Tobias Doerks

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. pmc Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins
    Tobias Doerks
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS ONE 7:e34302. 2012
  2. pmc DCD - a novel plant specific domain in proteins involved in development and programmed cell death
    Raimund Tenhaken
    Plant Molecular Biology, University of Frankfurt, Marie Curie Str, 9, 60439 Frankfurt, Germany
    BMC Bioinformatics 6:169. 2005
  3. pmc Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes
    Tobias Doerks
    EMBL, 69012 Heidelberg, Meyerhofstrasse 1 and Max Delbrueck Centrum, Robert Roessle Strasse 10, D 13092 Berlin, Germany
    Nucleic Acids Res 32:6321-6. 2004
  4. pmc SMART 4.0: towards genomic data integration
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 32:D142-4. 2004
  5. 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
  6. 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
  7. pmc Orthology prediction methods: a quality assessment using curated protein families
    Kalliopi Trachana
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Bioessays 33:769-80. 2011
  8. 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
  9. 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
  10. pmc Discovering functional novelty in metagenomes: examples from light-mediated processes
    Amoolya H Singh
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    J Bacteriol 191:32-41. 2009

Collaborators

Detail Information

Publications25

  1. pmc Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins
    Tobias Doerks
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS ONE 7:e34302. 2012
    ..All together, we have raised the fraction of the proteome with at least some functional annotation to 88% which should considerably enhance the interpretation of large-scale experiments targeting this medically important organism...
  2. pmc DCD - a novel plant specific domain in proteins involved in development and programmed cell death
    Raimund Tenhaken
    Plant Molecular Biology, University of Frankfurt, Marie Curie Str, 9, 60439 Frankfurt, Germany
    BMC Bioinformatics 6:169. 2005
    ..We delineate the NRP-gene in soybean, which is specifically induced during this programmed cell death and contains a novel protein domain, which is commonly found in different plant proteins...
  3. pmc Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes
    Tobias Doerks
    EMBL, 69012 Heidelberg, Meyerhofstrasse 1 and Max Delbrueck Centrum, Robert Roessle Strasse 10, D 13092 Berlin, Germany
    Nucleic Acids Res 32:6321-6. 2004
    ..However, we were able to assign pathways, cellular processes or physical complexes for 273 groups (encompassing 3624 previously functionally uncharacterized proteins)...
  4. pmc SMART 4.0: towards genomic data integration
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 32:D142-4. 2004
    ..Other improvements include the ability to query SMART by Gene Ontology terms, improved structure database searching and batch retrieval of multiple entries...
  5. 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/...
  6. 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...
  7. pmc Orthology prediction methods: a quality assessment using curated protein families
    Kalliopi Trachana
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Bioessays 33:769-80. 2011
    ..embl.de/orthobench/) should facilitate the improvement of current orthology assignment protocols, which is of utmost importance for many fields of biology and should be tackled by a broad scientific community...
  8. 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%)...
  9. 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...
  10. pmc Discovering functional novelty in metagenomes: examples from light-mediated processes
    Amoolya H Singh
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    J Bacteriol 191:32-41. 2009
    ..While the discoveries illustrate the opportunities in function discovery, we also discuss the immense conceptual and practical challenges that come along with this new type of data...
  11. 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
    ....
  12. 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/..
  13. pmc SMART 6: recent updates and new developments
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 37:D229-32. 2009
    ..In addition to the standard web access to the database, users can now query SMART using distributed annotation system (DAS) or through a simple object access protocol (SOAP) based web service...
  14. pmc A computational screen for type I polyketide synthases in metagenomics shotgun data
    Konrad U Foerstner
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS ONE 3:e3515. 2008
    ..Polyketides are a diverse group of biotechnologically important secondary metabolites that are produced by multi domain enzymes called polyketide synthases (PKS)...
  15. pmc A nitrile hydratase in the eukaryote Monosiga brevicollis
    Konrad U Foerstner
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS ONE 3:e3976. 2008
    ..The newly discovered NHase might open biotechnological routes due to its unconventional structure, its new type of host and its apparent integration into eukaryotic protein networks...
  16. ncbi CASH--a beta-helix domain widespread among carbohydrate-binding proteins
    Francesca D Ciccarelli
    Max Delbrueck Centrum, PO Box 740238, D 13092 Berlin, Germany
    Trends Biochem Sci 27:59-62. 2002
    ..The CASH domain is characterized by internal repetitions of glycines and hydrophobic residues that correspond to the repetitive units of a predicted or observed right-handed beta-helix structure of the pectate lyase superfamily...
  17. doi A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL
    Susanne Haemmerling
    Department of Paediatric Oncology, Haematology and Immunology, University of Heidelberg Medical Centre, Heidelberg, Germany
    Br J Haematol 157:180-7. 2012
    ..The 15q24 microdeletion may thus represent the first genetic hit to initiate leukaemogenesis and implicates PML and SUMO3 as novel components of the leukaemogenic network in TMD/AMKL...
  18. pmc Systematic association of genes to phenotypes by genome and literature mining
    Jan O Korbel
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS Biol 3:e134. 2005
    ..Among the clusters, we observe an enrichment of pathogenicity-related associations, suggesting that the approach reveals many novel genes likely to play a role in infectious diseases...
  19. ncbi Protein domain analysis in the era of complete genomes
    Richard R Copley
    EMBL, Meyerhofstrasse 1, Heidelberg, Germany
    FEBS Lett 513:129-34. 2002
    ....
  20. pmc SMART 7: recent updates to the protein domain annotation resource
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 40:D302-5. 2012
    ..An advanced full text search engine was implemented, covering the complete annotations for SMART and Pfam domains, as well as the complete set of protein descriptions, allowing users to quickly find relevant information...
  21. pmc mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes
    Isabelle Behm-Ansmant
    European Molecular Biology Laboratory EMBL, Heidelberg, Germany
    Genes Dev 20:1885-98. 2006
    ..Our findings indicate that GW182 links the miRNA pathway to mRNA degradation by interacting with AGO1 and promoting decay of at least a subset of miRNA targets...
  22. ncbi BSD: a novel domain in transcription factors and synapse-associated proteins
    Tobias Doerks
    EMBL, 69012 Heidelberg, Meyerhofstr 1, and Max Delbrueck Centrum, Berlin, Germany
    Trends Biochem Sci 27:168-70. 2002
    ..The BSD domain is characterized by three predicted alpha helices, which probably form a three-helical bundle, as well as by conserved tryptophan and phenylalanine residues, located at the C terminus of the domain...
  23. pmc Systematic identification of novel protein domain families associated with nuclear functions
    Tobias Doerks
    European Molecular Biology Laboratory, 69114 Heidelberg, Germany
    Genome Res 12:47-56. 2002
    ....
  24. ncbi Computational characterization of multiple Gag-like human proteins
    Monica Campillos
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Trends Genet 22:585-9. 2006
    ....
  25. pmc Recent improvements to the SMART domain-based sequence annotation resource
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 30:242-4. 2002
    ..SMART output can now be easily included in users' documents. A SMART mirror has been created at http://smart.ox.ac.uk...