Christian von Mering

Summary

Affiliation: University of Zurich
Country: Switzerland

Publications

  1. pmc STRING 7--recent developments in the integration and prediction of protein interactions
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 35:D358-62. 2007
  2. ncbi eggNOG v4.0: nested orthology inference across 3686 organisms
    Sean Powell
    European Molecular Biology Laboratory, Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany, University of Zurich and Swiss Institute of Bioinformatics, Institute of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zurich, Switzerland, Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109 5234, USA, Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, C Dr Aiguader 88, 08003 Barcelona, Spain, Universitat Pompeu Fabra UPF, 08003 Barcelona, Spain, CUBE Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3FG, UK, Biotechnology Center, TU Dresden, 01062 Dresden, Germany, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Atlanta
    Nucleic Acids Res 42:D231-9. 2014
  3. ncbi Immunity-related genes and gene families in Anopheles gambiae
    George K Christophides
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Science 298:159-65. 2002
  4. pmc STRING 8--a global view on proteins and their functional interactions in 630 organisms
    Lars J Jensen
    European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 37:D412-6. 2009
  5. pmc eggNOG: automated construction and annotation of orthologous groups of genes
    Lars Juhl Jensen
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 36:D250-4. 2008
  6. ncbi STITCH 4: integration of protein-chemical interactions with user data
    Michael Kuhn
    Biotechnology Center, TU Dresden, 01062 Dresden, Germany, Institute of Molecular Life Sciences, University of Zurich and Swiss Institute of Bioinformatics, Winterthurerstrasse 190, 8057 Zurich, Switzerland, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany and Max Delbrück Centre for Molecular Medicine, Robert Rossle Strasse 10, 13092 Berlin, Germany
    Nucleic Acids Res 42:D401-7. 2014
  7. ncbi Toward automatic reconstruction of a highly resolved tree of life
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Science 311:1283-7. 2006
  8. ncbi Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs
    Jan O Korbel
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nat Biotechnol 22:911-7. 2004
  9. pmc STITCH: interaction networks of chemicals and proteins
    Michael Kuhn
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 36:D684-8. 2008
  10. pmc eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
    Sean Powell
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 40:D284-9. 2012

Detail Information

Publications27

  1. pmc STRING 7--recent developments in the integration and prediction of protein interactions
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 35:D358-62. 2007
    ..Novel features include AJAX-based web-navigation, inclusion of additional resources such as BioGRID, and detailed protein domain annotation. STRING is available at http://string.embl.de/..
  2. ncbi eggNOG v4.0: nested orthology inference across 3686 organisms
    Sean Powell
    European Molecular Biology Laboratory, Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany, University of Zurich and Swiss Institute of Bioinformatics, Institute of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zurich, Switzerland, Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109 5234, USA, Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, C Dr Aiguader 88, 08003 Barcelona, Spain, Universitat Pompeu Fabra UPF, 08003 Barcelona, Spain, CUBE Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3FG, UK, Biotechnology Center, TU Dresden, 01062 Dresden, Germany, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Atlanta
    Nucleic Acids Res 42:D231-9. 2014
    ..Users can access the complete database of orthologous groups via a web interface, as well as through bulk download. ..
  3. ncbi Immunity-related genes and gene families in Anopheles gambiae
    George K Christophides
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Science 298:159-65. 2002
    ..Representative expression profiles confirm that sequence diversification is accompanied by specific responses to different immune challenges. Alternative RNA splicing may also contribute to expansion of the immune repertoire...
  4. pmc STRING 8--a global view on proteins and their functional interactions in 630 organisms
    Lars J Jensen
    European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 37:D412-6. 2009
    ..Version 8.0 of STRING covers about 2.5 million proteins from 630 organisms, providing the most comprehensive view on protein-protein interactions currently available. STRING can be reached at http://string-db.org/...
  5. pmc eggNOG: automated construction and annotation of orthologous groups of genes
    Lars Juhl Jensen
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 36:D250-4. 2008
    ..Users can query the resource for individual genes via a web interface or download the complete set of orthologous groups at http://eggnog.embl.de...
  6. ncbi STITCH 4: integration of protein-chemical interactions with user data
    Michael Kuhn
    Biotechnology Center, TU Dresden, 01062 Dresden, Germany, Institute of Molecular Life Sciences, University of Zurich and Swiss Institute of Bioinformatics, Winterthurerstrasse 190, 8057 Zurich, Switzerland, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany and Max Delbrück Centre for Molecular Medicine, Robert Rossle Strasse 10, 13092 Berlin, Germany
    Nucleic Acids Res 42:D401-7. 2014
    ..This improves the performance within protein families, where scores are now transferred only to orthologous proteins, but not to paralogous proteins. STITCH can be accessed with a web-interface, an API and downloadable files. ..
  7. ncbi Toward automatic reconstruction of a highly resolved tree of life
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Science 311:1283-7. 2006
    ..For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor...
  8. ncbi Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs
    Jan O Korbel
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nat Biotechnol 22:911-7. 2004
    ..The method thus enables the prediction of target processes and regulatory features for several hundred transcriptional regulators...
  9. pmc STITCH: interaction networks of chemicals and proteins
    Michael Kuhn
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 36:D684-8. 2008
    ..5 million genes across 373 genomes and their interactions contained in the STRING database. STITCH is available at http://stitch.embl.de/...
  10. pmc eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
    Sean Powell
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 40:D284-9. 2012
    ..Each group is amended by multiple sequence alignments and maximum-likelihood trees and broad functional descriptions are provided for 450,904 orthologous groups (62.5%)...
  11. pmc STRING: known and predicted protein-protein associations, integrated and transferred across organisms
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 33:D433-7. 2005
    ..STRING currently holds 730,000 proteins in 180 fully sequenced organisms, and is available at http://string.embl.de/...
  12. ncbi Shared components of protein complexes--versatile building blocks or biochemical artefacts?
    Roland Krause
    Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Bioessays 26:1333-43. 2004
    ....
  13. pmc Identification and analysis of evolutionarily cohesive functional modules in protein networks
    Monica Campillos
    The European Molecular Biology Laboratory EMBL, 69117 Heidelberg, Germany
    Genome Res 16:374-82. 2006
    ....
  14. pmc ArrayProspector: a web resource of functional associations inferred from microarray expression data
    Lars Juhl Jensen
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Nucleic Acids Res 32:W445-8. 2004
    ..The resource allows every association to be inspected visually and can be accessed at http://www.bork.embl.de/ArrayProspector...
  15. pmc Environments shape the nucleotide composition of genomes
    Konrad U Foerstner
    European Molecular Biology Laboratory, Heidelberg, Germany
    EMBO Rep 6:1208-13. 2005
    ....
  16. pmc Prediction of effective genome size in metagenomic samples
    Jeroen Raes
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Genome Biol 8:R10. 2007
    ..7 Mb; for bacteria in a nutrient-poor, organism-sparse ocean surface water sample, EGS is as low as 1.6 Mb. The method also permits evaluation of completion status and assembly bias in single-genome sequencing projects...
  17. ncbi Protein interaction networks from yeast to human
    Peer Bork
    European Molecular Biology Laboratory, Structural and Computational Biology Programme, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Curr Opin Struct Biol 14:292-9. 2004
    ....
  18. ncbi A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens
    Roland Krause
    Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Bioinformatics 19:1901-8. 2003
    ..A non-redundant collection of protein complexes from experimental data would be useful for biological interpretation, but manual assembly is tedious and often inconsistent...
  19. ncbi Consistency of genome-based methods in measuring Metazoan evolution
    Evgeny M Zdobnov
    EMBL Heidelberg, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    FEBS Lett 579:3355-61. 2005
    ..The deviations from the clock-like scenario in some lineages are observed consistently by several measures, implicitly confirming their reliability...
  20. pmc Complex genomic rearrangements lead to novel primate gene function
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, 69012 Heidelberg, Germany
    Genome Res 15:343-51. 2005
    ..We have experimentally verified that at least one of the newly formed proteins has a cellular localization different from RanBP2's, and we show that positive selection did act on specific domains during evolution...
  21. pmc STRING v9.1: protein-protein interaction networks, with increased coverage and integration
    Andrea Franceschini
    Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland
    Nucleic Acids Res 41:D808-15. 2013
    ....
  22. pmc Assessing systems properties of yeast mitochondria through an interaction map of the organelle
    Fabiana Perocchi
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS Genet 2:e170. 2006
    ..Our network thus advances the understanding of the mitochondrial system in yeast and identifies properties of genes underlying human mitochondrial disorders...
  23. pmc STRING: a database of predicted functional associations between proteins
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 31:258-61. 2003
    ..The database predicts functional interactions at an expected level of accuracy of at least 80% for more than half of the genes; it is online at http://www.bork.embl-heidelberg.de/STRING/...
  24. ncbi Global analysis of bacterial transcription factors to predict cellular target processes
    Tobias Doerks
    EMBL, 69117 Heidelberg, Meyerhofstr 1, Germany
    Trends Genet 20:126-31. 2004
    ....
  25. pmc Genome evolution reveals biochemical networks and functional modules
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Proc Natl Acad Sci U S A 100:15428-33. 2003
    ..The results indicate that modularity in protein networks is intrinsically encoded in present-day genomes...
  26. ncbi Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster
    Evgeny M Zdobnov
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Science 298:149-59. 2002
    ....
  27. ncbi Comparative assessment of large-scale data sets of protein-protein interactions
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nature 417:399-403. 2002
    ..To measure their accuracy and potential as well as to identify biases, strengths and weaknesses, we compare the methods with each other and with a reference set of previously reported protein interactions...