P Bork

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. 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
  2. pmc Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulation
    Christian Perotti
    Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
    Breast Cancer Res 10:R94. 2008
  3. ncbi request reprint Predicting function: from genes to genomes and back
    P Bork
    European Molecular Biology Laboratory, Meyerhofstr 1, Heidelberg, PF 10 2209, Germany
    J Mol Biol 283:707-25. 1998
  4. ncbi request reprint Evolution of tuf genes: ancient duplication, differential loss and gene conversion
    W C Lathe
    EMBL, Heidelberg, Germany
    FEBS Lett 502:113-6. 2001
  5. ncbi request reprint 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
  6. ncbi request reprint Protein sequence motifs
    P Bork
    European Molecular Biology Laboratory, Heidelberg, Germany
    Curr Opin Struct Biol 6:366-76. 1996
  7. pmc The protein phosphatase 2C (PP2C) superfamily: detection of bacterial homologues
    P Bork
    European Molecular Biology Laboratory, Heidelberg, Germany
    Protein Sci 5:1421-5. 1996
  8. ncbi request reprint Predicting functions from protein sequences--where are the bottlenecks?
    P Bork
    EMBL, Heidelberg, Germany
    Nat Genet 18:313-8. 1998
  9. pmc TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved modular architecture
    A Herold
    European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    Mol Cell Biol 20:8996-9008. 2000
  10. 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

Collaborators

Detail Information

Publications121 found, 100 shown here

  1. 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...
  2. pmc Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulation
    Christian Perotti
    Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
    Breast Cancer Res 10:R94. 2008
    ..We hypothesise that the identification of these genes should yield insights into the mechanisms by which prolactin participates in cancer formation or progression, and possibly how it regulates normal mammary gland development...
  3. ncbi request reprint Predicting function: from genes to genomes and back
    P Bork
    European Molecular Biology Laboratory, Meyerhofstr 1, Heidelberg, PF 10 2209, Germany
    J Mol Biol 283:707-25. 1998
    ..The final goal will be to elucidate the mapping between genotype and phenotype...
  4. ncbi request reprint Evolution of tuf genes: ancient duplication, differential loss and gene conversion
    W C Lathe
    EMBL, Heidelberg, Germany
    FEBS Lett 502:113-6. 2001
    ..Phylogenetic and genomic location analysis of 20 complete eubacterial genomes suggests that this ancient duplication has been differentially lost and maintained in eubacteria...
  5. ncbi request reprint 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
    ....
  6. ncbi request reprint Protein sequence motifs
    P Bork
    European Molecular Biology Laboratory, Heidelberg, Germany
    Curr Opin Struct Biol 6:366-76. 1996
    ..A systematically derived motif database is therefore feasible, allowing the classification of the majority of the newly appearing protein sequences into known families...
  7. pmc The protein phosphatase 2C (PP2C) superfamily: detection of bacterial homologues
    P Bork
    European Molecular Biology Laboratory, Heidelberg, Germany
    Protein Sci 5:1421-5. 1996
    ..Phylogenetic analysis of all the proteins indicates a widespread sequence family for which a considerable number of isoenzymes can be inferred...
  8. ncbi request reprint Predicting functions from protein sequences--where are the bottlenecks?
    P Bork
    EMBL, Heidelberg, Germany
    Nat Genet 18:313-8. 1998
    ..While current homology detection methods can cope with the data flow, the identification, verification and annotation of functional features need to be drastically improved...
  9. pmc TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved modular architecture
    A Herold
    European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    Mol Cell Biol 20:8996-9008. 2000
    ..Both human p15 homologues bind TAP, NXF2, and NXF3. Together, our results indicate that the TAP-p15 mRNA export pathway has diversified in higher eukaryotes compared to yeast, perhaps reflecting a greater substrate complexity...
  10. 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...
  11. ncbi request reprint A P-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of sequence motifs and enzyme activity
    P Bork
    European Molecular Biology Laboratory, Heidelberg, Germany
    Proteins 20:347-55. 1994
    ....
  12. ncbi request reprint Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways
    R R Copley
    Biocomputing, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
    J Mol Biol 303:627-41. 2000
    ..The results favour widespread recruitment of enzymes between pathways, rather than a "backwards evolution" model, and support the idea that modern proteins may have arisen from common ancestors that bound key metabolites...
  13. ncbi request reprint The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins
    Z Liu
    European Molecular Biology Laboratory, Heidelberg, Germany
    Structure 7:1557-66. 1999
    ..However, in the Werner and Bloom syndrome helicases the HRDC domain may have a role in their functional differences by mediating diverse molecular interactions...
  14. ncbi request reprint Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase
    B Eisenhaber
    European Molecular Biology Laboratory, Heidelberg, Germany
    Protein Eng 11:1155-61. 1998
    ..The volume of the active site cleft accommodating the four residues omega - 1...omega + 2 appears to be approximately 540 A3...
  15. 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...
  16. pmc Predicting protein function by genomic context: quantitative evaluation and qualitative inferences
    M Huynen
    European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Genome Res 10:1204-10. 2000
    ..Using a combination of genomic context and homology searches, new functional features can be predicted for 10% of M. genitalium genes...
  17. pmc STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene
    B Snel
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Nucleic Acids Res 28:3442-4. 2000
    ..The usefulness of STRING is illustrated with an example that suggests a functional context for an RNA methylase with unknown specificity...
  18. ncbi request reprint Integration of genome data and protein structures: prediction of protein folds, protein interactions and "molecular phenotypes" of single nucleotide polymorphisms
    S Sunyaev
    European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Curr Opin Struct Biol 11:125-30. 2001
    ..Furthermore, by utilising the new incoming data on single nucleotide polymorphisms by mapping them onto three-dimensional structures of proteins, problems concerning population, medical and evolutionary genetics can be addressed...
  19. pmc Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase, and galactokinase families of sugar kinases
    P Bork
    European Molecular Biology Laboratory, Heidelberg, Germany
    Protein Sci 2:31-40. 1993
    ..The flexible combination of active sites and three-dimensional folds observed in nature can be exploited by protein engineers in designing and optimizing enzymatic function...
  20. 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...
  21. ncbi request reprint Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Bioinformatics 23:127-8. 2007
    ..Various types of data such as genome sizes or protein domain repertoires can be mapped onto the tree. Export to several bitmap and vector graphics formats is supported. AVAILABILITY: iTOL is available at http://itol.embl.de..
  22. 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...
  23. ncbi request reprint Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii
    Florian Raible
    Developmental Unit, European Molecular Biological Laboratory EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Science 310:1325-6. 2005
    ..A comparison of coding exon sequences confirms the ancestral nature of Platynereis and human genes. Thus, the urbilaterian ancestor had complex, intron-rich genes that have been retained in Platynereis and human...
  24. 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
    ....
  25. ncbi request reprint Comparison of ARM and HEAT protein repeats
    M A Andrade
    European Molecular Biology Laboratory, Heidelberg, Germany
    J Mol Biol 309:1-18. 2001
    ..Our results illustrate that ARM and HEAT-repeat proteins, while having a common phylogenetic origin, have since diverged significantly. We discuss evolutionary scenarios that could account for the great diversity of repeats observed...
  26. pmc Measuring genome evolution
    M A Huynen
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, and Max Delbrück Centrum for Molecular Medicine, 13122 Berlin Buch, Germany
    Proc Natl Acad Sci U S A 95:5849-56. 1998
    ..Finally, we show that some genomes are more highly organized than others: they show a higher degree of the clustering of genes that have orthologs in other genomes...
  27. 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...
  28. ncbi request reprint The CUB domain. A widespread module in developmentally regulated proteins
    P Bork
    EMBL, Heidelberg, Germany
    J Mol Biol 231:539-45. 1993
    ....
  29. ncbi request reprint Exploitation of gene context
    M Huynen
    European Molecular Biology Laboratory, Max Delbrück Centrum for Molecular Medicine, Heidelberg, Berlin Buch, 69117, 13122, Germany
    Curr Opin Struct Biol 10:366-70. 2000
    ..This type of information complements functional features that are predicted by classical homology-based search techniques...
  30. ncbi request reprint Drosophila kelch motif is derived from a common enzyme fold
    P Bork
    European Molecular Biological Laboratory, Heidelberg, Germany
    J Mol Biol 236:1277-82. 1994
    ..This structure may be very widely distributed throughout the biological world in sialidases and some other enzymes. In bacteria, a mobile noncatalytic domain is often associated with these same enzymes...
  31. ncbi request reprint Inversions and the dynamics of eukaryotic gene order
    M A Huynen
    EMBL, Biocomputing, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Trends Genet 17:304-6. 2001
    ..Nevertheless, qualitatively interesting examples of conservation of gene order in eukaryotes can be observed...
  32. 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...
  33. 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...
  34. 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...
  35. ncbi request reprint 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...
  36. 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/..
  37. pmc SMART 5: domains in the context of genomes and networks
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 34:D257-60. 2006
    ..Furthermore, intrinsically disordered protein regions can be identified and displayed. The network context is now displayed in the results page for more than 350 000 proteins, enabling easy analyses of domain interactions...
  38. ncbi request reprint BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments
    Mikita Suyama
    Biocomputing, European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69012 Heidelberg, Germany
    Bioinformatics 20:1968-70. 2004
    ..The results are provided in text and PostScript formats to allow an automatic and visual evaluation of the respective region...
  39. ncbi request reprint Variation and evolution of the citric-acid cycle: a genomic perspective
    M A Huynen
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Trends Microbiol 7:281-91. 1999
    ..Several distinct, incomplete cycles reflect adaptations to different environments. Their distribution over the phylogenetic tree hints at precursors in the evolution of the citric-acid cycle...
  40. pmc Pathway alignment: application to the comparative analysis of glycolytic enzymes
    T Dandekar
    EMBL, P O Box 102209, D 69012 Heidelberg, Germany
    Biochem J 343:115-24. 1999
    ..Archaean, bacterial and parasite specific adaptations are identified and described...
  41. ncbi request reprint Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches
    T Dandekar
    European Molecular Biology Laboratory, Postfach 102209, D 69012 Heidelberg, Germany
    Bioinformatics 14:271-8. 1998
    ..To reveal unidentified regulatory signals, we combine information from experiments with computational approaches. Depending on available knowledge, three different strategies are employed...
  42. ncbi request reprint Prediction of potential GPI-modification sites in proprotein sequences
    B Eisenhaber
    European Molecular Biology Laboratory, Meyerhofstrasse1, Heidelberg, D 69012, Federal Republic of Germany
    J Mol Biol 292:741-58. 1999
    ..embl-heidelberg.de/beisenha/gpi/gpi_p rediction. html The algorithm has been implemented in the prototype software "big-Pi predictor" which may find application as a genome annotation and target selection tool...
  43. ncbi request reprint Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries
    F Eisenhaber
    Max Delbruck Centrum fur Molekulare Medizin, Robert Rossle Strasse 10, 13122 Berlin Buch, Germany
    Bioinformatics 15:528-35. 1999
    ..This person can extract from the text considerably more information than is immediately apparent due to his extended biological background knowledge and logical reasoning...
  44. 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...
  45. ncbi request reprint 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
    ....
  46. ncbi request reprint Exploring MEDLINE abstracts with XplorMed
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Heidelberg, Germany
    Drugs Today (Barc) 38:381-9. 2002
    ..XplorMed is available http://www.bork. embl-heidelberg.de/xplormed...
  47. 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...
  48. 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
    ....
  49. pmc Information extraction from full text scientific articles: where are the keywords?
    Parantu K Shah
    Biocomputing, European Molecular Biology Laboratory, Heidelberg, Germany
    BMC Bioinformatics 4:20. 2003
    ..Several questions arise as to whether the effort of scanning full text articles is worthy, or whether the information that can be extracted from the different sections of an article can be relevant...
  50. 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/...
  51. pmc Update on XplorMed: A web server for exploring scientific literature
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Meyerhofstr 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 31:3866-8. 2003
    ..Here we describe new features added to XplorMed during the last 2 years (http://www.bork.embl-heidelberg.de/xplormed/)...
  52. ncbi request reprint 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...
  53. 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/...
  54. ncbi request reprint Genome and protein evolution in eukaryotes
    Richard R Copley
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Curr Opin Chem Biol 6:39-45. 2002
    ..The overall picture is of a huge diversity of gene content within eukaryotic genomes, reflecting different functional demands in different species...
  55. 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...
  56. ncbi request reprint Genomes in flux: the evolution of archaeal and proteobacterial gene content
    Berend Snel
    European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Genome Res 12:17-25. 2002
    ..Gene loss, unlike the other processes, correlates fairly well with time. This clock-like behavior suggests that gene loss is under negative selection, while the processes that add genes are under positive selection...
  57. 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
    ....
  58. ncbi request reprint SHOT: a web server for the construction of genome phylogenies
    Jan O Korbel
    EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
    Trends Genet 18:158-62. 2002
    ..SHOT is a useful tool for analysing the tree of life from a genomic point of view. It is available at http://www.Bork.EMBL-Heidelberg.de/SHOT...
  59. pmc The identification of functional modules from the genomic association of genes
    Berend Snel
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Proc Natl Acad Sci U S A 99:5890-5. 2002
    ..Comparative genome analysis, thus, allows identification of a level of functional interaction between that of pairwise interactions, and of the complete genome...
  60. ncbi request reprint Computing fuzzy associations for the analysis of biological literature
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Heidelberg, Germany
    Biotechniques 32:1380-2, 1384-5. 2002
    ..Those relations are used to derive ensembles of related words and their associated subsets of abstracts. The algorithm can be used publicly at http:// www.bork.embl-heidelberg.de/xplormed/...
  61. 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
    ....
  62. pmc NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria
    Miguel A Andrade
    European Molecular Biology Laboratory, Meyerhofstr, 1, 69117 Heidelberg, Germany
    Genome Biol 3:RESEARCH0047. 2002
    ..To find potential targets for drugs active against pathogenic bacteria, we have searched all completely sequenced genomes of pathogenic bacteria for genes relevant for iron transport...
  63. pmc SAM as a protein interaction domain involved in developmental regulation
    J Schultz
    EMBL, Heidelberg, Germany
    Protein Sci 6:249-53. 1997
    ..A conserved tyrosine in the SAM sequences of the EPH related RPTKs is likely to mediate cell-cell initiated signal transduction via the binding of SH2 containing proteins to phosphotyrosine...
  64. ncbi request reprint Evolution of prokaryotic gene order: genome rearrangements in closely related species
    M Suyama
    EMBL, Meyerhofstr. 1, D-69012 Heidelberg, Germany
    Trends Genet 17:10-3. 2001
    ..Here, we compare closely related genomes to identify the rate with which gene order is disrupted and to infer the genes involved in the genome rearrangement...
  65. ncbi request reprint Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching
    A Shevchenko
    Peptide and Protein Group, European Molecular Biology Laboratory, Heidelberg, Germany
    Anal Chem 73:1917-26. 2001
    ....
  66. pmc Environments shape the nucleotide composition of genomes
    Konrad U Foerstner
    European Molecular Biology Laboratory, Heidelberg, Germany
    EMBO Rep 6:1208-13. 2005
    ....
  67. ncbi request reprint LSAT: learning about alternative transcripts in MEDLINE
    Parantu K Shah
    European Molecular Biology Laboratory, Heidelberg, Germany
    Bioinformatics 22:857-65. 2006
    ..In this work, we choose the task of extracting information around this complex topic using a two-step procedure involving machine learning and information extraction...
  68. 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/...
  69. ncbi request reprint 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...
  70. doi request reprint Proteome organization in a genome-reduced bacterium
    Sebastian Kühner
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Science 326:1235-40. 2009
    ..The data set provides a blueprint of the minimal cellular machinery required for life...
  71. doi request reprint AQUA: automated quality improvement for multiple sequence alignments
    Jean Muller
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Bioinformatics 26:263-5. 2010
    ..Availability: AQUA is implemented in Tcl/Tk and runs in command line on all platforms. The source code is available under the GNU GPL license. Source code, README and Supplementary data are available at http://www.bork.embl.de/Docu/AQUA...
  72. pmc PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
    Mikita Suyama
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Nucleic Acids Res 34:W609-12. 2006
    ..Another distinct feature is that the user can specify a subregion of the input alignment in order to specifically analyze functional domains or exons of interest. The PAL2NAL server is available at http://www.bork.embl.de/pal2nal...
  73. ncbi request reprint 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
    ....
  74. 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...
  75. pmc Human non-synonymous SNPs: server and survey
    Vasily Ramensky
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 30:3894-900. 2002
    ..The strongest selective pressure was detected for proteins involved in transcription regulation...
  76. ncbi request reprint The WHy domain mediates the response to desiccation in plants and bacteria
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, 69012 Heidelberg, Meyerhofstrasse 1, Germany
    Bioinformatics 21:1304-7. 2005
    ..Although many resistance genes (R genes) associated to HR have been identified, very little is known about the molecular mechanisms activated after their expression...
  77. pmc 4DXpress: a database for cross-species expression pattern comparisons
    Yannick Haudry
    European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 36:D847-53. 2008
    ..4DXpress will be an invaluable tool for developmental as well as for computational biologists interested in gene regulation and evolution. 4DXpress is available at http://ani.embl.de/4DXpress...
  78. ncbi request reprint The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstr 1, 69012 Heidelberg, Germany
    Genomics 81:437-41. 2003
    ....
  79. pmc The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstr, 1, 69012 Heidelberg, Germany
    BMC Bioinformatics 4:64. 2003
    ..The characterization of their domain composition and organization provides useful information on the specific role of each region of their sequence...
  80. ncbi request reprint XplorMed: a tool for exploring MEDLINE abstracts
    C Perez-Iratxeta
    European Molecular Biology Laboratory, Meyerhofstr 1, 69012 Heidelberg, Germany
    Trends Biochem Sci 26:573-5. 2001
    ..The exploratory tool XplorMed has been developed to analyse the result of any MEDLINE query. It suggests main groups of related topics and documents, sparing the user the need of reading all abstracts...
  81. 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...
  82. ncbi request reprint Prediction of deleterious human alleles
    S Sunyaev
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
    Hum Mol Genet 10:591-7. 2001
    ..The average human genotype carries approximately 10(3) damaging non-synonymous SNPs that together cause a substantial reduction in fitness...
  83. pmc Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins
    M Suyama
    EMBL, Heidelberg, Germany
    EMBO Rep 1:53-8. 2000
    ..Furthermore, the C-terminus of TAP was found to contain a ubiquitin-associated (UBA) domain. By site-directed mutagenesis we show that a conserved loop in this domain plays an essential role in mediating TAP-nucleoporin interaction...
  84. ncbi request reprint The WW domain: a signalling site in dystrophin?
    P Bork
    EMBL, Heidelberg, Germany
    Trends Biochem Sci 19:531-3. 1994
  85. ncbi request reprint Sircah: a tool for the detection and visualization of alternative transcripts
    Eoghan D Harrington
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Bioinformatics 24:1959-60. 2008
    ..The results can be visualized in a variety of ways, allowing the creation of publication quality images...
  86. doi request reprint Evolution of biomolecular networks: lessons from metabolic and protein interactions
    Takuji Yamada
    European Molecular Biology Laboratory, Heidelberg, Germany
    Nat Rev Mol Cell Biol 10:791-803. 2009
    ..However, many evolutionary constraints can be uncovered only if temporal and spatial aspects are included in the network analysis...
  87. ncbi request reprint Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome
    Florian Raible
    Computational Unit, EMBL, 69117 Heidelberg, Germany
    Dev Biol 300:461-75. 2006
    ..Notably, these structures also express different opsins, indicating that sea urchins possess an intricate molecular set-up to sense their environment...
  88. 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)...
  89. pmc Evolution and regulation of cellular periodic processes: a role for paralogues
    Kalliopi Trachana
    European Molecular Biology Laboratory Heidelberg, Heidelberg, Germany
    EMBO Rep 11:233-8. 2010
    ..Lineage-specific functional repertoires of periodic-associated paralogues imply that this mode of regulation might have evolved independently in several organisms...
  90. 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/...
  91. ncbi request reprint Common exon duplication in animals and its role in alternative splicing
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Hum Mol Genet 11:1561-7. 2002
    ..The common nature of recent exon duplication indicates that it might have a significant role in the fast evolution of eukaryotic genes. It also provides a general mechanism for the regulation of protein function...
  92. ncbi request reprint Structure-based assembly of protein complexes in yeast
    Patrick Aloy
    European Molecular Biology Laboratory, Structural and Computational Biology Programme, 1, 69117 Heidelberg, Germany
    Science 303:2026-9. 2004
    ..We also consider interactions between complexes (cross-talk) and use these to construct a structure-based network of molecular machines in the cell...
  93. ncbi request reprint A protocol for the update of references to scientific literature in biological databases
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Heidelberg, Germany
    Appl Bioinformatics 2:189-91. 2003
    ..Human experts found the references that the algorithm scored highly were more relevant to the database entry than those scored lowly, suggesting that the algorithm was useful...
  94. 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)...
  95. ncbi request reprint A versatile structural domain analysis server using profile weight matrices
    Steffen Schmidt
    EMBL, Postfach 102209, D 69012 Heidelberg, Germany
    J Chem Inf Comput Sci 42:405-7. 2002
    ..The WWW server is at http://www.bork.embl-heidelberg.de/AnDom, and profiles can be downloaded at ftp.bork.embl-heidelberg.de/pub/users/ schmidt/AnDom...
  96. ncbi request reprint The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold
    Francesca D Ciccarelli
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69012 Heidelberg, Germany
    Trends Biochem Sci 28:349-52. 2003
  97. ncbi request reprint Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells
    S M Woerner
    Division of Molecular Diagnostics and Therapy, Department of Surgery, University of Heidelberg, Heidelberg, Germany
    Int J Cancer 93:12-9. 2001
    ..The approach outlined here identified a new set of genes frequently affected by mutations in MSI-positive tumor cells. It will lead to novel and highly specific diagnostic and therapeutic targets for microsatellite unstable cancers...
  98. pmc An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins
    P Bork
    European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany
    Proc Natl Acad Sci U S A 89:7290-4. 1992
    ..A common evolutionary origin for all of the proteins in this class is proposed...
  99. ncbi request reprint Association of genes to genetically inherited diseases using data mining
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Meyerhofstr 1, Heidelberg 69012, Germany
    Nat Genet 31:316-9. 2002
    ..The scoring also indicates that for some diseases, the chance of identifying the underlying gene is higher...
  100. pmc A complex prediction: three-dimensional model of the yeast exosome
    Patrick Aloy
    EMBL, Meyerhofstrasse, Heidelberg, Germany
    EMBO Rep 3:628-35. 2002
    ..The model suggests numerous experiments to probe exosome function, particularly with respect to subunits making direct atomic contacts and conserved, possibly functional residues within the predicted central pore of the complex...
  101. pmc Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes
    Mikita Suyama
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS Comput Biol 2:e76. 2006
    ..The genes and unprocessed pseudogenes obtained here will enable further studies on the mechanisms involved in gene duplication as well as of the fate of duplicated genes...