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Ron Shamir

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Computational Biology

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Saccharomyces cerevisiae

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Oligonucleotide Array Sequence Analysis

Chemicals & Drugs

Genes & Molecular Sequences

Physiology

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Molecular Evolution

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Publications

TOP 3
Ozery-Flato Michal; Shamir Ron
Sorting cancer karyotypes by elementary operations.
Bruckner Sharon; Hüffner Falk; Karp Richard M; Shamir Ron; Sharan Roded
TORQUE: topology-free querying of protein interaction networks.
Ulitsky Igor; Shamir Ron
Identifying functional modules using expression profiles and confidence-scored protein interactions.

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All Publications

2009: Ozery-Flato Michal; Shamir Ron
Sorting cancer karyotypes by elementary operations.
Journal of computational biology : a journal of computational molecular cell biology 2009;16(10):1445-60.
2009: Bruckner Sharon; Hüffner Falk; Karp Richard M; Shamir Ron; Sharan Roded
TORQUE: topology-free querying of protein interaction networks.
Nucleic acids research 2009;37(Web Server issue):W106-8.
2009: Ulitsky Igor; Shamir Ron
Identifying functional modules using expression profiles and confidence-scored protein interactions.
Bioinformatics (Oxford, England) 2009;25(9):1158-64.
2009: Halperin Yonit; Linhart Chaim; Ulitsky Igor; Shamir Ron
Allegro: analyzing expression and sequence in concert to discover regulatory programs.
Nucleic acids research 2009;37(5):1566-79.
2009: Gutkin Michael; Shamir Ron; Dror Gideon
SlimPLS: a method for feature selection in gene expression-based disease classification.
PloS one 2009;4(7):e6416.
2008: Karlebach Guy; Shamir Ron
Modelling and analysis of gene regulatory networks.
Nature reviews. Molecular cell biology 2008;9(10):770-80.
2008: Müller Franz-Josef; Laurent Louise C; Kostka Dennis; Ulitsky Igor; Williams Roy; Lu Christina; Park In-Hyun; Rao Mahendra S; Shamir Ron; Schwartz Philip H; Schmidt Nils O; Loring Jeanne F
Regulatory networks define phenotypic classes of human stem cell lines.
Nature 2008;455(7211):401-5.
2008: Ozery-Flato Michal; Shamir Ron
Sorting genomes with centromeres by translocations.
Journal of computational biology : a journal of computational molecular cell biology 2008;15(7):793-812.
2008: Linhart Chaim; Halperin Yonit; Shamir Ron
Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets.
Genome research 2008;18(7):1180-9.
2008: Laurent Louise C; Chen Jing; Ulitsky Igor; Mueller Franz-Josef; Lu Christina; Shamir Ron; Fan Jian-Bing; Loring Jeanne F
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: Barzuza Tamar; Beckmann Jacques S; Shamir Ron; Pe'er Itsik
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: Raijman Daniela; Shamir Ron; Tanay Amos
Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites.
PLoS computational biology 2008;4(1):e7.
2008: Ulitsky Igor; Shamir Ron
Detecting pathways transcriptionally correlated with clinical parameters.
Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference 2008;7():249-58.
2008: Ulitsky Igor; Shlomi Tomer; Kupiec Martin; Shamir Ron
From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions.
Molecular systems biology 2008;4():209.
2008: Elkon Ran; Vesterman Rita; Amit Nira; Ulitsky Igor; Zohar Idan; Weisz Mali; Mass Gilad; Orlev Nir; Sternberg Giora; Blekhman Ran; Assa Jackie; Shiloh Yosef; Shamir Ron
SPIKE--a database, visualization and analysis tool of cellular signaling pathways.
BMC bioinformatics 2008;9():110.
2007: Levine Arie; Kugathasan Subra; Annese Vito; Biank Vincent; Leshinsky-Silver Esther; Davidovich Ofir; Kimmel Gad; Shamir Ron; Palmieri Orazio; Karban Amir; Broeckel Ulrich; Cucchiara Salvatore
Pediatric onset Crohn's colitis is characterized by genotype-dependent age-related susceptibility.
Inflammatory bowel diseases 2007;13(12):1509-15.
2007: Kimmel Gad; Jordan Michael I; Halperin Eran; Shamir Ron; Karp Richard M
A randomization test for controlling population stratification in whole-genome association studies.
American journal of human genetics 2007;81(5):895-905.
2007: Leshinsky-Silver E; Karban A; Cohen S; Fridlander M; Davidowich O; Kimmel G; Shamir R; Levine A
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: Karban Amir; Itay Maza; Davidovich Ofir; Leshinsky-Silver Esther; Kimmel Gad; Fidder Herma; Shamir Ron; Waterman Matti; Eliakim Rami; Levine Arie
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: Ozery-Flato Michal; Shamir Ron
Sorting by reciprocal translocations via reversals theory.
Journal of computational biology : a journal of computational molecular cell biology 2007;14(4):408-22.
2007: Blum Roy; Elkon Ran; Yaari Shira; Zundelevich Adi; Jacob-Hirsch Jasmine; Rechavi Gideon; Shamir Ron; Kloog Yoel
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: Steinfeld Israel; Shamir Ron; Kupiec Martin
A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription.
Nature genetics 2007;39(3):303-9.
2007: Gat-Viks Irit; Shamir Ron
Refinement and expansion of signaling pathways: the osmotic response network in yeast.
Genome research 2007;17(3):358-67.
2007: Elkon Ran; Linhart Chaim; Halperin Yonit; Shiloh Yosef; Shamir Ron
Functional genomic delineation of TLR-induced transcriptional networks.
BMC genomics 2007;8():394.
2007: Linhart Chaim; Shamir Ron
Degenerate primer design: theoretical analysis and the HYDEN program.
Methods in molecular biology (Clifton, N.J.) 2007;402():221-44.
2007: Ulitsky Igor; Shamir Ron
Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks.
Molecular systems biology 2007;3():104.
2007: Ulitsky Igor; Shamir Ron
Identification of functional modules using network topology and high-throughput data.
BMC systems biology 2007;1():8.
2007: Sharan Roded; Ulitsky Igor; Shamir Ron
Network-based prediction of protein function.
Molecular systems biology 2007;3():88.
2007: Davidovich Ofir; Kimmel Gad; Shamir Ron
GEVALT: an integrated software tool for genotype analysis.
BMC bioinformatics 2007;8():36.
2006: Kimmel Gad; Shamir Ron
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: Belle Archana; Tanay Amos; Bitincka Ledion; Shamir Ron; O'Shea Erin K
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: Blum Roy; Nakdimon Itay; Goldberg Liat; Elkon Ran; Shamir Ron; Rechavi Gideon; Kloog Yoel
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: Gal Inabr; Kimmel Gad; Gershoni-Baruch Ruth; Papa Moshe Z; Dagan Efrat; Shamir Ron; Friedman Eitan
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: Koren M; Kimmel G; Ben-Asher E; Gal I; Papa M Z; Beckmann J S; Lancet D; Shamir R; Friedman E
ATM haplotypes and breast cancer risk in Jewish high-risk women.
British journal of cancer 2006;94(10):1537-43.
2006: Gat-Viks Irit; Tanay Amos; Raijman Daniela; Shamir Ron
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: Rashi-Elkeles S; Elkon R; Weizman N; Linhart C; Amariglio N; Sternberg G; Rechavi G; Barzilai A; Shamir R; Shiloh Y
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: Sorek Rotem; Dror Gideon; Shamir Ron
Assessing the number of ancestral alternatively spliced exons in the human genome.
BMC genomics 2006;7():273.
2005: Kimmel Gad; Shamir Ron
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: Linhart Chaim; Elkon Ran; Shiloh Yosef; Shamir Ron
Deciphering transcriptional regulatory elements that encode specific cell cycle phasing by comparative genomics analysis.
Cell cycle (Georgetown, Tex.) 2005;4(12):1788-97.
2005: Barzuza Tamar; Beckmann Jacques S; Shamir Ron; Pe'er Itsik
Typing without calling the allele: a strategy for inferring SNP haplotypes.
European journal of human genetics : EJHG 2005;13(8):898-901.
2005: Sharan Roded; Ideker Trey; Kelley Brian; Shamir Ron; Karp Richard M
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: Halperin Eran; Kimmel Gad; Shamir Ron
Tag SNP selection in genotype data for maximizing SNP prediction accuracy.
Bioinformatics (Oxford, England) 2005;21 Suppl 1():i195-203.
2005: Tanay Amos; Regev Aviv; Shamir Ron
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: Linhart Chaim; Shamir Ron
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: Kimmel Gad; Shamir Ron
The incomplete perfect phylogeny haplotype problem.
Journal of bioinformatics and computational biology 2005;3(2):359-84.
2005: Dror Gideon; Sorek Rotem; Shamir Ron
Accurate identification of alternatively spliced exons using support vector machine.
Bioinformatics (Oxford, England) 2005;21(7):897-901.
2005: Kimmel Gad; Shamir Ron
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: Tanay Amos; Steinfeld Israel; Kupiec Martin; Shamir Ron
Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium.
Molecular systems biology 2005;1():2005.0002.
2005: Dudley Aimée Marie; Janse Daniel Maarten; Tanay Amos; Shamir Ron; Church George McDonald
A global view of pleiotropy and phenotypically derived gene function in yeast.
Molecular systems biology 2005;1():2005.0001.
2005: Shalgi Reut; Lapidot Michal; Shamir Ron; Pilpel Yitzhak
A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs.
Genome biology 2005;6(10):R86.
2005: Shamir Ron; Maron-Katz Adi; Tanay Amos; Linhart Chaim; Steinfeld Israel; Sharan Roded; Shiloh Yosef; Elkon Ran
EXPANDER--an integrative program suite for microarray data analysis.
BMC bioinformatics 2005;6():232.
2005: Elkon Ran; Rashi-Elkeles Sharon; Lerenthal Yaniv; Linhart Chaim; Tenne Tamar; Amariglio Ninette; Rechavi Gideon; Shamir Ron; Shiloh Yosef
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: Sorek Rotem; Shemesh Ronen; Cohen Yuval; Basechess Ortal; Ast Gil; Shamir Ron
A non-EST-based method for exon-skipping prediction.
Genome research 2004;14(8):1617-23.
2004: Akavia Adi; Senderowitz Hanoch; Lerner Alon; Shamir Ron
Designing a multiroute synthesis scheme in combinatorial chemistry.
Journal of combinatorial chemistry 2004;6(4):540-8.
2004: Tanay Amos; Gat-Viks Irit; Shamir Ron
A global view of the selection forces in the evolution of yeast cis-regulation.
Genome research 2004;14(5):829-34.
2004: Tanay Amos; Sharan Roded; Kupiec Martin; Shamir Ron
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: Olender Tsviya; Fuchs Tania; Linhart Chaim; Shamir Ron; Adams Mark; Kalush Francis; Khen Miriam; Lancet Doron
The canine olfactory subgenome.
Genomics 2004;83(3):361-72.
2004: Orlev Nir; Shamir Ron; Shiloh Yosef
PIVOT: protein interacions visualizatiOn tool.
Bioinformatics (Oxford, England) 2004;20(3):424-5.
2004: Sorek Rotem; Shamir Ron; Ast Gil
How prevalent is functional alternative splicing in the human genome?
Trends in genetics : TIG 2004;20(2):68-71.
2004: Shamir Ron
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: Gat-Viks Irit; Tanay Amos; Shamir Ron
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: Elkon Ran; Zeller Karen I; Linhart Chaim; Dang Chi V; Shamir Ron; Shiloh Yosef
In silico identification of transcriptional regulators associated with c-Myc.
Nucleic acids research 2004;32(17):4955-61.
2004: Tanay Amos; Shamir Ron
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: Gat-Viks I; Shamir R; Karp R M; Sharan R
Reconstructing chain functions in genetic networks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2004;():498-509.
2003: Gat-Viks I; Sharan R; Shamir R
Scoring clustering solutions by their biological relevance.
Bioinformatics (Oxford, England) 2003;19(18):2381-9.
2003: Pupko Tal; Sharan Roded; Hasegawa Masami; Shamir Ron; Graur Dan
Detecting excess radical replacements in phylogenetic trees.
Gene 2003;319():127-35.
2003: Pe'er Itsik; Arbili Naama; Liu Yi; Enck Colby; Gelfand Craig A; Shamir Ron
Advanced computational techniques for re-sequencing DNA with polymerase signaling assay arrays.
Nucleic acids research 2003;31(19):5667-75.
2003: Sharan Roded; Maron-Katz Adi; Shamir Ron
CLICK and EXPANDER: a system for clustering and visualizing gene expression data.
Bioinformatics (Oxford, England) 2003;19(14):1787-99.
2003: Elkon Ran; Linhart Chaim; Sharan Roded; Shamir Ron; Shiloh Yosef
Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells.
Genome research 2003;13(5):773-80.
2003: Ozery-Flato Michal; Shamir Ron
Two notes on genome rearrangement.
Journal of bioinformatics and computational biology 2003;1(1):71-94.
2003: Halperin Eran; Halperin Shay; Hartman Tzvika; Shamir Ron
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: Ben-Dor Amir; Karp Richard M; Schwikowski Benno; Shamir Ron
The restriction scaffold problem.
Journal of computational biology : a journal of computational molecular cell biology 2003;10(3-4):385-98.
2003: Gat-Viks I; Shamir R
Chain functions and scoring functions in genetic networks.
Bioinformatics (Oxford, England) 2003;19 Suppl 1():i108-17.
2002: Pe'er Itsik; Arbili Naama; Shamir Ron
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: Fuchs Tania; Malecova Barbora; Linhart Chaim; Sharan Roded; Khen Miriam; Herwig Ralf; Shmulevich Dmitry; Elkon Rani; Steinfath Matthias; O'Brien John K; Radelof Uwe; Lehrach Hans; Lancet Doron; Shamir Ron
DEFOG: a practical scheme for deciphering families of genes.
Genomics 2002;80(3):295-302.
2002: Linhart Chaim; Shamir Ron
The degenerate primer design problem.
Bioinformatics (Oxford, England) 2002;18 Suppl 1():S172-81.
2002: Tanay Amos; Sharan Roded; Shamir Ron
Discovering statistically significant biclusters in gene expression data.
Bioinformatics (Oxford, England) 2002;18 Suppl 1():S136-44.
2002: Sharan R; Elkon R; Shamir R
Cluster analysis and its applications to gene expression data.
Ernst Schering Research Foundation workshop 2002;(38):83-108.
2002: Shamir Ron; Tsur Dekel
Large scale sequencing by hybridization.
Journal of computational biology : a journal of computational molecular cell biology 2002;9(2):413-28.
2001: Ben-Dor A; Pe'er I; Shamir R; Sharan R
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: Tanay A; Shamir R
Computational expansion of genetic networks.
Bioinformatics (Oxford, England) 2001;17 Suppl 1():S270-8.
2000: Hartuv E; Schmitt A O; Lange J; Meier-Ewert S; Lehrach H; Shamir R
An algorithm for clustering cDNA fingerprints.
Genomics 2000;66(3):249-56.
2000: Pupko T; Pe'er I; Shamir R; Graur D
A fast algorithm for joint reconstruction of ancestral amino acid sequences.
Molecular biology and evolution 2000;17(6):890-6.
2000: Karp R M; Shamir R
Algorithms for optical mapping.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(1-2):303-16.
2000: Karp R M; Pe'er I; Shamir R
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: Sharan R; Shamir R
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: Pe'er I; Shamir R
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: Karp R M; Pe'er I; Shamir R
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: Ben-Dor A; Shamir R; Yakhini Z
Clustering gene expression patterns.
Journal of computational biology : a journal of computational molecular cell biology 1999;6(3-4):281-97.
1999: Mayraz G; Shamir R
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: Goldberg P W; Golumbic M C; Kaplan H; Shamir R
Four strikes against physical mapping of DNA.
Journal of computational biology : a journal of computational molecular cell biology 1995;2(1):139-52.

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Ron Shamir

Research Profile (preview)

Concepts & Ideas

Occupations

Activities & Behaviors

Living Beings

Procedures

Devices

Chemicals & Drugs

Genes & Molecular Sequences

Physiology

Phenomena

Network (preview)

Publications

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All Publications