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Author Details

Ioannis Xenarios
University of Lausanne
1994
199
62
Timothy Clark (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36908398Exploiting parallelization in positional Burrows-Wheeler transform (PBWT) algorithms for efficient haplotype matching and compression.Bioinform Adv2023
37594081Reference genomes for BALB/c Nude and NOD/SCID mouse models.G3 (Bethesda)2023
36717752Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency.Nat Metab2023
36908398Exploiting parallelization in positional Burrows-Wheeler transform (PBWT) algorithms for efficient haplotype matching and compression.Bioinform Adv2023
36619367Continuous population-level monitoring of SARS-CoV-2 seroprevalence in a large European metropolitan region.iScience2023
37594081Reference genomes for BALB/c Nude and NOD/SCID mouse models.G3 (Bethesda)2023
36717752Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency.Nat Metab2023
36619367Continuous population-level monitoring of SARS-CoV-2 seroprevalence in a large European metropolitan region.iScience2023
34757834External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories.J Clin Microbiol2022
35651602Sex-Biased Control of Inflammation and Metabolism by a Mitochondrial Nod-Like Receptor.Front Immunol2022
36216966An anti-influenza combined therapy assessed by single cell RNA-sequencing.Commun Biol2022
36155976Towards mouse genetic-specific RNA-sequencing read mapping.PLoS Comput Biol2022
35748697XSI-a genotype compression tool for compressive genomics in large biobanks.Bioinformatics2022
35992159Dissection of the macrophage response towards infection by the <i>Leishmania</i>-viral endosymbiont duo and dynamics of the type I interferon response.Front Cell Infect Microbiol2022
34757834External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories.J Clin Microbiol2022
35651602Sex-Biased Control of Inflammation and Metabolism by a Mitochondrial Nod-Like Receptor.Front Immunol2022
35748697XSI-a genotype compression tool for compressive genomics in large biobanks.Bioinformatics2022
35992159Dissection of the macrophage response towards infection by the <i>Leishmania</i>-viral endosymbiont duo and dynamics of the type I interferon response.Front Cell Infect Microbiol2022
36155976Towards mouse genetic-specific RNA-sequencing read mapping.PLoS Comput Biol2022
36216966An anti-influenza combined therapy assessed by single cell RNA-sequencing.Commun Biol2022
32313939Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.Brief Bioinform2021
32313939Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.Brief Bioinform2021
33995353Unsupervised Analysis of Flow Cytometry Data in a Clinical Setting Captures Cell Diversity and Allows Population Discovery.Front Immunol2021
33929935Blood virosphere in febrile Tanzanian children.Emerg Microbes Infect2021
34488035Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland.Epidemics2021
33929935Blood virosphere in febrile Tanzanian children.Emerg Microbes Infect2021
34488035Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland.Epidemics2021
33995353Unsupervised Analysis of Flow Cytometry Data in a Clinical Setting Captures Cell Diversity and Allows Population Discovery.Front Immunol2021
31631325Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release.Biotechnol Bioeng2020
32077582Contribution of exome sequencing to the identification of genes involved in the response to clopidogrel in cardiovascular patients.J Thromb Haemost2020
32076073Fisetin protects against cardiac cell death through reduction of ROS production and caspases activity.Sci Rep2020
31688925Enzyme annotation in UniProtKB using Rhea.Bioinformatics2020
31790143Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region.Bioinformatics2020
32184981New genome assembly of the barn owl (<i>Tyto alba alba</i>).Ecol Evol2020
31631325Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release.Biotechnol Bioeng2020
32157095Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes.Nat Commun2020
32034905HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes.Gigascience2020
31922550PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling.Bioinformatics2020
32656337Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion.Sci Adv2020
33139591Virosaurus A Reference to Explore and Capture Virus Genetic Diversity.Viruses2020
32952936Predicting combinations of immunomodulators to enhance dendritic cell-based vaccination based on a hybrid experimental and computational platform.Comput Struct Biotechnol J2020
31790143Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region.Bioinformatics2020
32077582Contribution of exome sequencing to the identification of genes involved in the response to clopidogrel in cardiovascular patients.J Thromb Haemost2020
32076073Fisetin protects against cardiac cell death through reduction of ROS production and caspases activity.Sci Rep2020
31922550PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling.Bioinformatics2020
31688925Enzyme annotation in UniProtKB using Rhea.Bioinformatics2020
32034905HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes.Gigascience2020
33139591Virosaurus A Reference to Explore and Capture Virus Genetic Diversity.Viruses2020
32656337Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion.Sci Adv2020
32952936Predicting combinations of immunomodulators to enhance dendritic cell-based vaccination based on a hybrid experimental and computational platform.Comput Struct Biotechnol J2020
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Collaborators

Alan Bridge
carnegie mellon university
Co-authored papers 26
Lydie Bougueleret
carnegie mellon university
Co-authored papers 25
Sylvain Poux
carnegie mellon university
Co-authored papers 14
Philippe Le Mercier
carnegie mellon university
Co-authored papers 14
Nicole Redaschi
Co-authored papers 13
David Eisenberg
university of california los angeles
Co-authored papers 13
Elisabeth Coudert
Centre Medical Universitaire
Co-authored papers 12
Marco Pagni
Co-authored papers 11
Anne Niknejad
University of Lausanne
Co-authored papers 10
Edouard de Castro
Co-authored papers 10
Patrick Masson
carnegie mellon university
Co-authored papers 9
Chantal Hulo
carnegie mellon university
Co-authored papers 9
Henning Hermjakob
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 9
Kristian B Axelsen
Centre Medical Universitaire
Co-authored papers 9
Anne Morgat
Centre Medical Universitaire
Co-authored papers 8
Catherine Rivoire
carnegie mellon university
Co-authored papers 7
Andrea H Auchincloss
carnegie mellon university
Co-authored papers 7
Rolf Apweiler
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 7
Lukasz Salwinski
university of california los angeles
Co-authored papers 7
Peer Bork
University of Wurzburg
Co-authored papers 6
Alexandre Reymond
Co-authored papers 6
Anne Estreicher
carnegie mellon university - 1 rue Michel Servet CH-1 Geneva 4
Co-authored papers 6
Guillaume Keller
carnegie mellon university
Co-authored papers 5
Nevila Hyka-Nouspikel
Centre Medical Universitaire
Co-authored papers 5
Edward M Marcotte
University of Texas
Co-authored papers 5
Paul D Thomas
University of Southern California
Co-authored papers 5
Amos Bairoch
University of Geneva
Co-authored papers 5
Brigitte Boeckmann
Co-authored papers 5
Lorenzo Cerutti
Co-authored papers 5
Lucila Aimo
Centre Medical Universitaire
Co-authored papers 5
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