Ron Shamir - researchr alias

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2011

2010

Detecting Highways of Horizontal Gene TransferMukul S. Bansal, J. Peter Gogarten, Ron Shamir. recomb 2010: 109-120 [doi]

Discovering Transcriptional Modules by Combined Analysis of Expression Profiles and Regulatory SequencesYonit Halperin, Chaim Linhart, Igor Ulitsky, Ron Shamir. recomb 2010: 578-579 [doi]

2009

Topology-Free Querying of Protein Interaction NetworksSharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan. recomb 2009: 74-89 [doi]

Torque: topology-free querying of protein interaction networksSharon Bruckner, Falk HÃ¼ffner, Richard M. Karp, Ron Shamir, Roded Sharan. nar, 37(Web-Server-Issue):106-108, 2009. [doi]

Matching with don t-cares and a small number of mismatchesChaim Linhart, Ron Shamir. ipl, 109(5):273-277, 2009. [doi]

Faster pattern matching with character classes using prime number encodingChaim Linhart, Ron Shamir. jcss, 75(3):155-162, 2009. [doi]

Assessing the Quality of Whole Genome Alignments in BacteriaFiras Swidan, Ron Shamir. abi, 2009, 2009. [doi]

Identifying functional modules using expression profiles and confidence-scored protein interactionsIgor Ulitsky, Ron Shamir. bioinformatics, 25(9):1158-1164, 2009. [doi]

2008

Computational Problems in Perfect Phylogeny Haplotyping: Typing without Calling the AlleleTamar Barzuza, Jacques S. Beckmann, Ron Shamir, Itsik Pe er. tcbb, 5(1):101-109, 2008. [doi]

SPIKE - a database, visualization and analysis tool of cellular signaling pathwaysRan 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. bmcbi, 9, 2008. [doi]

Sorting Genomes with Centromeres by TranslocationsMichal Ozery-Flato, Ron Shamir. jcb, 15(7):793-812, 2008. [doi]

Sorting Cancer Karyotypes by Elementary OperationsMichal Ozery-Flato, Ron Shamir. recomb 2008: 211-225 [doi]

Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression ProfilesIgor Ulitsky, Richard M. Karp, Ron Shamir. recomb 2008: 347-359 [doi]

A Faster Algorithm for RNA Co-foldingMichal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir. wabi 2008: 174-185 [doi]

2007

GEVALT: An integrated software tool for genotype analysisOfir Davidovich, Gad Kimmel, Ron Shamir. bmcbi, 8, 2007. [doi]

PrefaceSorin Istrail, Pavel A. Pevzner, Ron Shamir. DAM, 155(6-7):673-674, 2007. [doi]

Special issue on computational molecular biologyRichard M. Karp, Ming Li, Pavel A. Pevzner, Ron Shamir. jcss, 73(7):1023, 2007. [doi]

Sorting by Reciprocal Translocations via Reversals TheoryMichal Ozery-Flato, Ron Shamir. jcb, 14(4):408-422, 2007. [doi]

Rearrangements in Genomes with Centromeres Part I: TranslocationsMichal Ozery-Flato, Ron Shamir. recomb 2007: 339-353 [doi]

Improved algorithms for the random cluster graph modelRon Shamir, Dekel Tsur. rsa, 31(4):418-449, 2007. [doi]

2006

2005

Accurate identification of alternatively spliced exons using support vector machineGideon Dror, Rotem Sorek, Ron Shamir. bioinformatics, 21(7):897-901, 2005. [doi]

The Factor Graph Network Model for Biological SystemsIrit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir. recomb 2005: 31-47 [doi]

Tag SNP selection in genotype data for maximizing SNP prediction accuracyEran Halperin, Gad Kimmel, Ron Shamir. ismb 2005: 195-203 [doi]

Guest Editors forewordRichard M. Karp, Ming Li, Pavel A. Pevzner, Ron Shamir. jcss, 70(3):283, 2005. [doi]

The Incomplete Perfect Phylogeny Haplotype ProblemGad Kimmel, Ron Shamir. jbcb, 3(2):359-384, 2005. [doi]

A Block-Free Hidden Markov Model for Genotypes and Its Application to Disease AssociationGad Kimmel, Ron Shamir. jcb, 12(10):1243-1260, 2005. [doi]

The Degenerate Primer Design Problem: Theory and ApplicationsChaim Linhart, Ron Shamir. jcb, 12(4):431-456, 2005. [doi]

::::EXPANDER ::::- an integrative program suite for microarray data analysisRon Shamir, Adi Maron-Katz, Amos Tanay, Chaim Linhart, Israel Steinfeld, Roded Sharan, Yosef Shiloh, Ran Elkon. bmcbi, 6:232, 2005. [doi]

Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction DataRoded Sharan, Trey Ideker, Brian P. Kelley, Ron Shamir, Richard M. Karp. jcb, 12(6):835-846, 2005. [doi]

2004

Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPsTamar Barzuza, Jacques S. Beckmann, Ron Shamir, Itsik Pe er. cpm 2004: 14-31 [doi]

Incomplete Directed Perfect PhylogenyItsik Pe er, Tal Pupko, Ron Shamir, Roded Sharan. siamcomp, 33(3):590-607, 2004. [doi]

Reconstructing Chain Functions in Genetic NetworksIrit Gat-Viks, Ron Shamir, Richard M. Karp, Roded Sharan. psb 2004: 498-509 [doi]

Modeling and Analysis of Heterogeneous Regulation in Biological NetworksIrit Gat-Viks, Amos Tanay, Ron Shamir. recomb 2005: 98-113 [doi]

Modeling and Analysis of Heterogeneous Regulation in Biological NetworksIrit Gat-Viks, Amos Tanay, Ron Shamir. jcb, 11(6):1034-1049, 2004. [doi]

A note on tolerance graph recognitionRyan B. Hayward, Ron Shamir. DAM, 143(1-3):307-311, 2004. [doi]

Maximum likelihood resolution of multi-block genotypesGad Kimmel, Ron Shamir. recomb 2004: 2-9 [doi]

Computational Problems in Noisy SNP and Haplotype Analysis: Block Scores, Block Identification, and Population StratificationGad Kimmel, Roded Sharan, Ron Shamir. informs, 16(4):360-370, 2004. [doi]

PIVOT: Protein Interacions VisualizatiOn ToolNir Orlev, Ron Shamir, Yosef Shiloh. bioinformatics, 20(3):424-425, 2004. [doi]

A fully dynamic algorithm for modular decomposition and recognition of cographsRon Shamir, Roded Sharan. DAM, 136(2-3):329-340, 2004. [doi]

Computational Dissection of Regulatory Networks Using Diverse High-Throughput DataRon Shamir. csb 2004: 2-3 [doi]

Cluster graph modification problemsRon Shamir, Roded Sharan, Dekel Tsur. DAM, 144(1-2):173-182, 2004. [doi]

Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction dataRoded Sharan, Trey Ideker, Brian P. Kelley, Ron Shamir, Richard M. Karp. recomb 2004: 282-289 [doi]

Multilevel Modeling and Inference of Transcription RegulationAmos Tanay, Ron Shamir. jcb, 11(2/3):357-375, 2004. [doi]

2003

The Restriction Scaffold ProblemAmir Ben-Dor, Richard M. Karp, Benno Schwikowski, Ron Shamir. jcb, 10(3/4):385-398, 2003. [doi]

Scoring clustering solutions by their biological relevanceIrit Gat-Viks, Roded Sharan, Ron Shamir. bioinformatics, 19(18):2381-2389, 2003.

Chain functions and scoring functions in genetic networksIrit Gat-Viks, Ron Shamir. ismb 2003: 108-117 [doi]

Handling Long Targets and Errors in Sequencing by HybridizationEran Halperin, Shay Halperin, Tzvika Hartman, Ron Shamir. jcb, 10(3/4):483-497, 2003. [doi]

Identifying Blocks and Sub-populations in Noisy SNP DataGad Kimmel, Roded Sharan, Ron Shamir. wabi 2003: 303-319 [doi]

Two Notes on Genome RearrangementMichal Ozery-Flato, Ron Shamir. jbcb, 1(1):71-94, 2003. [doi]

CLICK and EXPANDER: a system for clustering and visualizing gene expression dataRoded Sharan, Adi Maron-Katz, Ron Shamir. bioinformatics, 19(14):1787-1799, 2003.

Modeling transcription programs: inferring binding site activity and dose-response model optimizationAmos Tanay, Ron Shamir. recomb 2003: 301-310 [doi]

2002

On the Complexity of Positional Sequencing by HybridizationAmir Ben-Dor, Itsik Pe er, Ron Shamir, Roded Sharan. jcb, 8(4):361-371, 2002.

The restriction scaffold problemAmir Ben-Dor, Richard M. Karp, Benno Schwikowski, Ron Shamir. recomb 2002: 58-66 [doi]

On the Generality of Phylogenies from Incomplete Directed CharactersItsik Pe er, Ron Shamir, Roded Sharan. swat 2002: 358-367 [doi]

Handling long targets and errors in sequencing by hybridizationEran Halperin, Shay Halperin, Tzvika Hartman, Ron Shamir. recomb 2002: 176-185 [doi]

ForewordMing Li, Pavel A. Pevzner, Ron Shamir. jcss, 65(3):441, 2002. [doi]

The degenerate primer design problemChaim Linhart, Ron Shamir. ismb 2002: 172-181

Large Scale Sequencing by HybridizationRon Shamir, Dekel Tsur. jcb, 9(2):413-428, 2002.

Improved Algorithms for the Random Cluster Graph ModelRon Shamir, Dekel Tsur. swat 2002: 230-239 [doi]

Cluster Graph Modification ProblemsRon Shamir, Roded Sharan, Dekel Tsur. criwg 2002: 379-390 [doi]

Discovering statistically significant biclusters in gene expression dataAmos Tanay, Roded Sharan, Ron Shamir. ismb 2002: 136-144

2001

2000

Spectrum Alignment: Efficient Resequencing by HybridizationItsik Pe er, Ron Shamir. ismb 2000: 260-268

Incomplete Directed Perfect PhylogenyItsik Pe er, Ron Shamir, Roded Sharan. cpm 2000: 143-153 [doi]

A clustering algorithm based on graph connectivityErez Hartuv, Ron Shamir. ipl, 76(4-6):175-181, 2000. [doi]

ForewordSorin Istrail, Pavel A. Pevzner, Ron Shamir. DAM, 104(1-3):1-2, 2000.

Algorithms for Optical MappingRichard M. Karp, Ron Shamir. jcb, 7(1-2):303-316, 2000.

An Algorithm Combining Discrete and Continuous Methods for Optical MappingRichard M. Karp, Itsik Pe er, Ron Shamir. jcb, 7(5):745-760, 2000.

A Polynomial Approximation Algorithm for the Minimum Fill-In ProblemAssaf Natanzon, Ron Shamir, Roded Sharan. siamcomp, 30(4):1067-1079, 2000. [doi]

Preface: Special RECOMB 2000 IssueRon Shamir. jcb, 7(3-4):329-330, 2000.

Center CLICK: A Clustering Algorithm with Applications to Gene Expression AnalysisRoded Sharan, Ron Shamir. ismb 2000: 307-316

1999

On the Complexity of Positional Sequencing by HybridizationAmir Ben-Dor, Itsik Pe er, Ron Shamir, Roded Sharan. cpm 1999: 88-100 [doi]

Clustering Gene Expression PatternsAmir Ben-Dor, Ron Shamir, Zohar Yakhini. jcb, 6(3/4):281-297, 1999.

An algorithm for clustering cDNAs for gene expression analysisErez Hartuv, Armin O. Schmitt, Jörg Lange, Sebastian Meier-Ewert, Hans Lehrach, Ron Shamir. recomb 1999: 188-197 [doi]

A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval GraphsPavol Hell, Ron Shamir, Roded Sharan. esa 1999: 527-539 [doi]

Bounded Degree Interval Sandwich ProblemsHaim Kaplan, Ron Shamir. algorithmica, 24(2):96-104, 1999. [doi]

A Faster and Simpler Algorithm for Sorting Signed Permutations by ReversalsHaim Kaplan, Ron Shamir, Robert Endre Tarjan. siamcomp, 29(3):880-892, 1999.

Tractability of Parameterized Completion Problems on Chordal, Strongly Chordal, and Proper Interval GraphsHaim Kaplan, Ron Shamir, Robert Endre Tarjan. siamcomp, 28(5):1906-1922, 1999.

An Algorithm Combining Discrete and Continuous Methods for Optical MappingRichard M. Karp, Itsik Pe er, Ron Shamir. ismb 1999: 159-168

Construction of Physical Maps from Oligonucleotide Fingerprints DataGuy Mayraz, Ron Shamir. jcb, 6(2):237-252, 1999.

Construction of physical maps from oligonucleotide fingerprints dataGuy Mayraz, Ron Shamir. recomb 1999: 268-277 [doi]

Complexity Classification of Some Edge Modification ProblemsAssaf Natanzon, Ron Shamir, Roded Sharan. criwg 1999: 65-77 [doi]

Faster Subtree IsomorphismRon Shamir, Dekel Tsur. jal, 33(2):267-280, 1999.

1998

ForewordSorin Istrail, Pavel A. Pevzner, Ron Shamir. DAM, 88(1-3):3-6, 1998. [doi]

A Polynomial Approximation Algorithm for the Minimum Fill-In ProblemAssaf Natanzon, Ron Shamir, Roded Sharan. stoc 1998: 41-47 [doi]

The Maximum Subforest Problem: Approximation and Exact Algorithms (Extended Abstract)Ron Shamir, Dekel Tsur. soda 1998: 394-399

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