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Ron Shamir

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Oligonucleotide Array Sequence Analysis

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Publications

TOP 3
Yaron Orenstein; Eran Mick; Ron Shamir
RAP: Accurate and Fast Motif Finding Based on Protein-Binding Microarray Data.
David Amar; Hershel Safer; Ron Shamir
Dissection of regulatory networks that are altered in disease via differential co-expression.
Mukul S Bansal; J Peter Gogarten; Timothy J Harlow; Guy Banay; Ron Shamir
Systematic inference of highways of horizontal gene transfer in prokaryotes.

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All Publications

2013: Yaron Orenstein; Eran Mick; Ron Shamir
RAP: Accurate and Fast Motif Finding Based on Protein-Binding Microarray Data.
Journal of computational biology : a journal of computational molecular cell biology 2013;20(5):375-82.
2013: David Amar; Hershel Safer; Ron Shamir
Dissection of regulatory networks that are altered in disease via differential co-expression.
PLoS computational biology 2013;9(3):e1002955.
2013: Mukul S Bansal; J Peter Gogarten; Timothy J Harlow; Guy Banay; Ron Shamir
Systematic inference of highways of horizontal gene transfer in prokaryotes.
Bioinformatics (Oxford, England) 2013;29(5):571-9.
2012: Ofer Lavi; Gideon Dror; Ron Shamir
Network-induced classification kernels for gene expression profile analysis.
Journal of computational biology : a journal of computational molecular cell biology 2012;19(6):694-709.
2012: Yaron Orenstein; Chaim Linhart; Ron Shamir
Assessment of algorithms for inferring positional weight matrix motifs of transcription factor binding sites using protein binding microarray data.
PloS one 2012;7(9):e46145.
2012: Roye Rozov; Eran Halperin; Ron Shamir
MGMR: leveraging RNA-Seq population data to optimize expression estimation.
BMC bioinformatics 2012;13 Suppl 6():S2.
2012: Shelly Hagag; Paula Kubitschek-Barreira; Leila Lopes-Bezerra; Gabriela W P Neves; William Nierman; Itamar Shalit; Ron Shamir; David Amar; Nir Osherov
Transcriptional and proteomic analysis of the Aspergillus fumigatus ΔprtT protease-deficient mutant.
PloS one 2012;7(4):e33604.
2012: Guy Karlebach; Ron Shamir
Constructing logical models of gene regulatory networks by integrating transcription factor-DNA interactions with expression data: an entropy-based approach.
Journal of computational biology : a journal of computational molecular cell biology 2012;19(1):30-41.
2012: Chaim Linhart; Limor Broday; Yonit Halperin; Amir Darom; Shahar Kidron; Ron Shamir
A novel candidate cis-regulatory motif pair in the promoters of germline and oogenesis genes in C. elegans.
Genome research 2012;22(1):76-83.
2011: Mukul S Bansal; J Peter Gogarten; Guy Banay; Ron Shamir
Detecting highways of horizontal gene transfer.
Journal of computational biology : a journal of computational molecular cell biology 2011;18(9):1087-114.
2011: Sharon Rashi-Elkeles; Gideon Rechavi; Ron Shamir; Seagull Shavit; Ninette Amariglio; Ran Elkon; Ana Kupershtein; Yaniv lerenthal; Chaim Linhart; Yosef Shiloh
Transcriptional modulation induced by ionizing radiation: p53 remains a central player.
Molecular oncology 2011;5(4):336-48.
2011: Pavel A Pevzner; Ron Shamir
Preface: 2nd Satellite Meeting on Bioinformatics Education, Research in Computational Molecular Biology (RECOMB-BE 2010).
Journal of computational biology : a journal of computational molecular cell biology 2011;18(7):865.
2011: Mukul S Bansal; Ron Shamir
A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2011;8(3):848-50.
2011: Louise C Laurent; Igor Ulitsky; Ileana Slavin; Ha Tran; Andrew Schork; Robert Morey; Candace Lynch; Julie V Harness; Sunray Lee; Maria J Barrero; Sherman Ku; Marina Martynova; Ruslan Semechkin; Vasiliy Galat; Joel M Gottesfeld; Juan Carlos Izpisua-Belmonte; Chuck Murry; Hans S Keirstead; Hyun-Sook Park; Uli Schmidt; Andrew L Laslett; Franz-Josef Muller; Caroline M Nievergelt; Ron Shamir; Jeanne F Loring
Dynamic changes in the copy number of pluripotency and cell proliferation genes in human ESCs and iPSCs during reprogramming and time in culture.
Cell stem cell 2011;8(1):106-18.
2011: Liraz Marom; Ron Shamir; Igor Ulitsky; Yuval Cabilly; Orna Elroy-Stein
A point mutation in translation initiation factor eIF2B leads to function--and time-specific changes in brain gene expression.
PloS one 2011;6(10):e26992.
2011: Michal Ozery-Flato; Shai Izraeli; Chaim Linhart; Luba Trakhtenbrot; Ron Shamir
Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy.
Genome biology 2011;12(6):R61.
2011: Tal Elkan-Miller; Igor Ulitsky; Ronna Hertzano; Anya Rudnicki; Amiel A Dror; Danielle R Lenz; Ran Elkon; Martin Irmler; Johannes Beckers; Ron Shamir; Karen B Avraham
Integration of transcriptomics, proteomics, and microRNA analyses reveals novel microRNA regulation of targets in the mammalian inner ear.
PloS one 2011;6(4):e18195.
2011: haim, chaim sharon; David Amar; Emma Levdansky; Gabriel Mircus; Yona Shadkchan; Ron Shamir; Nir Osherov
PrtT-regulated proteins secreted by Aspergillus fumigatus activate MAPK signaling in exposed A549 lung cells leading to necrotic cell death.
PloS one 2011;6(3):e17509.
2011: 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 research 2011;39(Database issue):D793-9.
2010: Michal Ziv-Ukelson; Irit Gat-Viks; Ydo Wexler; Ron Shamir
A faster algorithm for simultaneous alignment and folding of RNA.
Journal of computational biology : a journal of computational molecular cell biology 2010;17(8):1051-65.
2010: Igor Ulitsky; Louise C Laurent; Ron Shamir
Towards computational prediction of microRNA function and activity.
Nucleic acids research 2010;38(15):e160.
2010: Pablo S Aguilar; Florian Fröhlich; Michael Rehman; Mike Shales; Igor Ulitsky; Agustina Olivera-Couto; Hannes Braberg; Ron Shamir; Peter Walter; Matthias Mann; Christer S Ejsing; Nevan J Krogan; Tobias C Walther
A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking.
Nature structural & molecular biology 2010;17(7):901-8.
2010: Shira Yaari-Stark; Maayan Shaked; Yael Nevo-Caspi; Jasmine Jacob-Hircsh; Ron Shamir; Gideon Rechavi; Yoel Kloog
Ras inhibits endoplasmic reticulum stress in human cancer cells with amplified Myc.
International journal of cancer. Journal international du cancer 2010;126(10):2268-81.
2010: Sharon Bruckner; Falk Hüffner; Richard M Karp; Ron Shamir; Roded Sharan
Topology-free querying of protein interaction networks.
Journal of computational biology : a journal of computational molecular cell biology 2010;17(3):237-52.
2010: Igor Ulitsky; Adi Maron-Katz; Seagull Shavit; Dorit Sagir; Chaim Linhart; Ran Elkon; Amos Tanay; Roded Sharan; Yosef Shiloh; Ron Shamir
Expander: from expression microarrays to networks and functions.
Nature protocols 2010;5(2):303-22.
2010: Igor Ulitsky; Akshay Krishnamurthy; Richard M Karp; Ron Shamir
DEGAS: de novo discovery of dysregulated pathways in human diseases.
PloS one 2010;5(10):e13367.
2010: Guy Karlebach; Ron Shamir
Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case.
BMC systems biology 2010;4():15.
2010: Gal Hagit Romano; Yonat Gurvich; Ofer Lavi; Igor Ulitsky; Ron Shamir; Martin Kupiec
Different sets of QTLs influence fitness variation in yeast.
Molecular systems biology 2010;6():346.
2010: Irit Gat-Viks; Renana Meller; Martin Kupiec; Ron Shamir
Understanding gene sequence variation in the context of transcription regulation in yeast.
PLoS genetics 2010;6(1):e1000800.
2009: Michal Ozery-Flato; Ron Shamir
Sorting cancer karyotypes by elementary operations.
Journal of computational biology : a journal of computational molecular cell biology 2009;16(10):1445-60.
2009: Pavel Pevzner; Ron Shamir
Computing has changed biology--biology education must catch up.
Science (New York, N.Y.) 2009;325(5940):541-2.
2009: Sharon Bruckner; Falk Hüffner; Richard M Karp; Ron Shamir; Roded Sharan
TORQUE: topology-free querying of protein interaction networks.
Nucleic acids research 2009;37(Web Server issue):W106-8.
2009: Igor Ulitsky; Ron Shamir
Identifying functional modules using expression profiles and confidence-scored protein interactions.
Bioinformatics (Oxford, England) 2009;25(9):1158-64.
2009: Yonit Halperin; Chaim Linhart; Igor Ulitsky; Ron Shamir
Allegro: analyzing expression and sequence in concert to discover regulatory programs.
Nucleic acids research 2009;37(5):1566-79.
2009: Firas Swidan; Ron Shamir
Assessing the quality of whole genome alignments in bacteria.
Advances in bioinformatics 2009;():749027.
2009: Igor Ulitsky; Nevan J Krogan; Ron Shamir
Towards accurate imputation of quantitative genetic interactions.
Genome biology 2009;10(12):R140.
2009: Michael Gutkin; Ron Shamir; Gideon Dror
SlimPLS: a method for feature selection in gene expression-based disease classification.
PloS one 2009;4(7):e6416.
2008: Guy Karlebach; Ron Shamir
Modelling and analysis of gene regulatory networks.
Nature reviews. Molecular cell biology 2008;9(10):770-80.
2008: Franz-Josef Müller; Louise C Laurent; Dennis Kostka; Igor Ulitsky; Roy Williams; Christina Lu; In-Hyun Park; Mahendra S Rao; Ron Shamir; Philip H Schwartz; Nils O Schmidt; Jeanne F Loring
Regulatory networks define phenotypic classes of human stem cell lines.
Nature 2008;455(7211):401-5.
2008: Michal Ozery-Flato; Ron Shamir
Sorting genomes with centromeres by translocations.
Journal of computational biology : a journal of computational molecular cell biology 2008;15(7):793-812.
2008: Chaim Linhart; Yonit Halperin; Ron Shamir
Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets.
Genome research 2008;18(7):1180-9.
2008: Louise C Laurent; Jing Chen; Igor Ulitsky; Franz-Josef Mueller; Christina Lu; Ron Shamir; Jian-Bing Fan; Jeanne F Loring
Comprehensive microRNA profiling reveals a unique human embryonic stem cell signature dominated by a single seed sequence.
Stem cells (Dayton, Ohio) 2008;26(6):1506-16.
2008: Igor Ulitsky; Ron Shamir
Detecting pathways transcriptionally correlated with clinical parameters.
Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference 2008;7():249-58.
2008: Igor Ulitsky; Tomer Shlomi; Martin Kupiec; Ron Shamir
From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions.
Molecular systems biology 2008;4():209.
2008: 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 2008;9():110.
2008: Tamar Barzuza; Jacques Beckmann; Ron Shamir; Itsik Pe'er
Computational problems in perfect phylogeny haplotyping: typing without calling the allele.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2008;5(1):101-9.
2008: Daniela Raijman; Ron Shamir; Amos Tanay
Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites.
PLoS computational biology 2008;4(1):e7.
2008: Igor Ulitsky; Irit Gat-Viks; Ron Shamir
MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data.
Genome biology 2008;9(1):R1.
2007: Arie Levine; Subra Kugathasan; Vito Annese; Vincent Biank; Esther Leshinsky-Silver; Ofir Davidovich; Gad Kimmel; Ron Shamir; Orazio Palmieri; Palmieri Orazio; Amir Karban; Ulrich Broeckel; Salvatore Cucchiara
Pediatric onset Crohn's colitis is characterized by genotype-dependent age-related susceptibility.
Inflammatory bowel diseases 2007;13(12):1509-15.
2007: Gad Kimmel; Michael I Jordan; Eran Halperin; Ron Shamir; Richard M Karp
A randomization test for controlling population stratification in whole-genome association studies.
American journal of human genetics 2007;81(5):895-905.
2007: Esther Leshinsky-Silver; Amir Karban; S Cohen; M Fridlander; O Davidowich; Gad Kimmel; Ron Shamir; Arie Levine
Lack of association of the 3'-UTR polymorphism in the NFKBIA gene with Crohn's disease in an Israeli cohort.
International journal of colorectal disease 2007;22(9):1021-5.
2007: Amir Karban; Maza Itay; Ofir Davidovich; Esther Leshinsky-Silver; Gad Kimmel; Herma H Fidder; Ron Shamir; Matti Waterman; Rami Eliakim; Arie Levine
Risk factors for perianal Crohn's disease: the role of genotype, phenotype, and ethnicity.
The American journal of gastroenterology 2007;102(8):1702-8.
2007: Michal Ozery-Flato; Ron Shamir
Sorting by reciprocal translocations via reversals theory.
Journal of computational biology : a journal of computational molecular cell biology 2007;14(4):408-22.
2007: Roy Blum; Ran Elkon; Shira Yaari; Adi Zundelevich; Jasmine Jacob-Hirsch; Gideon Rechavi; Ron Shamir; Yoel Kloog
Gene expression signature of human cancer cell lines treated with the ras inhibitor salirasib (S-farnesylthiosalicylic acid).
Cancer research 2007;67(7):3320-8.
2007: Israel Steinfeld; Ron Shamir; Martin Kupiec
A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription.
Nature genetics 2007;39(3):303-9.
2007: Irit Gat-Viks; Ron Shamir
Refinement and expansion of signaling pathways: the osmotic response network in yeast.
Genome research 2007;17(3):358-67.
2007: Ran Elkon; Chaim Linhart; Yonit Halperin; Yosef Shiloh; Ron Shamir
Functional genomic delineation of TLR-induced transcriptional networks.
BMC genomics 2007;8():394.
2007: Chaim Linhart; Ron Shamir
Degenerate primer design: theoretical analysis and the HYDEN program.
Methods in molecular biology (Clifton, N.J.) 2007;402():221-44.
2007: Igor Ulitsky; Ron Shamir
Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks.
Molecular systems biology 2007;3():104.
2007: Igor Ulitsky; Ron Shamir
Identification of functional modules using network topology and high-throughput data.
BMC systems biology 2007;1():8.
2007: Roded Sharan; Igor Ulitsky; Ron Shamir
Network-based prediction of protein function.
Molecular systems biology 2007;3():88.
2007: Ofir Davidovich; Gad Kimmel; Ron Shamir
GEVALT: an integrated software tool for genotype analysis.
BMC bioinformatics 2007;8():36.
2006: Gad Kimmel; Ron Shamir
A fast method for computing high-significance disease association in large population-based studies.
American journal of human genetics 2006;79(3):481-92.
2006: Archana Belle; Amos Tanay; Ledion Bitincka; Ron Shamir; Erin K O'Shea
Quantification of protein half-lives in the budding yeast proteome.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(35):13004-9.
2006: Roy Blum; Itay Nakdimon; Liat Goldberg; Ran Elkon; Ron Shamir; Gideon Rechavi; Yoel Kloog
E2F1 identified by promoter and biochemical analysis as a central target of glioblastoma cell-cycle arrest in response to Ras inhibition.
International journal of cancer. Journal international du cancer 2006;119(3):527-38.
2006: M Koren; G Kimmel; E Ben-Asher; Inbar Gal; Moshe Z Papa; Jacques Beckmann; D Lancet; Ron Shamir; Eitan Friedman
ATM haplotypes and breast cancer risk in Jewish high-risk women.
British journal of cancer 2006;94(10):1537-43.
2006: Inbar Gal; Gad Kimmel; Ruth Gershoni-Baruch; Moshe Z Papa; Efrat Dagan; Ron Shamir; Eitan Friedman
A specific RAD51 haplotype increases breast cancer risk in Jewish non-Ashkenazi high-risk women.
European journal of cancer (Oxford, England : 1990) 2006;42(8):1129-34.
2006: Sharon Rashi-Elkeles; Ran Elkon; Nir Weizman; Chaim Linhart; Ninette Amariglio; G Sternberg; Gideon Rechavi; Ari Barzilai; Ron Shamir; Yosef Shiloh
Parallel induction of ATM-dependent pro- and antiapoptotic signals in response to ionizing radiation in murine lymphoid tissue.
Oncogene 2006;25(10):1584-92.
2006: Irit Gat-Viks; Amos Tanay; Daniela Raijman; Ron Shamir
A probabilistic methodology for integrating knowledge and experiments on biological networks.
Journal of computational biology : a journal of computational molecular cell biology 2006;13(2):165-81.
2006: Rotem Sorek; Gideon Dror; Ron Shamir
Assessing the number of ancestral alternatively spliced exons in the human genome.
BMC genomics 2006;7():273.
2005: Gad Kimmel; Ron Shamir
A block-free hidden Markov model for genotypes and its application to disease association.
Journal of computational biology : a journal of computational molecular cell biology 2005;12(10):1243-60.
2005: Chaim Linhart; Ran Elkon; Yosef Shiloh; Ron Shamir
Deciphering transcriptional regulatory elements that encode specific cell cycle phasing by comparative genomics analysis.
Cell cycle (Georgetown, Tex.) 2005;4(12):1788-97.
2005: Tamar Barzuza; Jacques Beckmann; Ron Shamir; Itsik Pe'er
Typing without calling the allele: a strategy for inferring SNP haplotypes.
European journal of human genetics : EJHG 2005;13(8):898-901.
2005: 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 : a journal of computational molecular cell biology 2005;12(6):835-46.
2005: Eran Halperin; Gad Kimmel; Ron Shamir
Tag SNP selection in genotype data for maximizing SNP prediction accuracy.
Bioinformatics (Oxford, England) 2005;21 Suppl 1():i195-203.
2005: Amos Tanay; Aviv Regev; Ron Shamir
Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(20):7203-8.
2005: Chaim Linhart; Ron Shamir
The degenerate primer design problem: theory and applications.
Journal of computational biology : a journal of computational molecular cell biology 2005;12(4):431-56.
2005: Gad Kimmel; Ron Shamir
The incomplete perfect phylogeny haplotype problem.
Journal of bioinformatics and computational biology 2005;3(2):359-84.
2005: Gideon Dror; Rotem Sorek; Ron Shamir
Accurate identification of alternatively spliced exons using support vector machine.
Bioinformatics (Oxford, England) 2005;21(7):897-901.
2005: Gad Kimmel; Ron Shamir
GERBIL: Genotype resolution and block identification using likelihood.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(1):158-62.
2005: Amos Tanay; Israel Steinfeld; Martin Kupiec; Ron Shamir
Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium.
Molecular systems biology 2005;1():2005.0002.
2005: Aimée M Dudley; Daniel M Janse; Amos Tanay; Ron Shamir; George M Church
A global view of pleiotropy and phenotypically derived gene function in yeast.
Molecular systems biology 2005;1():2005.0001.
2005: Reut Shalgi; Michal Lapidot; Ron Shamir; Yitzhak Pilpel
A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs.
Genome biology 2005;6(10):R86.
2005: 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 2005;6():232.
2005: Ran Elkon; Sharon Rashi-Elkeles; Yaniv lerenthal; Chaim Linhart; Tamar Tenne; Ninette Amariglio; Gideon Rechavi; Ron Shamir; Yosef Shiloh
Dissection of a DNA-damage-induced transcriptional network using a combination of microarrays, RNA interference and computational promoter analysis.
Genome biology 2005;6(5):R43.
2004: Rotem Sorek; Ronen Shemesh; Yuval Cohen; Ortal Basechess; Gil Ast; Ron Shamir
A non-EST-based method for exon-skipping prediction.
Genome research 2004;14(8):1617-23.
2004: Adi Akavia; Hanoch Senderowitz; Alon Lerner; Ron Shamir
Designing a multiroute synthesis scheme in combinatorial chemistry.
Journal of combinatorial chemistry 2004;6(4):540-8.
2004: Amos Tanay; Irit Gat-Viks; Ron Shamir
A global view of the selection forces in the evolution of yeast cis-regulation.
Genome research 2004;14(5):829-34.
2004: Amos Tanay; Roded Sharan; Martin Kupiec; Ron Shamir
Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(9):2981-6.
2004: Tsviya Olender; Tania Fuchs; Chaim Linhart; Ron Shamir; Mark Adams; Francis Kalush; Miriam Khen; Doron Lancet
The canine olfactory subgenome.
Genomics 2004;83(3):361-72.
2004: Nir Orlev; Ron Shamir; Yosef Shiloh
PIVOT: protein interacions visualizatiOn tool.
Bioinformatics (Oxford, England) 2004;20(3):424-5.
2004: Rotem Sorek; Ron Shamir; Gil Ast
How prevalent is functional alternative splicing in the human genome?
Trends in genetics : TIG 2004;20(2):68-71.
2004: Ron Shamir
Revealing the structure and dynamics of cis-regulation using heterogeneous, genome-wide, multi-species data.
Genome informatics. International Conference on Genome Informatics 2004;15(2):300-1.
2004: Irit Gat-Viks; Amos Tanay; Ron Shamir
Modeling and analysis of heterogeneous regulation in biological networks.
Journal of computational biology : a journal of computational molecular cell biology 2004;11(6):1034-49.
2004: Ran Elkon; Karen I Zeller; Chaim Linhart; Chi Dang; Ron Shamir; Yosef Shiloh
In silico identification of transcriptional regulators associated with c-Myc.
Nucleic acids research 2004;32(17):4955-61.
2004: Amos Tanay; Ron Shamir
Multilevel modeling and inference of transcription regulation.
Journal of computational biology : a journal of computational molecular cell biology 2004;11(2-3):357-75.
2004: Irit Gat-Viks; Ron Shamir; Richard M Karp; Roded Sharan
Reconstructing chain functions in genetic networks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2004;():498-509.
2003: Irit Gat-Viks; Roded Sharan; Ron Shamir
Scoring clustering solutions by their biological relevance.
Bioinformatics (Oxford, England) 2003;19(18):2381-9.
2003: Tal Pupko; Roded Sharan; Masami Hasegawa; Ron Shamir; Dan Graur
Detecting excess radical replacements in phylogenetic trees.
Gene 2003;319():127-35.
2003: Itsik Pe'er; Naama Arbili; Yi Liu; Colby Enck; Craig A Gelfand; Ron Shamir
Advanced computational techniques for re-sequencing DNA with polymerase signaling assay arrays.
Nucleic acids research 2003;31(19):5667-75.
2003: Roded Sharan; Adi Maron-Katz; Ron Shamir
CLICK and EXPANDER: a system for clustering and visualizing gene expression data.
Bioinformatics (Oxford, England) 2003;19(14):1787-99.
2003: Ran Elkon; Chaim Linhart; Roded Sharan; Ron Shamir; Yosef Shiloh
Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells.
Genome research 2003;13(5):773-80.
2003: Michal Ozery-Flato; Ron Shamir
Two notes on genome rearrangement.
Journal of bioinformatics and computational biology 2003;1(1):71-94.
2003: Eran Halperin; Shay Halperin; Tzvika Hartman; Ron Shamir
Handling long targets and errors in sequencing by hybridization.
Journal of computational biology : a journal of computational molecular cell biology 2003;10(3-4):483-97.
2003: Amir Ben-Dor; Richard M Karp; Benno Schwikowski; Ron Shamir
The restriction scaffold problem.
Journal of computational biology : a journal of computational molecular cell biology 2003;10(3-4):385-98.
2003: Irit Gat-Viks; Ron Shamir
Chain functions and scoring functions in genetic networks.
Bioinformatics (Oxford, England) 2003;19 Suppl 1():i108-17.
2002: Itsik Pe'er; Naama Arbili; Ron Shamir
A computational method for resequencing long DNA targets by universal oligonucleotide arrays.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(24):15492-6.
2002: Tania Fuchs; Barbora Malecova; Chaim Linhart; Roded Sharan; Miriam Khen; Ralf Herwig; Dmitry Shmulevich; Ran Elkon; Matthias Steinfath; John K O'Brien; Uwe Radelof; Hans Lehrach; Doron Lancet; Ron Shamir
DEFOG: a practical scheme for deciphering families of genes.
Genomics 2002;80(3):295-302.
2002: Chaim Linhart; Ron Shamir
The degenerate primer design problem.
Bioinformatics (Oxford, England) 2002;18 Suppl 1():S172-81.
2002: Amos Tanay; Roded Sharan; Ron Shamir
Discovering statistically significant biclusters in gene expression data.
Bioinformatics (Oxford, England) 2002;18 Suppl 1():S136-44.
2002: Roded Sharan; Ran Elkon; Ron Shamir
Cluster analysis and its applications to gene expression data.
Ernst Schering Research Foundation workshop 2002;(38):83-108.
2002: Ron Shamir; Dekel Tsur
Large scale sequencing by hybridization.
Journal of computational biology : a journal of computational molecular cell biology 2002;9(2):413-28.
2001: Amir Ben-Dor; I Pe'er; Ron Shamir; Roded Sharan
On the complexity of positional sequencing by hybridization.
Journal of computational biology : a journal of computational molecular cell biology 2001;8(4):361-71.
2001: Amos Tanay; Ron Shamir
Computational expansion of genetic networks.
Bioinformatics (Oxford, England) 2001;17 Suppl 1():S270-8.
2000: E Hartuv; A O Schmitt; J Lange; S Meier-Ewert; Hans Lehrach; Ron Shamir
An algorithm for clustering cDNA fingerprints.
Genomics 2000;66(3):249-56.
2000: Tal Pupko; Itsik Pe'er; Ron Shamir; Dan Graur
A fast algorithm for joint reconstruction of ancestral amino acid sequences.
Molecular biology and evolution 2000;17(6):890-6.
2000: Richard M Karp; Ron Shamir
Algorithms for optical mapping.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(1-2):303-16.
2000: Richard M Karp; I Pe'er; Ron Shamir
An algorithm combining discrete and continuous methods for optical mapping.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(5):745-60.
2000: R Sharan; Ron Shamir
CLICK: a clustering algorithm with applications to gene expression analysis.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 2000;8():307-16.
2000: Itsik Pe'er; Ron Shamir
Spectrum alignment: efficient resequencing by hybridization.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 2000;8():260-8.
1999: Amir Ben-Dor; Ron Shamir; Zohar Yakhini
Clustering gene expression patterns.
Journal of computational biology : a journal of computational molecular cell biology 1999;6(3-4):281-97.
1999: R M Karp; I Pe'er; Ron Shamir
An algorithm combining discrete and continuous methods for optical mapping.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1999;():159-68.
1999: G Mayraz; Ron Shamir
Construction of physical maps from oligonucleotide fingerprints data.
Journal of computational biology : a journal of computational molecular cell biology 1999;6(2):237-52.
1995: P W Goldberg; M C Golumbic; H Kaplan; Ron Shamir
Four strikes against physical mapping of DNA.
Journal of computational biology : a journal of computational molecular cell biology 1995;2(1):139-52.