| 2009 |
|---|
| 118 | EE | Chaim Linhart,
Ron Shamir:
Matching with don't-cares and a small number of mismatches.
Inf. Process. Lett. 109(5): 273-277 (2009) |
| 117 | EE | Chaim Linhart,
Ron Shamir:
Faster pattern matching with character classes using prime number encoding.
J. Comput. Syst. Sci. 75(3): 155-162 (2009) |
| 2008 |
|---|
| 116 | EE | Igor Ulitsky,
Richard M. Karp,
Ron Shamir:
Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles.
RECOMB 2008: 347-359 |
| 115 | EE | Michal Ozery-Flato,
Ron Shamir:
Sorting Cancer Karyotypes by Elementary Operations.
RECOMB-CG 2008: 211-225 |
| 114 | EE | Michal Ziv-Ukelson,
Irit Gat-Viks,
Ydo Wexler,
Ron Shamir:
A Faster Algorithm for RNA Co-folding.
WABI 2008: 174-185 |
| 113 | EE | 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) |
| 112 | EE | Michal Ozery-Flato,
Ron Shamir:
Sorting Genomes with Centromeres by Translocations.
Journal of Computational Biology 15(7): 793-812 (2008) |
| 2007 |
|---|
| 111 | EE | Michal Ozery-Flato,
Ron Shamir:
Rearrangements in Genomes with Centromeres Part I: Translocations.
RECOMB 2007: 339-353 |
| 110 | EE | Sorin Istrail,
Pavel A. Pevzner,
Ron Shamir:
Preface.
Discrete Applied Mathematics 155(6-7): 673-674 (2007) |
| 109 | EE | 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 | EE | Michal Ozery-Flato,
Ron Shamir:
Sorting by Reciprocal Translocations via Reversals Theory.
Journal of Computational Biology 14(4): 408-422 (2007) |
| 107 | EE | Ron Shamir,
Dekel Tsur:
Improved algorithms for the random cluster graph model.
Random Struct. Algorithms 31(4): 418-449 (2007) |
| 2006 |
|---|
| 106 | EE | Michal Ozery-Flato,
Ron Shamir:
An O(n3/2sqrt(log n)) Algorithm for Sorting by Reciprocal Translocations.
CPM 2006: 258-269 |
| 105 | EE | Michal Ozery-Flato,
Ron Shamir:
Sorting by Translocations Via Reversals Theory.
Comparative Genomics 2006: 87-98 |
| 104 | EE | Ron Shamir:
Some Computational Challenges in Today's Bio-medicine.
ESA 2006: 3 |
| 103 | EE | Tzvika Hartman,
Ron Shamir:
A simpler and faster 1.5-approximation algorithm for sorting by transpositions.
Inf. Comput. 204(2): 275-290 (2006) |
| 102 | EE | 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 | EE | 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 | EE | 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 | EE | Irit Gat-Viks,
Amos Tanay,
Daniela Raijman,
Ron Shamir:
The Factor Graph Network Model for Biological Systems.
RECOMB 2005: 31-47 |
| 98 | EE | 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 | EE | Gideon Dror,
Rotem Sorek,
Ron Shamir:
Accurate identification of alternatively spliced exons using support vector machine.
Bioinformatics 21(7): 897-901 (2005) |
| 96 | EE | Gad Kimmel,
Ron Shamir:
The Incomplete Perfect Phylogeny Haplotype Problem.
J. Bioinformatics and Computational Biology 3(2): 359-384 (2005) |
| 95 | EE | Richard M. Karp,
Ming Li,
Pavel A. Pevzner,
Ron Shamir:
Guest Editors' foreword.
J. Comput. Syst. Sci. 70(3): 283- (2005) |
| 94 | EE | 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 | EE | Chaim Linhart,
Ron Shamir:
The Degenerate Primer Design Problem: Theory and Applications.
Journal of Computational Biology 12(4): 431-456 (2005) |
| 92 | EE | 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 | EE | 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 | EE | Ron Shamir:
Computational Dissection of Regulatory Networks Using Diverse High-Throughput Data.
CSB 2004: 2-3 |
| 89 | EE | Irit Gat-Viks,
Ron Shamir,
Richard M. Karp,
Roded Sharan:
Reconstructing Chain Functions in Genetic Networks.
Pacific Symposium on Biocomputing 2004: 498-509 |
| 88 | EE | Gad Kimmel,
Ron Shamir:
Maximum likelihood resolution of multi-block genotypes.
RECOMB 2004: 2-9 |
| 87 | EE | 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 | EE | Irit Gat-Viks,
Amos Tanay,
Ron Shamir:
Modeling and Analysis of Heterogeneous Regulation in Biological Networks.
Regulatory Genomics 2004: 98-113 |
| 85 | EE | Nir Orlev,
Ron Shamir,
Yosef Shiloh:
PIVOT: Protein Interacions VisualizatiOn Tool.
Bioinformatics 20(3): 424-425 (2004) |
| 84 | EE | 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 | EE | Ryan B. Hayward,
Ron Shamir:
A note on tolerance graph recognition.
Discrete Applied Mathematics 143(1-3): 307-311 (2004) |
| 82 | EE | Ron Shamir,
Roded Sharan,
Dekel Tsur:
Cluster graph modification problems.
Discrete Applied Mathematics 144(1-2): 173-182 (2004) |
| 81 | EE | 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 | EE | Amos Tanay,
Ron Shamir:
Multilevel Modeling and Inference of Transcription Regulation.
Journal of Computational Biology 11(2/3): 357-375 (2004) |
| 79 | EE | 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 | EE | Itsik Pe'er,
Tal Pupko,
Ron Shamir,
Roded Sharan:
Incomplete Directed Perfect Phylogeny.
SIAM J. Comput. 33(3): 590-607 (2004) |
| 2003 |
|---|
| 77 | EE | Irit Gat-Viks,
Ron Shamir:
Chain functions and scoring functions in genetic networks.
ISMB (Supplement of Bioinformatics) 2003: 108-117 |
| 76 | EE | Amos Tanay,
Ron Shamir:
Modeling transcription programs: inferring binding site activity and dose-response model optimization.
RECOMB 2003: 301-310 |
| 75 | EE | 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 | EE | Michal Ozery-Flato,
Ron Shamir:
Two Notes on Genome Rearrangement.
J. Bioinformatics and Computational Biology 1(1): 71-94 (2003) |
| 71 | EE | 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 | EE | 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 | EE | Eran Halperin,
Shay Halperin,
Tzvika Hartman,
Ron Shamir:
Handling long targets and errors in sequencing by hybridization.
RECOMB 2002: 176-185 |
| 66 | EE | Amir Ben-Dor,
Richard M. Karp,
Benno Schwikowski,
Ron Shamir:
The restriction scaffold problem.
RECOMB 2002: 58-66 |
| 65 | EE | Ron Shamir,
Dekel Tsur:
Improved Algorithms for the Random Cluster Graph Model.
SWAT 2002: 230-239 |
| 64 | EE | Itsik Pe'er,
Ron Shamir,
Roded Sharan:
On the Generality of Phylogenies from Incomplete Directed Characters.
SWAT 2002: 358-367 |
| 63 | EE | Ron Shamir,
Roded Sharan,
Dekel Tsur:
Cluster Graph Modification Problems.
WG 2002: 379-390 |
| 62 | EE | 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 | EE | Ron Shamir,
Dekel Tsur:
Large scale sequencing by hybridization.
RECOMB 2001: 269-277 |
| 57 | EE | 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 | EE | 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 | EE | 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 | EE | 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 | EE | 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 | EE | 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 | EE | Amir Ben-Dor,
Itsik Pe'er,
Ron Shamir,
Roded Sharan:
On the Complexity of Positional Sequencing by Hybridization.
CPM 1999: 88-100 |
| 43 | EE | 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 | EE | 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 | EE | Guy Mayraz,
Ron Shamir:
Construction of physical maps from oligonucleotide fingerprints data.
RECOMB 1999: 268-277 |
| 39 | EE | Assaf Natanzon,
Ron Shamir,
Roded Sharan:
Complexity Classification of Some Edge Modification Problems.
WG 1999: 65-77 |
| 38 | EE | 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 | EE | 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 | EE | Assaf Natanzon,
Ron Shamir,
Roded Sharan:
A Polynomial Approximation Algorithm for the Minimum Fill-In Problem.
STOC 1998: 41-47 |
| 29 | EE | Sorin Istrail,
Pavel A. Pevzner,
Ron Shamir:
Foreword.
Discrete Applied Mathematics 88(1-3): 3-6 (1998) |
| 28 | EE | Itsik Pe'er,
Ron Shamir:
The median problems for breakpoints are NP-complete
Electronic Colloquium on Computational Complexity (ECCC) 5(71): (1998) |
| 1997 |
|---|
| 27 | EE | Ron Shamir,
Dekel Tsur:
Faster subtree isomorphism.
ISTCS 1997: 126-131 |
| 26 | EE | 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 | EE | Itsik Pe'er,
Ron Shamir:
Realizing Interval Graphs with Size and Distance Constraints.
SIAM J. Discrete Math. 10(4): 662-687 (1997) |
| 23 | EE | 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 | EE | 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 | EE | Ron Shamir:
A fast algorithm for constructing monge sequences in transportation problems with forbidden arcs.
Discrete Mathematics 114(1-3): 435-444 (1993) |
| 10 | EE | 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 | EE | 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 | EE | 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) |
