Peer Bork

Summary

Publications

  1. ncbi request reprint Towards cellular systems in 4D
    Peer Bork
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Cell 121:507-9. 2005
  2. ncbi request reprint Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families
    Parantu K Shah
    European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany
    Gene 407:199-215. 2008
  3. 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
  4. 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
  5. 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
  6. 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
  7. pmc Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis
    Sean D Hooper
    Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
    Mol Syst Biol 3:72. 2007
  8. 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
  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. 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

Detail Information

Publications86

  1. ncbi request reprint Towards cellular systems in 4D
    Peer Bork
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Cell 121:507-9. 2005
  2. ncbi request reprint Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families
    Parantu K Shah
    European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany
    Gene 407:199-215. 2008
    ..Utilization of such multi-fold approaches results in 10-fold increase of function annotation for Drosophila serine proteases and demonstrates value in increasing annotations in multiple genomes...
  3. 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...
  4. 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...
  5. 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...
  6. 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...
  7. pmc Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis
    Sean D Hooper
    Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
    Mol Syst Biol 3:72. 2007
    ..By mapping the groups to the protein network, we also predict and experimentally confirm new functional associations...
  8. 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..
  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. 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...
  11. 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...
  12. 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...
  13. 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...
  14. 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...
  15. 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...
  16. doi request reprint Drug target identification using side-effect similarity
    Monica Campillos
    European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Science 321:263-6. 2008
    ..Nine of these were tested and confirmed in cell assays, documenting the feasibility of using phenotypic information to infer molecular interactions and hinting at new uses of marketed drugs...
  17. ncbi request reprint Proteome survey reveals modularity of the yeast cell machinery
    Anne Claude Gavin
    Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 440:631-6. 2006
    ..This study provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling...
  18. 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
    ....
  19. 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...
  20. doi 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...
  21. pmc A network of conserved co-occurring motifs for the regulation of alternative splicing
    Mikita Suyama
    Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 38:7916-26. 2010
    ..These results indicate that even more alternative splicing events will be found with the progress of large-scale and high-throughput analyses for various tissue samples and developmental stages...
  22. 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
    ....
  23. 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/...
  24. 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...
  25. 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/...
  26. 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...
  27. 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...
  28. 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...
  29. pmc A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae
    Oriol Gallego
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Heidelberg, Germany
    Mol Syst Biol 6:430. 2010
    ....
  30. pmc Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium
    Vera van Noort
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Heidelberg, Germany
    Mol Syst Biol 8:571. 2012
    ..The results imply previously unreported hidden layers of post-transcriptional regulation intertwining phosphorylation with lysine acetylation and other mechanisms that define the functional state of a cell...
  31. 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%)...
  32. pmc iPath2.0: interactive pathway explorer
    Takuji Yamada
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 39:W412-5. 2011
    ..0's maps. These customized maps give users an intuitive overview of their own data, guiding the analysis of various genomics and metagenomics projects...
  33. 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)...
  34. pmc Enterotypes of the human gut microbiome
    Manimozhiyan Arumugam
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 473:174-80. 2011
    ..For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers...
  35. doi request reprint Large-scale prediction of drug-target relationships
    Michael Kuhn
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    FEBS Lett 582:1283-90. 2008
    ..We finally discuss how phenotypic data could help to expand our understanding of the complex mechanisms of drug action...
  36. ncbi request reprint Computational characterization of multiple Gag-like human proteins
    Monica Campillos
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Trends Genet 22:585-9. 2006
    ....
  37. doi request reprint SmashCommunity: a metagenomic annotation and analysis tool
    Manimozhiyan Arumugam
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Bioinformatics 26:2977-8. 2010
    ..It provides tools to estimate the quantitative phylogenetic and functional compositions of metagenomes, to compare compositions of multiple metagenomes and to produce intuitive visual representations of such analyses...
  38. ncbi request reprint Get the most out of your metagenome: computational analysis of environmental sequence data
    Jeroen Raes
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Curr Opin Microbiol 10:490-8. 2007
    ....
  39. doi request reprint Predicting biological networks from genomic data
    Eoghan D Harrington
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    FEBS Lett 582:1251-8. 2008
    ..Here, we review the computational methods available to predict biological networks from genomic sequence data and discuss how they relate to high-throughput experimental methods...
  40. pmc Protein coding potential of retroviruses and other transposable elements in vertebrate genomes
    Evgeny M Zdobnov
    EMBL Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 33:946-54. 2005
    ..To automatically annotate RETRA genes in other vertebrate genomes, we provide as a tool a set of marker protein domains and a manually refined list of domesticated or ancestral RETRA genes for rescuing genes with vertebrate functions...
  41. ncbi request reprint 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...
  42. pmc Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 39:W475-8. 2011
    ..Export to various bitmap and vector graphics formats is supported. Batch access interface is available for programmatic access or inclusion of interactive trees into other web services...
  43. 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
    ....
  44. pmc Country-specific antibiotic use practices impact the human gut resistome
    Kristoffer Forslund
    European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Genome Res 23:1163-9. 2013
    ..The results are robust over time as the antibiotic resistance determinants of individuals persist in the human gut flora for at least a year. ..
  45. pmc Consistent mutational paths predict eukaryotic thermostability
    Vera van Noort
    European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
    BMC Evol Biol 13:7. 2013
    ..With Chaetomium thermophilum, Thielavia terrestris and Thielavia heterothallica three genome sequences of thermophilic eukaryotes have been published...
  46. pmc OGEE: an online gene essentiality database
    Wei Hua Chen
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 40:D901-6. 2012
    ..Linked tools allow the user to compare gene essentiality among different gene groups, or compare features of essential genes to non-essential genes, and visualize the results. OGEE is freely available at http://ogeedb.embl.de...
  47. pmc Genomic variation landscape of the human gut microbiome
    Siegfried Schloissnig
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 493:45-50. 2013
    ..This indicates that individual-specific strains are not easily replaced and that an individual might have a unique metagenomic genotype, which may be exploitable for personalized diet or drug intake...
  48. pmc PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins
    Pablo Minguez
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 41:D306-11. 2013
    ..PTMcode is presented as a protein-based searchable database with an interactive web interface providing the context of the co-regulation of nearly 75 000 residues in >10 000 proteins...
  49. 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...
  50. 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...
  51. pmc Structural similarity to bridge sequence space: finding new families on the bridges
    Parantu K Shah
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Protein Sci 14:1305-14. 2005
    ..We quantify the associated increase in structural information in Swissprot and discuss examples illustrating the applicability of this approach to understand functional and evolutionary relationships between protein families...
  52. 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...
  53. doi request reprint iPath: interactive exploration of biochemical pathways and networks
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, Heidelberg, Germany
    Trends Biochem Sci 33:101-3. 2008
    ..For example, by merging human genome data with two important gut commensals, iPath can pinpoint the complementarity of the host-symbiont metabolic capacities...
  54. 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
    ....
  55. ncbi request reprint Protein function space: viewing the limits or limited by our view?
    Jeroen Raes
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Curr Opin Struct Biol 17:362-9. 2007
    ..However, when we consider protein families, continued sequencing seems to yield an ever-increasing number of novel families. Until we reconcile these two views, the limits of protein space will remain obscured...
  56. ncbi request reprint Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii
    Mikita Suyama
    EMBL, Heidelberg, Germany
    FEBS Lett 579:5281-6. 2005
    ....
  57. pmc RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the nuclear pore complex and functions in nuclear mRNA export
    Daniel Forler
    EMBL, 69117 Heidelberg, Germany
    Mol Cell Biol 24:1155-67. 2004
    ..In RanBP2-depleted cells, NXF1 diffuses freely through the cytoplasm. Consequently, the nuclear levels of the protein decrease and export of bulk mRNA is impaired...
  58. 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...
  59. 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...
  60. pmc A genome-wide survey of human pseudogenes
    David Torrents
    EMBL, Heidelberg 69117, Germany
    Genome Res 13:2559-67. 2003
    ..It is likely that the human pseudogenes identified here represent only a small fraction of the total, which probably exceeds the number of genes...
  61. ncbi request reprint Alternative splicing and evolution
    Stephanie Boue
    EMBL, Heidelberg, Germany
    Bioessays 25:1031-4. 2003
    ..It suggests that alternative splicing plays a major role in genome evolution allowing new exons to evolve with less constraint...
  62. 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...
  63. ncbi request reprint Functional organization of the yeast proteome by systematic analysis of protein complexes
    Anne Claude Gavin
    Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 415:141-7. 2002
    ..This higher-order map contains fundamental biological information and offers the context for a more reasoned and informed approach to drug discovery...
  64. 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/...
  65. pmc Is there biological research beyond Systems Biology? A comparative analysis of terms
    Peer Bork
    Mol Syst Biol 1:2005.0012. 2005
  66. ncbi request reprint Function prediction and protein networks
    Martijn A Huynen
    Nijmegen Center for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
    Curr Opin Cell Biol 15:191-8. 2003
    ..Finally, the interaction networks that can be obtained by combining the predicted pair-wise interactions have enough internal structure to detect higher levels of organization, such as 'functional modules'...
  67. ncbi request reprint Increase of functional diversity by alternative splicing
    Evgenia V Kriventseva
    European Bioinformatics Institute EMBL EBI, Hinxton Wellcome Trust Genome Campus, Hinxton, Cambridge, UK CB10 1SD
    Trends Genet 19:124-8. 2003
    ..Thus, it seems that positive selection has had a major role in the evolution of alternative splicing...
  68. ncbi request reprint Bioinformatics in the post-sequence era
    Minoru Kanehisa
    Bioinformatics Center, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nat Genet 33:305-10. 2003
    ....
  69. ncbi request reprint The genome sequence of the malaria mosquito Anopheles gambiae
    Robert A Holt
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 298:129-49. 2002
    ..An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect...
  70. ncbi request reprint InterPro: an integrated documentation resource for protein families, domains and functional sites
    Nicola J Mulder
    EMBL Outstation, European Bioinformatics Institute, Hinxton, Cambridge, UK
    Brief Bioinform 3:225-35. 2002
    ..Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (2,141,621 InterPro hits from 586,124 SWISS-PROT and TrEMBL protein sequences). The database is freely accessible for text- and sequence-based searches...
  71. pmc Predicting protein cellular localization using a domain projection method
    Richard Mott
    Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, United Kingdom
    Genome Res 12:1168-74. 2002
    ..This method is complementary to approaches that use amino-acid composition or identify sorting sequences; these methods may be combined to further enhance prediction accuracy...
  72. 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...
  73. ncbi request reprint The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data
    Henning Hermjakob
    European Bioinformatics Institute, EBI Hinxton, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Biotechnol 22:177-83. 2004
    ....
  74. 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...
  75. pmc NetworKIN: a resource for exploring cellular phosphorylation networks
    Rune Linding
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    Nucleic Acids Res 36:D695-9. 2008
    ..The database currently contains a predicted phosphorylation network with 20,224 site-specific interactions involving 3978 phosphoproteins and 73 human kinases from 20 families...
  76. pmc Systematic discovery of in vivo phosphorylation networks
    Rune Linding
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    Cell 129:1415-26. 2007
    ..Applying this approach to DNA damage signaling, we show that 53BP1 and Rad50 are phosphorylated by CDK1 and ATM, respectively. We describe a scalable strategy to evaluate predictions, which suggests that BCLAF1 is a GSK-3 substrate...
  77. pmc Update of the G2D tool for prioritization of gene candidates to inherited diseases
    Carolina Perez-Iratxeta
    Ontario Genomics Innovation Centre, Ottawa Health Research Institute, 501 Smyth, Ottawa, ON, Canada K1H 8L6
    Nucleic Acids Res 35:W212-6. 2007
    ..This means that some of them will correspond to well-known characterized genes, and others will overlap with predicted genes, thus providing a wider analysis. G2D is publicly available at http://www.ogic.ca/projects/g2d_2/..
  78. pmc Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals
    Sven Danckwardt
    Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
    EMBO J 26:2658-69. 2007
    ..These data uncover a novel mechanism that functionally links the splicing and 3' end formation machineries of multiple cellular mRNAs in an USE-dependent manner...
  79. ncbi request reprint Literature mining for the biologist: from information retrieval to biological discovery
    Lars Juhl Jensen
    European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    Nat Rev Genet 7:119-29. 2006
    ..However, the latter will require the integration of literature and high-throughput data, which should encourage close collaborations between biologists and computational linguists...
  80. 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...
  81. ncbi request reprint Medusa: a simple tool for interaction graph analysis
    Sean D Hooper
    European Molecular Biology Laboratory Heidelberg, Germany
    Bioinformatics 21:4432-3. 2005
    ..It features an intuitive user interface developed with the help of biologists. Medusa is optimized for accessing protein interaction data from STRING, but can be used for any type of graph from any scientific field...
  82. doi request reprint Biochemistry. Not comparable, but complementary
    Lars Juhl Jensen
    European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    Science 322:56-7. 2008
  83. ncbi request reprint Comparative metagenomics of microbial communities
    Susannah Green Tringe
    Department of Energy DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
    Science 308:554-7. 2005
    ..The identification of environment-specific genes through a gene-centric comparative analysis presents new opportunities for interpreting and diagnosing environments...
  84. ncbi request reprint Comparison of computational methods for the identification of cell cycle-regulated genes
    Ulrik de Lichtenberg
    Center for Biological Sequence Analysis, Technical University of Denmark DK 2800 Lyngby, Denmark
    Bioinformatics 21:1164-71. 2005
    ..We present a simple permutation-based method that performs better than most existing methods...
  85. ncbi request reprint Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome
    Adam J Liska
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Proteomics 4:2707-21. 2004
    ..These findings were made possible due to the application of sequence-similarity methods, which extended mass spectrometric protein identification capabilities by 2-fold compared to conventional methods...
  86. ncbi request reprint Genome-wide experimental determination of barriers to horizontal gene transfer
    Rotem Sorek
    Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
    Science 318:1449-52. 2007
    ..coli, a computational analysis of gene-transfer rates across available bacterial and archaeal genomes supports that the barriers observed in our study are general across the tree of life...