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Author Details

Simon Kasif
Boston University
1993
84
37
PMIDPaper TitleJournal TitlePublished Year
37323575Targeted <i>in silico</i> characterization of fusion transcripts in tumor and normal tissues via FusionInspector.Cell Rep Methods2023
37323575Targeted <i>in silico</i> characterization of fusion transcripts in tumor and normal tissues via FusionInspector.Cell Rep Methods2023
34845204High-throughput mediation analysis of human proteome and metabolome identifies mediators of post-bariatric surgical diabetes control.Nat Commun2021
34966926Interpretable network propagation with application to expanding the repertoire of human proteins that interact with SARS-CoV-2.Gigascience2021
34845204High-throughput mediation analysis of human proteome and metabolome identifies mediators of post-bariatric surgical diabetes control.Nat Commun2021
34966926Interpretable network propagation with application to expanding the repertoire of human proteins that interact with SARS-CoV-2.Gigascience2021
32878640Analysis of brain region-specific co-expression networks reveals clustering of established and novel genes associated with Alzheimer disease.Alzheimers Res Ther2020
33253151We need to keep a reproducible trace of facts, predictions, and hypotheses from gene to function in the era of big data.PLoS Biol2020
32878640Analysis of brain region-specific co-expression networks reveals clustering of established and novel genes associated with Alzheimer disease.Alzheimers Res Ther2020
33253151We need to keep a reproducible trace of facts, predictions, and hypotheses from gene to function in the era of big data.PLoS Biol2020
29684019One for all and all for One: Improving replication of genetic studies through network diffusion.PLoS Genet2018
29684019One for all and all for One: Improving replication of genetic studies through network diffusion.PLoS Genet2018
29241534Integrating Extracellular Flux Measurements and Genome-Scale Modeling Reveals Differences between Brown and White Adipocytes.Cell Rep2017
29241534Integrating Extracellular Flux Measurements and Genome-Scale Modeling Reveals Differences between Brown and White Adipocytes.Cell Rep2017
27689005Defects in muscle branched-chain amino acid oxidation contribute to impaired lipid metabolism.Mol Metab2016
26635392COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.Nucleic Acids Res2016
27689005Defects in muscle branched-chain amino acid oxidation contribute to impaired lipid metabolism.Mol Metab2016
26635392COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.Nucleic Acids Res2016
25737951Metabolic modeling of muscle metabolism identifies key reactions linked to insulin resistance phenotypes.Mol Metab2015
25737951Metabolic modeling of muscle metabolism identifies key reactions linked to insulin resistance phenotypes.Mol Metab2015
25644941Identification of rare germline copy number variations over-represented in five human cancer types.Mol Cancer2015
25644941Identification of rare germline copy number variations over-represented in five human cancer types.Mol Cancer2015
24726434Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells.Cell2014
24726434Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells.Cell2014
24753616Hypermutable DNA chronicles the evolution of human colon cancer.Proc Natl Acad Sci U S A2014
25071837Objective: biochemical function.Front Genet2014
25071837Objective: biochemical function.Front Genet2014
24753616Hypermutable DNA chronicles the evolution of human colon cancer.Proc Natl Acad Sci U S A2014
23707066An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma.Cell Rep2013
23825549Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori.PLoS One2013
23862675Systems biology characterization of engineered tissues.Annu Rev Biomed Eng2013
24013487The COMBREX project: design, methodology, and initial results.PLoS Biol2013
23967053To supplement or not to supplement: a metabolic network framework for human nutritional supplements.PLoS One2013
23707066An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma.Cell Rep2013
23825549Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori.PLoS One2013
23862675Systems biology characterization of engineered tissues.Annu Rev Biomed Eng2013
23967053To supplement or not to supplement: a metabolic network framework for human nutritional supplements.PLoS One2013
24013487The COMBREX project: design, methodology, and initial results.PLoS Biol2013
22675498Deep sequencing of the oral microbiome reveals signatures of periodontal disease.PLoS One2012
22675498Deep sequencing of the oral microbiome reveals signatures of periodontal disease.PLoS One2012
23111013Thousands of missed genes found in bacterial genomes and their analysis with COMBREX.Biol Direct2012
23111013Thousands of missed genes found in bacterial genomes and their analysis with COMBREX.Biol Direct2012
21097892COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.Nucleic Acids Res2011
21097892COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.Nucleic Acids Res2011
20016491Biochemical networks: the evolution of gene annotation.Nat Chem Biol2010
20713682A systems biology approach identifies inflammatory abnormalities between mouse strains prior to development of metabolic disease.Diabetes2010
20472640Functional characterization of the YmcB and YqeV tRNA methylthiotransferases of Bacillus subtilis.Nucleic Acids Res2010
20016491Biochemical networks: the evolution of gene annotation.Nat Chem Biol2010
20580212Predicting malaria interactome classifications from time-course transcriptomic data along the intraerythrocytic developmental cycle.Artif Intell Med2010
20713682A systems biology approach identifies inflammatory abnormalities between mouse strains prior to development of metabolic disease.Diabetes2010
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Collaborators

Co-authored papers 10
Yong Loo Lin School of Medicine, National University of Singapore
Co-authored papers 7
Center for Computational Biology, Johns Hopkins University
Co-authored papers 7
Center for Computational Biology, Johns Hopkins School of Medicine
Co-authored papers 6
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Joslin Diabetes Center, Harvard Medical School
Co-authored papers 4
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Co-authored papers 4
Harvard Medical School
Co-authored papers 4
University of Massachusetts Medical School
Co-authored papers 3
Institute for Genome Sciences, University of Maryland School of Medicine
Co-authored papers 3
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The Research Institute at Nationwide Children's Hospital
Co-authored papers 3
Broad Institute of MIT and Harvard
Co-authored papers 3
Co-authored papers 3
Harvard Medical School
Co-authored papers 3
Co-authored papers 3
Co-authored papers 3
Co-authored papers 3
Co-authored papers 3
Co-authored papers 2
Vanderbilt-Ingram Cancer Center, Vanderbilt University
Co-authored papers 2
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 2
Tulane University School of Medicine
Co-authored papers 2
Harvard University, USA Broad Institute, USA Harvard Stem Cell Institute
Co-authored papers 2
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Boston University Chobanian & Avedisian School of Medicine
Co-authored papers 2
Co-authored papers 2
Co-authored papers 2