T Doerks

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. ncbi request reprint DDT -- a novel domain in different transcription and chromosome remodeling factors
    T Doerks
    European Molecular Biology Laboratory, 69012 Heidelberg, Germany
    Trends Biochem Sci 26:145-6. 2001
  2. 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
  3. pmc eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
    J Muller
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 38:D190-5. 2010
  4. pmc Quantitative assessment of protein function prediction from metagenomics shotgun sequences
    E D Harrington
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Proc Natl Acad Sci U S A 104:13913-8. 2007
  5. ncbi request reprint Quantitative phylogenetic assessment of microbial communities in diverse environments
    C von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Science 315:1126-30. 2007
  6. ncbi request reprint 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
  7. 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
  8. 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
  9. 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
  10. ncbi request reprint 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

Collaborators

Detail Information

Publications15

  1. ncbi request reprint DDT -- a novel domain in different transcription and chromosome remodeling factors
    T Doerks
    European Molecular Biology Laboratory, 69012 Heidelberg, Germany
    Trends Biochem Sci 26:145-6. 2001
    ..This domain is characterized by a number of conserved aromatic and charged residues and is predicted to consist of three alpha helices. Recent studies indicate a likely DNA-binding function for the DDT domain...
  2. 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
    ....
  3. pmc eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
    J Muller
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 38:D190-5. 2010
    ..Users can access the complete set of orthologous groups via a web interface at: http://eggnog.embl.de...
  4. pmc Quantitative assessment of protein function prediction from metagenomics shotgun sequences
    E D Harrington
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Proc Natl Acad Sci U S A 104:13913-8. 2007
    ..Our results further suggest that, although functions can be inferred for most proteins on earth, many functions remain to be discovered in numerous small, rare protein families...
  5. ncbi request reprint Quantitative phylogenetic assessment of microbial communities in diverse environments
    C von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Science 315:1126-30. 2007
    ..The method also enables determination of preferred habitats for entire microbial clades and provides evidence that such habitat preferences are often remarkably stable over time...
  6. ncbi request reprint 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...
  7. 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...
  8. 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...
  9. 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/..
  10. ncbi request reprint 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...
  11. 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...
  12. 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...
  13. ncbi request reprint 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...
  14. ncbi request reprint Protein domain analysis in the era of complete genomes
    Richard R Copley
    EMBL, Meyerhofstrasse 1, Heidelberg, Germany
    FEBS Lett 513:129-34. 2002
    ....
  15. ncbi request reprint 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
    ....