomplete Perfect Phylogeny Haplotype Problem. J. Bioinformatics and Computational Biology 3(2): 359-384 (2005) | |
| 95 | Richard M. Karp, Ming Li, Pavel A. Pevzner, Ron Shamir: Guest Editors' foreword. J. Comput. Syst. Sci. 70(3): 283- (2005) | |
| 94 | Gad Kimmel, Ron Shamir: A Block-Free Hidden Markov Model for Genotypes and Its Application to Disease Association. Journal of Computational Biology 12(10): 1243-1260 (2005) | |
| 93 | Chaim Linhart, Ron Shamir: The Degenerate Primer Design Problem: Theory and Applications. Journal of Computational Biology 12(4): 431-456 (2005) | |
| 92 | 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. Journal of Computational Biology 12(6): 835-846 (2005) | |
| 2004 | ||
| 91 | 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 | |
| 90 | Ron Shamir: Computational Dissection of Regulatory Networks Using Diverse High-Throughput Data. CSB 2004: 2-3 | |
| 89 | Irit Gat-Viks, Ron Shamir, Richard M. Karp, Roded Sharan: Reconstructing Chain Functions in Genetic Networks. Pacific Symposium on Biocomputing 2004: 498-509 | |
| 88 | Gad Kimmel, Ron Shamir: Maximum likelihood resolution of multi-block genotypes. RECOMB 2004: 2-9 | |
| 87 | 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 | |
| 86 | Irit Gat-Viks, Amos Tanay, Ron Shamir: Modeling and Analysis of Heterogeneous Regulation in Biological Networks. Regulatory Genomics 2004: 98-113 | |
| 85 | Nir Orlev, Ron Shamir, Yosef Shiloh: PIVOT: Protein Interacions VisualizatiOn Tool. Bioinformatics 20(3): 424-425 (2004) | |
| 84 | Ron Shamir, Roded Sharan: A fully dynamic algorithm for modular decomposition and recognition of cographs. Discrete Applied Mathematics 136(2-3): 329-340 (2004) | |
| 83 | Ryan B. Hayward, Ron Shamir: A note on tolerance graph recognition. Discrete Applied Mathematics 143(1-3): 307-311 (2004) | |
| 82 | Ron Shamir, Roded Sharan, Dekel Tsur: Cluster graph modification problems. Discrete Applied Mathematics 144(1-2): 173-182 (2004) | |
| 81 | Gad Kimmel, Roded Sharan, Ron Shamir: Computational Problems in Noisy SNP and Haplotype Analysis: Block Scores, Block Identification, and Population Stratification. INFORMS Journal on Computing 16(4): 360-370 (2004) | |
| 80 | Amos Tanay, Ron Shamir: Multilevel Modeling and Inference of Transcription Regulation. Journal of Computational Biology 11(2/3): 357-375 (2004) | |
| 79 | Irit Gat-Viks, Amos Tanay, Ron Shamir: Modeling and Analysis of Heterogeneous Regulation in Biological Networks. Journal of Computational Biology 11(6): 1034-1049 (2004) | |
| 78 | Itsik Pe'er, Tal Pupko, Ron Shamir, Roded Sharan: Incomplete Directed Perfect Phylogeny. SIAM J. Comput. 33(3): 590-607 (2004) | |
| 2003 | ||
| 77 | Irit Gat-Viks, Ron Shamir: Chain functions and scoring functions in genetic networks. ISMB (Supplement of Bioinformatics) 2003: 108-117 | |
| 76 | Amos Tanay, Ron Shamir: Modeling transcription programs: inferring binding site activity and dose-response model optimization. RECOMB 2003: 301-310 | |
| 75 | Gad Kimmel, Roded Sharan, Ron Shamir: Identifying Blocks and Sub-populations in Noisy SNP Data. WABI 2003: 303-319 | |
| 74 | Roded Sharan, Adi Maron-Katz, Ron Shamir: CLICK and EXPANDER: a system for clustering and visualizing gene expression data. Bioinformatics 19(14): 1787-1799 (2003) | |
| 73 | Irit Gat-Viks, Roded Sharan, Ron Shamir: Scoring clustering solutions by their biological relevance. Bioinformatics 19(18): 2381-2389 (2003) | |
| 72 | Michal Ozery-Flato, Ron Shamir: Two Notes on Genome Rearrangement. J. Bioinformatics and Computational Biology 1(1): 71-94 (2003) | |
| 71 | Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Ron Shamir: The Restriction Scaffold Problem. Journal of Computational Biology 10(3/4): 385-398 (2003) | |
| 70 | Eran Halperin, Shay Halperin, Tzvika Hartman, Ron Shamir: Handling Long Targets and Errors in Sequencing by Hybridization. Journal of Computational Biology 10(3/4): 483-497 (2003) | |
| 2002 | ||
| 69 | Amos Tanay, Roded Sharan, Ron Shamir: Discovering statistically significant biclusters in gene expression data. ISMB 2002: 136-144 | |
| 68 | Chaim Linhart, Ron Shamir: The degenerate primer design problem. ISMB 2002: 172-181 | |
| 67 | Eran Halperin, Shay Halperin, Tzvika Hartman, Ron Shamir: Handling long targets and errors in sequencing by hybridization. RECOMB 2002: 176-185 | |
| 66 | Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Ron Shamir: The restriction scaffold problem. RECOMB 2002: 58-66 | |
| 65 | Ron Shamir, Dekel Tsur: Improved Algorithms for the Random Cluster Graph Model. SWAT 2002: 230-239 | |
| 64 | Itsik Pe'er, Ron Shamir, Roded Sharan: On the Generality of Phylogenies from Incomplete Directed Characters. SWAT 2002: 358-367 | |
| 63 | Ron Shamir, Roded Sharan, Dekel Tsur: Cluster Graph Modification Problems. WG 2002: 379-390 | |
| 62 | Ming Li, Pavel A. Pevzner, Ron Shamir: Foreword. J. Comput. Syst. Sci. 65(3): 441 (2002) | |
| 61 | Amir Ben-Dor, Itsik Pe'er, Ron Shamir, Roded Sharan: On the Complexity of Positional Sequencing by Hybridization. Journal of Computational Biology 8(4): 361-371 (2002) | |
| 60 | Ron Shamir, Dekel Tsur: Large Scale Sequencing by Hybridization. Journal of Computational Biology 9(2): 413-428 (2002) | |
| 2001 | ||
| 59 | Amos Tanay, Ron Shamir: Computational expansion of genetic networks. ISMB (Supplement of Bioinformatics) 2001: 270-278 | |
| 58 | Ron Shamir, Dekel Tsur: Large scale sequencing by hybridization. RECOMB 2001: 269-277 | |
| 57 | Tal Pupko, Roded Sharan, Masami Hasegawa, Ron Shamir, Dan Graur: A Chemical-Distance-Based Test for Positive Darwinian Selection. WABI 2001: 142-155 | |
| 56 | Assaf Natanzon, Ron Shamir, Roded Sharan: Complexity classification of some edge modification problems. Discrete Applied Mathematics 113(1): 109-128 (2001) | |
| 55 | Piotr Berman, Amir Ben-Dor, Itsik Pe'er, Roded Sharan, Ron Shamir: On the Complexity of Positional Sequencing by Hybridization Electronic Colloquium on Computational Complexity (ECCC) 8(54): (2001) | |
| 54 | 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) | |
| 2000 | ||
| 53 | Itsik Pe'er, Ron Shamir, Roded Sharan: Incomplete Directed Perfect Phylogeny. CPM 2000: 143-153 | |
| 52 | Itsik Pe'er, Ron Shamir: Spectrum Alignment: Efficient Resequencing by Hybridization. ISMB 2000: 260-268 | |
| 51 | Roded Sharan, Ron Shamir: Center CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis. ISMB 2000: 307-316 | |
| 50 | Sorin Istrail, Pavel A. Pevzner, Ron Shamir: Foreword. Discrete Applied Mathematics 104(1-3): 1-2 (2000) | |
| 49 | Erez Hartuv, Ron Shamir: A clustering algorithm based on graph connectivity. Inf. Process. Lett. 76(4-6): 175-181 (2000) | |
| 48 | Richard M. Karp, Ron Shamir: Algorithms for Optical Mapping. Journal of Computational Biology 7(1-2): 303-316 (2000) | |
| 47 | Ron Shamir: Preface: Special RECOMB 2000 Issue. Journal of Computational Biology 7(3-4): 329-330 (2000) | |
| 46 | Richard M. Karp, Itsik Pe'er, Ron Shamir: An Algorithm Combining Discrete and Continuous Methods for Optical Mapping. Journal of Computational Biology 7(5): 745-760 (2000) | |
| 45 | Assaf Natanzon, Ron Shamir, Roded Sharan: A Polynomial Approximation Algorithm for the Minimum Fill-In Problem. SIAM J. Comput. 30(4): 1067-1079 (2000) | |
| 1999 | ||
| 44 | Amir Ben-Dor, Itsik Pe'er, Ron Shamir, Roded Sharan: On the Complexity of Positional Sequencing by Hybridization. CPM 1999: 88-100 | |
| 43 | Pavol Hell, Ron Shamir, Roded Sharan: A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs. ESA 1999: 527-539 | |
| 42 | Richard M. Karp, Itsik Pe'er, Ron Shamir: An Algorithm Combining Discrete and Continuous Methods for Optical Mapping. ISMB 1999: 159-168 | |
| 41 | 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 | |
| 40 | Guy Mayraz, Ron Shamir: Construction of physical maps from oligonucleotide fingerprints data. RECOMB 1999: 268-277 | |
| 39 | Assaf Natanzon, Ron Shamir, Roded Sharan: Complexity Classification of Some Edge Modification Problems. WG 1999: 65-77 | |
| 38 | Haim Kaplan, Ron Shamir: Bounded Degree Interval Sandwich Problems. Algorithmica 24(2): 96-104 (1999) | |
| 37 | Ron Shamir, Dekel Tsur: Faster Subtree Isomorphism. J. Algorithms 33(2): 267-280 (1999) | |
| 36 | Guy Mayraz, Ron Shamir: Construction of Physical Maps from Oligonucleotide Fingerprints Data. Journal of Computational Biology 6(2): 237-252 (1999) | |
| 35 | Amir Ben-Dor, Ron Shamir, Zohar Yakhini: Clustering Gene Expression Patterns. Journal of Computational Biology 6(3/4): 281-297 (1999) | |
| 34 | 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) | |
| 33 | 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) | |
| 1998 | ||
| 32 | Richard M. Karp, Ron Shamir: Algorithms for optical mapping. RECOMB 1998: 117-124 | |
| 31 | Ron Shamir, Dekel Tsur: The Maximum Subforest Problem: Approximation and Exact Algorithms (Extended Abstract). SODA 1998: 394-399 | |
| 30 | Assaf Natanzon, Ron Shamir, Roded Sharan: A Polynomial Approximation Algorithm for the Minimum Fill-In Problem. STOC 1998: 41-47 | |
| 29 | Sorin Istrail, Pavel A. Pevzner, Ron Shamir: Foreword. Discrete Applied Mathematics 88(1-3): 3-6 (1998) | |
| 28 | Itsik Pe'er, Ron Shamir: The median problems for breakpoints are NP-complete Electronic Colloquium on Computational Complexity (ECCC) 5(71): (1998) | |
| 1997 | ||
| 27 | Ron Shamir, Dekel Tsur: Faster subtree isomorphism. ISTCS 1997: 126-131 | |
| 26 | Haim Kaplan, Ron Shamir, Robert Endre Tarjan: Faster and simpler algorithm for sorting signed permutations by reversals. RECOMB 1997: 163 | |
| 25 | Haim Kaplan, Ron Shamir, Robert Endre Tarjan: Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals. SODA 1997: 344-351 | |
| 24 | Itsik Pe'er, Ron Shamir: Realizing Interval Graphs with Size and Distance Constraints. SIAM J. Discrete Math. 10(4): 662-687 (1997) | |
| 23 | Itsik Pe'er, Ron Shamir: Satisfiability Problems on Intervals and Unit Intervals. Theor. Comput. Sci. 175(2): 349-372 (1997) | |
| 1996 | ||
| 22 | Haim Kaplan, Ron Shamir: Physical Maps and Interval Sandwich Problems: Bounded Degrees Help. ISTCS 1996: 195-201 | |
| 21 | Haim Kaplan, Ron Shamir: Pathwidth, Bandwidth, and Completion Problems to Proper Interval Graphs with Small Cliques. SIAM J. Comput. 25(3): 540-561 (1996) | |
| 1995 | ||
| 20 | Itsik Pe'er, Ron Shamir: Interval Graphs with Side (and Size) Constraints. ESA 1995: 142-154 | |
| 19 | Martin Charles Golumbic, Haim Kaplan, Ron Shamir: Graph Sandwich Problems. J. Algorithms 19(3): 449-473 (1995) | |
| 18 | Paul W. Goldberg, Martin Charles Golumbic, Haim Kaplan, Ron Shamir: Four Strikes Against Physical Mapping of DNA. Journal of Computational Biology 2(1): 139-152 (1995) | |
| 1994 | ||
| 17 | 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 | |
| 16 | Yaron Pinto, Ron Shamir: Efficient Algorithms for Minimum-Cost Flow Problems with Piecewise-Linear Convex Costs. Algorithmica 11(3): 256-276 (1994) | |
| 15 | Endre Boros, Peter L. Hammer, Mark E. Hartmann, Ron Shamir: Balancing Problems in Acyclic Networks. Discrete Applied Mathematics 49(1-3): 77-93 (1994) | |
| 14 | Haim Kaplan, Ron Shamir: The Domatic Number Problem on Some Perfect Graph Families. Inf. Process. Lett. 49(1): 51-56 (1994) | |
| 1993 | ||
| 13 | Martin Charles Golumbic, Haim Kaplan, Ron Shamir: Algorithms and Complexity of Sandwich Problems in Graphs (Extended Abstract). WG 1993: 57-69 | |
| 12 | Ilan Adler, Alan J. Hoffman, Ron Shamir: Monge and Feasibility Sequences in General Flow Problems. Discrete Applied Mathematics 44(1-3): 21-38 (1993) | |
| 11 | Ron Shamir: A fast algorithm for constructing monge sequences in transportation problems with forbidden arcs. Discrete Mathematics 114(1-3): 435-444 (1993) | |
| 10 | Martin Charles Golumbic, Ron Shamir: Complexity and Algorithms for Reasoning about Time: A Graph-Theoretic Approach. J. ACM 40(5): 1108-1133 (1993) | |
| 9 | 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) | |
| 1992 | ||
| 8 | Martin Charles Golumbic, Ron Shamir: Algorithms and Complexity for Reasoning about Time. AAAI 1992: 741-747 | |
| 7 | Martin Charles Golumbic, Ron Shamir: Interval Graphs, Interval Orders and the Consistency of Temporal Events. ISTCS 1992: 32-42 | |
| 6 | Endre Boros, Peter L. Hammer, Ron Shamir: A Polynomial Algorithm for Balancing Acyclic Data Flow Graphs. IEEE Trans. Computers 41(11): 1380-1385 (1992) | |
| 5 | 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) | |
| 1990 | ||
| 4 | Ron Shamir, Brenda L. Dietrich: Characterization and Algorithms for Greedily Solvable Transportation Problems. SODA 1990: 358-366 | |
| 3 | Dorit S. Hochbaum, Ron Shamir: Minimizing the number of tardy job units under release time constraints. Discrete Applied Mathematics 28(1): 45-57 (1990) | |
| 1989 | ||
| 2 | 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 | ||
| 1 | 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. Complexity 3(4): 372-387 (1987) | |