| * | 2009 |
|---|
| 69 | EE | Sharon Bruckner,
Falk Hüffner,
Richard M. Karp,
Ron Shamir,
Roded Sharan:
Topology-Free Querying of Protein Interaction Networks.
RECOMB 2009: 74-89 |
| 68 | EE | 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 |
|---|
| 67 | EE | Nir Yosef,
Roded Sharan,
William Stafford Noble:
Improved network-based identification of protein orthologs.
ECCB 2008: 200-206 |
| 66 | | Oron Vanunu,
Roded Sharan:
A Propagation-based Algorithm for Inferring Gene-Disease Assocations.
German Conference on Bioinformatics 2008: 54-52 |
| 65 | EE | Maxim Kalaev,
Vineet Bafna,
Roded Sharan:
Fast and Accurate Alignment of Multiple Protein Networks.
RECOMB 2008: 246-256 |
| 64 | EE | Alexander Medvedovsky,
Vineet Bafna,
Uri Zwick,
Roded Sharan:
An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks.
WABI 2008: 222-232 |
| 63 | EE | Maxim Kalaev,
Mike Smoot,
Trey Ideker,
Roded Sharan:
NetworkBLAST: comparative analysis of protein networks.
Bioinformatics 24(4): 594-596 (2008) |
| 62 | EE | Banu Dost,
Tomer Shlomi,
Nitin Gupta,
Eytan Ruppin,
Vineet Bafna,
Roded Sharan:
QNet: A Tool for Querying Protein Interaction Networks.
Journal of Computational Biology 15(7): 913-925 (2008) |
| 2007 |
|---|
| 61 | EE | Oved Ourfali,
Tomer Shlomi,
Trey Ideker,
Eytan Ruppin,
Roded Sharan:
SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments.
ISMB/ECCB (Supplement of Bioinformatics) 2007: 359-366 |
| 60 | EE | Banu Dost,
Tomer Shlomi,
Nitin Gupta,
Eytan Ruppin,
Vineet Bafna,
Roded Sharan:
QNet: A Tool for Querying Protein Interaction Networks.
RECOMB 2007: 1-15 |
| 59 | EE | Oleg Rokhlenko,
Tomer Shlomi,
Roded Sharan,
Eytan Ruppin,
Ron Y. Pinter:
Constraint-based functional similarity of metabolic genes: going beyond network topology.
Bioinformatics 23(16): 2139-2146 (2007) |
| 58 | EE | Eitan Hirsh,
Roded Sharan:
Identification of conserved protein complexes based on a model of protein network evolution.
Bioinformatics 23(2): 170-176 (2007) |
| 57 | EE | Nir Yosef,
Zohar Yakhini,
Anya Tsalenko,
Vessela Kristensen,
Anne-Lise Børresen-Dale,
Eytan Ruppin,
Roded Sharan:
A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data.
Bioinformatics 23(2): 91-98 (2007) |
| 56 | EE | Itay Mayrose,
Osnat Penn,
Elana Erez,
Nimrod D. Rubinstein,
Tomer Shlomi,
Natalia Tarnovitski Freund,
Erez M. Bublil,
Eytan Ruppin,
Roded Sharan,
Jonathan M. Gershoni,
Eric Martz,
Tal Pupko:
Pepitope: epitope mapping from affinity-selected peptides.
Bioinformatics 23(23): 3244-3246 (2007) |
| 55 | EE | Jens Gramm,
Till Nierhoff,
Roded Sharan,
Till Tantau:
Haplotyping with missing data via perfect path phylogenies.
Discrete Applied Mathematics 155(6-7): 788-805 (2007) |
| 54 | EE | Eric P. Xing,
Michael I. Jordan,
Roded Sharan:
Bayesian Haplotype Inference via the Dirichlet Process.
Journal of Computational Biology 14(3): 267-284 (2007) |
| 2006 |
|---|
| 53 | EE | Shaojie Zhang,
Ilya Borovok,
Yair Aharonowitz,
Roded Sharan,
Vineet Bafna:
A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements.
ISMB (Supplement of Bioinformatics) 2006: 557-565 |
| 52 | EE | Oleg Rokhlenko,
Tomer Shlomi,
Roded Sharan,
Eytan Ruppin,
Ron Y. Pinter:
Flux-Based vs. Topology-Based Similarity of Metabolic Genes.
WABI 2006: 274-285 |
| 51 | EE | Jens Gramm,
Tzvika Hartman,
Till Nierhoff,
Roded Sharan,
Till Tantau:
On the Complexity of SNP Block Partitioning Under the Perfect Phylogeny Model.
WABI 2006: 92-102 |
| 50 | EE | Tomer Shlomi,
Daniel Segal,
Eytan Ruppin,
Roded Sharan:
QPath: a method for querying pathways in a protein-protein interaction network.
BMC Bioinformatics 7: 199 (2006) |
| 49 | EE | Roded Sharan,
Bjarni V. Halldórsson,
Sorin Istrail:
Islands of Tractability for Parsimony Haplotyping.
IEEE/ACM Trans. Comput. Biology Bioinform. 3(3): 303-311 (2006) |
| 48 | EE | Anya Tsalenko,
Roded Sharan,
Vessela Kristensen,
Hege Edvardsen,
Anne-Lise Børresen-Dale,
Amir Ben-Dor,
Zohar Yakhini:
Analysis of Snp-expression Association Matrices.
J. Bioinformatics and Computational Biology 4(2): 259-274 (2006) |
| 47 | EE | Eleazar Eskin,
Roded Sharan,
Eran Halperin:
A Note on Phasing Long Genomic Regions Using Local Haplotype Predictions.
J. Bioinformatics and Computational Biology 4(3): 639-648 (2006) |
| 46 | EE | Jacob Scott,
Trey Ideker,
Richard M. Karp,
Roded Sharan:
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks.
Journal of Computational Biology 13(2): 133-144 (2006) |
| 45 | 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 |
|---|
| 44 | EE | Anya Tsalenko,
Roded Sharan,
Hege Edvardsen,
Vessela Kristensen,
Anne-Lise Børresen-Dale,
Amir Ben-Dor,
Zohar Yakhini:
Analysis of SNP-Expression Association Matrices.
CSB 2005: 135-143 |
| 43 | EE | Roded Sharan,
Bjarni V. Halldórsson,
Sorin Istrail:
Islands of Tractability for Parsimony Haplotyping.
CSB 2005: 65-72 |
| 42 | EE | Roded Sharan,
Eugene W. Myers:
A motif-based framework for recognizing sequence families.
ISMB (Supplement of Bioinformatics) 2005: 387-393 |
| 41 | EE | Jacob Scott,
Trey Ideker,
Richard M. Karp,
Roded Sharan:
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks.
RECOMB 2005: 1-13 |
| 40 | EE | Silpa Suthram,
Tomer Shlomi,
Eytan Ruppin,
Roded Sharan,
Trey Ideker:
Comparison of Protein-Protein Interaction Confidence Assignment Schemes.
Systems Biology and Regulatory Genomics 2005: 39-50 |
| 39 | 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) |
| 38 | EE | Tzvika Hartman,
Roded Sharan:
A 1.5-approximation algorithm for sorting by transpositions and transreversals.
J. Comput. Syst. Sci. 70(3): 300-320 (2005) |
| 37 | EE | Roded Sharan,
Jens Gramm,
Zohar Yakhini,
Amir Ben-Dor:
Multiplexing Schemes for Generic SNP Genotyping Assays.
Journal of Computational Biology 12(5): 514-533 (2005) |
| 36 | EE | Eran Segal,
Roded Sharan:
A Discriminative Model for Identifying Spatial cis-Regulatory Modules.
Journal of Computational Biology 12(6): 822-834 (2005) |
| 35 | 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 |
|---|
| 34 | EE | Eric P. Xing,
Roded Sharan,
Michael I. Jordan:
Bayesian haplo-type inference via the dirichlet process.
ICML 2004 |
| 33 | EE | Roded Sharan,
Amir Ben-Dor,
Zohar Yakhini:
Multiplexing Schemes for Generic SNP Genotyping Assays.
Pacific Symposium on Biocomputing 2004: 140-151 |
| 32 | EE | Irit Gat-Viks,
Ron Shamir,
Richard M. Karp,
Roded Sharan:
Reconstructing Chain Functions in Genetic Networks.
Pacific Symposium on Biocomputing 2004: 498-509 |
| 31 | EE | Eran Segal,
Roded Sharan:
A discriminative model for identifying spatial cis-regulatory modules.
RECOMB 2004: 141-149 |
| 30 | 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 |
| 29 | EE | Tzvika Hartman,
Roded Sharan:
A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals.
WABI 2004: 50-61 |
| 28 | 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) |
| 27 | EE | Ron Shamir,
Roded Sharan,
Dekel Tsur:
Cluster graph modification problems.
Discrete Applied Mathematics 144(1-2): 173-182 (2004) |
| 26 | 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) |
| 25 | EE | Amir Ben-Dor,
Tzvika Hartman,
Richard M. Karp,
Benno Schwikowski,
Roded Sharan,
Zohar Yakhini:
Towards Optimally Multiplexed Applications of Universal Arrays.
Journal of Computational Biology 11(2/3): 476-492 (2004) |
| 24 | | Roded Sharan,
Asa Ben-Hur,
Gabriela G. Loots,
Ivan Ovcharenko:
CREME: Cis-Regulatory Module Explorer for the human genome.
Nucleic Acids Research 32(Web-Server-Issue): 253-256 (2004) |
| 23 | | Brian P. Kelley,
Bingbing Yuan,
Fran Lewitter,
Roded Sharan,
Brent R. Stockwell,
Trey Ideker:
PathBLAST: a tool for alignment of protein interaction networks.
Nucleic Acids Research 32(Web-Server-Issue): 83-88 (2004) |
| 22 | EE | Itsik Pe'er,
Tal Pupko,
Ron Shamir,
Roded Sharan:
Incomplete Directed Perfect Phylogeny.
SIAM J. Comput. 33(3): 590-607 (2004) |
| 2003 |
|---|
| 21 | EE | Roded Sharan,
Ivan Ovcharenko,
Asa Ben-Hur,
Richard M. Karp:
CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments.
ISMB (Supplement of Bioinformatics) 2003: 283-291 |
| 20 | EE | Amir Ben-Dor,
Tzvika Hartman,
Benno Schwikowski,
Roded Sharan,
Zohar Yakhini:
Towards optimally multiplexed applications of universal DNA tag systems.
RECOMB 2003: 48-56 |
| 19 | EE | Gad Kimmel,
Roded Sharan,
Ron Shamir:
Identifying Blocks and Sub-populations in Noisy SNP Data.
WABI 2003: 303-319 |
| 18 | | 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) |
| 17 | | Irit Gat-Viks,
Roded Sharan,
Ron Shamir:
Scoring clustering solutions by their biological relevance.
Bioinformatics 19(18): 2381-2389 (2003) |
| 2002 |
|---|
| 16 | | Amos Tanay,
Roded Sharan,
Ron Shamir:
Discovering statistically significant biclusters in gene expression data.
ISMB 2002: 136-144 |
| 15 | EE | Itsik Pe'er,
Ron Shamir,
Roded Sharan:
On the Generality of Phylogenies from Incomplete Directed Characters.
SWAT 2002: 358-367 |
| 14 | EE | Ron Shamir,
Roded Sharan,
Dekel Tsur:
Cluster Graph Modification Problems.
WG 2002: 379-390 |
| 13 | | 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) |
| 2001 |
|---|
| 12 | EE | Tal Pupko,
Roded Sharan,
Masami Hasegawa,
Ron Shamir,
Dan Graur:
A Chemical-Distance-Based Test for Positive Darwinian Selection.
WABI 2001: 142-155 |
| 11 | | Assaf Natanzon,
Ron Shamir,
Roded Sharan:
Complexity classification of some edge modification problems.
Discrete Applied Mathematics 113(1): 109-128 (2001) |
| 10 | 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) |
| 9 | 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 |
|---|
| 8 | EE | Itsik Pe'er,
Ron Shamir,
Roded Sharan:
Incomplete Directed Perfect Phylogeny.
CPM 2000: 143-153 |
| 7 | | Roded Sharan,
Ron Shamir:
Center CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis.
ISMB 2000: 307-316 |
| 6 | 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 |
|---|
| 5 | EE | Amir Ben-Dor,
Itsik Pe'er,
Ron Shamir,
Roded Sharan:
On the Complexity of Positional Sequencing by Hybridization.
CPM 1999: 88-100 |
| 4 | EE | Pavol Hell,
Ron Shamir,
Roded Sharan:
A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs.
ESA 1999: 527-539 |
| 3 | EE | Assaf Natanzon,
Ron Shamir,
Roded Sharan:
Complexity Classification of Some Edge Modification Problems.
WG 1999: 65-77 |
| 1998 |
|---|
| 2 | EE | Assaf Natanzon,
Ron Shamir,
Roded Sharan:
A Polynomial Approximation Algorithm for the Minimum Fill-In Problem.
STOC 1998: 41-47 |
| 1996 |
|---|
| 1 | | Roded Sharan,
Avi Wigderson:
A New NCAlgorithm for Perfect Matching in Bipartite Cubic Graphs.
ISTCS 1996: 202-207 |
