Research Topics
Genomes and Genes | Christian von MeringSummaryAffiliation: University of Zurich Country: Switzerland Publications
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Detail Information
Publications
STRING 7--recent developments in the integration and prediction of protein interactionsChristian 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/..
Immunity-related genes and gene families in Anopheles gambiaeGeorge 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...- STRING 8--a global view on proteins and their functional interactions in 630 organismsLars 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/... - Toward automatic reconstruction of a highly resolved tree of lifeFrancesca 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... - eggNOG: automated construction and annotation of orthologous groups of genesLars 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... - Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairsJan 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... - STITCH: interaction networks of chemicals and proteinsMichael 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/... - eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic rangesSean 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%)... - Global analysis of bacterial transcription factors to predict cellular target processesTobias Doerks
EMBL, 69117 Heidelberg, Meyerhofstr 1, Germany
Trends Genet 20:126-31. 2004.... - 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.... - STRING: known and predicted protein-protein associations, integrated and transferred across organismsChristian 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/... - Identification and analysis of evolutionarily cohesive functional modules in protein networksMonica Campillos
The European Molecular Biology Laboratory EMBL, 69117 Heidelberg, Germany
Genome Res 16:374-82. 2006.... - ArrayProspector: a web resource of functional associations inferred from microarray expression dataLars 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... - Environments shape the nucleotide composition of genomesKonrad U Foerstner
European Molecular Biology Laboratory, Heidelberg, Germany
EMBO Rep 6:1208-13. 2005.... - Prediction of effective genome size in metagenomic samplesJeroen 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... - Consistency of genome-based methods in measuring Metazoan evolutionEvgeny 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... - A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screensRoland 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... - Protein interaction networks from yeast to humanPeer Bork
European Molecular Biology Laboratory, Structural and Computational Biology Programme, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Curr Opin Struct Biol 14:292-9. 2004.... - Complex genomic rearrangements lead to novel primate gene functionFrancesca 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... - STRING v9.1: protein-protein interaction networks, with increased coverage and integrationAndrea Franceschini
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland
Nucleic Acids Res 41:D808-15. 2013.... - Assessing systems properties of yeast mitochondria through an interaction map of the organelleFabiana 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... - STRING: a database of predicted functional associations between proteinsChristian 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/... - Genome evolution reveals biochemical networks and functional modulesChristian 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... - Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogasterEvgeny M Zdobnov
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Science 298:149-59. 2002.... - Comparative assessment of large-scale data sets of protein-protein interactionsChristian 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...