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Author Details

Ron Shamir
Tel Aviv University
1995
216
53
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37395437Integration of gene expression and DNA methylation data across different experiments.Nucleic Acids Res2023
37558282Efficient minimizer orders for large values of <i>k</i> using minimum decycling sets.Genome Res2023
37451831Evaluation of European-based polygenic risk score for breast cancer in Ashkenazi Jewish women in Israel.J Med Genet2023
37386027Single cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscape.Nat Commun2023
35139202The DOMINO web-server for active module identification analysis.Bioinformatics2022
35527644Data Set-Adaptive Minimizer Order Reduces Memory Usage in <i>k</i>-Mer Counting.J Comput Biol2022
36306319Parameterized syncmer schemes improve long-read mapping.PLoS Comput Biol2022
361248043CAC: improving the classification of phages and plasmids in metagenomic assemblies using assembly graphs.Bioinformatics2022
35100425CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps.Nucleic Acids Res2022
35173197A machine learning model for predicting deterioration of COVID-19 inpatients.Sci Rep2022
29726899Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions.Bioinformatics2021
33564068Classification of node-positive melanomas into prognostic subgroups using keratin, immune, and melanogenesis expression patterns.Oncogene2021
347402352020 Outstanding contributions to ISCB award: Judith Blake.Bioinformatics2021
347402342020 ISCB Innovatory Award: Xiaole Shirley Liu.Bioinformatics2021
34172093SCAPP: an algorithm for improved plasmid assembly in metagenomes.Microbiome2021
33471440DOMINO: a network-based active module identification algorithm with reduced rate of false calls.Mol Syst Biol2021
31602783Unravelling plasmidome distribution and interaction with its hosting microbiome.Environ Microbiol2020
31873850Using the kinetics of C-reactive protein response to improve the differential diagnosis between acute bacterial and viral infections.Infection2020
31681944PRODIGY: personalized prioritization of driver genes.Bioinformatics2020
333519292019 ISCB Overton Prize: Christophe Dessimoz.Bioinformatics2020
33351928Bonnie Berger named ISCB 2019 ISCB Accomplishments by a Senior Scientist Award recipient.Bioinformatics2020
333519272019 ISCB Innovator Award Recognizes William Stafford Noble.Bioinformatics2020
333519262019 Outstanding Contributions to ISCB Awarded to Barb Bryant.Bioinformatics2020
32931516MONET: Multi-omic module discovery by omic selection.PLoS Comput Biol2020
32243433PlasClass improves plasmid sequence classification.PLoS Comput Biol2020
32127354Melanoma-Secreted Lysosomes Trigger Monocyte-Derived Dendritic Cell Apoptosis and Limit Cancer Immunotherapy.Cancer Res2020
30698637NEMO: cancer subtyping by integration of partial multi-omic data.Bioinformatics2019
31878868PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets.BMC Bioinformatics2019
31464374Inaccuracy of the log-rank approximation in cancer data analysis.Mol Syst Biol2019
31393900Personalized prediction of adverse heart and kidney events using baseline and longitudinal data from SPRINT and ACCORD.PLoS One2019
31100387The EXPANDER Integrated Platform for Transcriptome Analysis.J Mol Biol2019
311649772019 ISCB Overton Prize: Christophe Dessimoz.F1000Res2019
311649752019 ISCB Innovator Award recognizes William Stafford Noble.F1000Res2019
31164973Bonnie Berger named ISCB 2019 ISCB Accomplishments by a Senior Scientist Award recipient.F1000Res2019
30496480Multi-omic and multi-view clustering algorithms: review and cancer benchmark.Nucleic Acids Res2019
29036597Faucet: streaming de novo assembly graph construction.Bioinformatics2018
30157915Genomic meta-analysis of the interplay between 3D chromatin organization and gene expression programs under basal and stress conditions.Epigenetics Chromatin2018
30210803GePMI: A statistical model for personal intestinal microbiome identification.NPJ Biofilms Microbiomes2018
298791122018 ISCB Overton Prize awarded to Cole Trapnell.PLoS Comput Biol2018
298791012018 ISCB Innovator Award recognizes M. Madan Babu.PLoS Comput Biol2018
29929553Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness.Hum Genomics2018
298688842018 ISCB Overton Prize awarded to Cole Trapnell.Bioinformatics2018
29868819Message from the ISCB: 2018 Outstanding Contributions to ISCB Award: Russ Altman.Bioinformatics2018
29868787Message from the ISCB: 2018 ISCB Accomplishments by a Senior Scientist Award.Bioinformatics2018
298687092018 ISCB Innovator Award recognizes M. Madan Babu.Bioinformatics2018
30295871Multi-omic and multi-view clustering algorithms: review and cancer benchmark.Nucleic Acids Res2018
30416739Erratum: Author Correction: GePMI: a statistical model for personal intestinal microbiome identification.NPJ Biofilms Microbiomes2018
29616063MorphDB: Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants.Front Plant Sci2018
29360930ADEPTUS: a discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases.Bioinformatics2018
297719162018 ISCB accomplishments by a senior scientist award.PLoS Comput Biol2018
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Collaborators

Igor Ulitsky
Weizmann Institute of Science
Co-authored papers 23
Roded Sharan
Tel Aviv University
Co-authored papers 20
Amos Tanay
Weizmann Institute of Science
Co-authored papers 16
Richard M Karp
University of California at Berkeley and International Computer Science Institute
Co-authored papers 10
Itsik Pe'er
Columbia University
Co-authored papers 9
Eran Halperin
Co-authored papers 8
Roye Rozov
Co-authored papers 5
Jacques S Beckmann
University of Lausanne
Co-authored papers 3
Itzhak Mizrahi
Co-authored papers 3
Doron Lancet
Co-authored papers 3
Guy Karlebach
Max Planck Institute for Psycholinguistics
Co-authored papers 3
Franz-Josef Müller
Co-authored papers 3
Dan Graur
University of Houston
Co-authored papers 2
Carl Kingsford
Carnegie Mellon University
Co-authored papers 2
Nevan J Krogan (CM4AI)
University of California San Francisco
Co-authored papers 2
Pavel A Pevzner
University of California
Co-authored papers 2
Rui Jiang
Co-authored papers 2
Jian-Bing Fan
Nanfang Hospital and Basic Medical College, Southern Medical University
Co-authored papers 1
Jenny Chang-Claude
German Cancer Research Center (DKFZ)
Co-authored papers 1
Rudolf Kaaks
Co-authored papers 1
Alexis Brice
Sorbonne University, Paris Brain Institute - ICM, Inserm, CNRS
Co-authored papers 1
Michael Rehman
Institute of Biochemistry, Friedrich-Alexander-University of Erlangen-Nurnberg
Co-authored papers 1
Marie-Laure Yaspo
Max Planck Institute for Molecular Genetics
Co-authored papers 1
Xiaohong R Yang
National Cancer Institute
Co-authored papers 1
Peter A Fasching
Otto-Friedrich-University Bamberg
Co-authored papers 1
Ronna Hertzano
University of Maryland School of Medicine
Co-authored papers 1
Assaf Gottlieb
Center for Precision Health, University of Texas Health Science Center at Houston
Co-authored papers 1
Bonnie Berger
Massachusetts Institute of Technology
Co-authored papers 1
Esther M John
Co-authored papers 1
Fuad A Iraqi
Co-authored papers 1
Release 1.2