Peer Bork

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. pmc Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours
    Takuji Yamada
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 8:581. 2012
  2. 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
  3. 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
  4. pmc Younger genes are less likely to be essential than older genes, and duplicates are less likely to be essential than singletons of the same age
    Wei Hua Chen
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Biol Evol 29:1703-6. 2012
  5. pmc Prediction of drug combinations by integrating molecular and pharmacological data
    Xing Ming Zhao
    European Molecular Biology Laboratory EMBL, Heidelberg, Germany
    PLoS Comput Biol 7:e1002323. 2011
  6. 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
  7. pmc Identifying single copy orthologs in Metazoa
    Christopher J Creevey
    Teagasc, Animal and Grassland Research and Innovation Centre, Grange, Dunsany, County Meath, Ireland
    PLoS Comput Biol 7:e1002269. 2011
  8. 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
  9. 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
  10. pmc A molecular study of microbe transfer between distant environments
    Sean D Hooper
    Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
    PLoS ONE 3:e2607. 2008

Collaborators

Detail Information

Publications94

  1. pmc Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours
    Takuji Yamada
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 8:581. 2012
    ....
  2. 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...
  3. 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...
  4. pmc Younger genes are less likely to be essential than older genes, and duplicates are less likely to be essential than singletons of the same age
    Wei Hua Chen
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Biol Evol 29:1703-6. 2012
    ..The "paradoxical" high essentiality among mouse gene duplicates is then caused by different age profiles of singletons and duplicates, with the latter tending to be derived from older genes...
  5. pmc Prediction of drug combinations by integrating molecular and pharmacological data
    Xing Ming Zhao
    European Molecular Biology Laboratory EMBL, Heidelberg, Germany
    PLoS Comput Biol 7:e1002323. 2011
    ..We believe that our proposed approach can help to limit the search space of drug combinations and provide a new way to effectively utilize existing drugs for new purposes...
  6. 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...
  7. pmc Identifying single copy orthologs in Metazoa
    Christopher J Creevey
    Teagasc, Animal and Grassland Research and Innovation Centre, Grange, Dunsany, County Meath, Ireland
    PLoS Comput Biol 7:e1002269. 2011
    ..In contrast, the vast majority of EST datasets with no corresponding genome sequence available are largely under-sampled and probably do not accurately represent the actual genomic complement of the organisms from which they are derived...
  8. 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...
  9. 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...
  10. pmc A molecular study of microbe transfer between distant environments
    Sean D Hooper
    Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
    PLoS ONE 3:e2607. 2008
    ..In this study, we compare two environmental sequencing projects to find molecular evidence of transfer of microbes over vast geographical distances...
  11. pmc Universally distributed single-copy genes indicate a constant rate of horizontal transfer
    Christopher J Creevey
    Animal and Bioscience Research Department, Teagasc, Grange, Dunsany, Ireland
    PLoS ONE 6:e22099. 2011
    ..This suggests that levels of HGT above this rate may be indicative of positively selected transfers that may allow niche adaptation or bestow other benefits to the recipient organism...
  12. pmc Network neighbors of drug targets contribute to drug side-effect similarity
    Lucas Brouwers
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS ONE 6:e22187. 2011
    ..Looking forward, such analyses will be extremely useful in the process of drug development to better understand adverse side effects...
  13. 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...
  14. 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...
  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. 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...
  17. pmc The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
    Damian Szklarczyk
    Faculty of Health Sciences, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Denmark
    Nucleic Acids Res 39:D561-8. 2011
    ..Version 9.0 of STRING covers more than 1100 completely sequenced organisms; the resource can be reached at http://string-db.org...
  18. pmc MOCAT: a metagenomics assembly and gene prediction toolkit
    Jens Roat Kultima
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS ONE 7:e47656. 2012
    ..MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/...
  19. pmc Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines
    Alessandro Ori
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 9:648. 2013
    ....
  20. 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...
  21. pmc Systematic identification of proteins that elicit drug side effects
    Michael Kuhn
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 9:663. 2013
    ..Taken together, we show that a large fraction of complex drug side effects are mediated by individual proteins and create a reference for such relations...
  22. 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...
  23. pmc Human monogenic disease genes have frequently functionally redundant paralogs
    Wei Hua Chen
    European Molecular Biology Laboratory EMBL Heidelberg, Heidelberg, Germany
    PLoS Comput Biol 9:e1003073. 2013
    ..Consequently the defective genes are linked to genetic disorders while they continue propagating within the population. Our results provide insight into the molecular basis underlying the spreading of duplicated disease genes...
  24. 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...
  25. 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...
  26. 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...
  27. pmc STITCH 3: zooming in on protein-chemical interactions
    Michael Kuhn
    Biotechnology Center, TU Dresden, 01062 Dresden, Germany
    Nucleic Acids Res 40:D876-80. 2012
    ..Combining the isomers increases the coverage, as interaction databases and publications found through text mining will often refer to compounds without specifying the stereoisomer. The database is accessible at http://stitch.embl.de/...
  28. pmc High-resolution transcription atlas of the mitotic cell cycle in budding yeast
    Marina V Granovskaia
    EMBL European Molecular Biology Laboratory, Department of Genome Biology, Meyerhofstr, Heidelberg, Germany
    Genome Biol 11:R24. 2010
    ..To explore the complex transcriptome architecture underlying the budding yeast cell cycle, we used 8 bp tiling arrays to generate a 5 minute-resolution, strand-specific expression atlas of the whole genome...
  29. pmc Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution
    Carlos Quijano
    Instituto de Investigaciones Biomedicas CSIC UAM, Arturo Duperier 4, 28029 Madrid, Spain
    Genome Biol 9:R176. 2008
    ..However, the contribution of gene duplication to gene order has not been analyzed in detail, as it is believed that co-expression due to recent duplicates would obscure other domains of co-expression...
  30. pmc Circular reasoning rather than cyclic expression
    Lars Juhl Jensen
    Genome Biol 9:403. 2008
    ..A response to Combined analysis reveals a core set of cycling genes by Y Lu, S Mahony, PV Benos, R Rosenfeld, I Simon, LL Breeden and Z Bar-Joseph. Genome Biol 2007, 8:R146...
  31. pmc Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?
    Albert Pallejà
    Biochemistry and Biotechnology Department, Rovira i Virgili University, C Marcel li Domingo s n, 43007 Tarragona, Catalunya, Spain
    BMC Genomics 9:335. 2008
    ..Here we examine the longest overlaps and assess whether they are the product of special functional constraints or of erroneous annotation...
  32. pmc Non-random retention of protein-coding overlapping genes in Metazoa
    Giulia Soldà
    1Department of Biology and Genetics for Medical Sciences, University of Milan, 20133 Milan, Italy
    BMC Genomics 9:174. 2008
    ..Here we report a comparative analysis of overlaps between genes coding for well-annotated proteins in five metazoan genomes (human, mouse, zebrafish, fruit fly and worm)...
  33. pmc G2D: a tool for mining genes associated with disease
    Carolina Perez-Iratxeta
    Ontario Genomics Innovation Centre, Ottawa Health Research Institute, ON K1H 8L6, Ottawa, Canada
    BMC Genet 6:45. 2005
    ..We previously developed an algorithm to prioritize genes on a chromosomal region according to their possible relation to an inherited disease using a combination of data mining on biomedical databases and gene sequence analysis...
  34. 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...
  35. 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...
  36. 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...
  37. pmc STITCH 2: an interaction network database for small molecules and proteins
    Michael Kuhn
    Biotechnology Center, TU Dresden, 01062 Dresden, Germany
    Nucleic Acids Res 38:D552-6. 2010
    ..STITCH 2.0 connects proteins from 630 organisms to over 74,000 different chemicals, including 2200 drugs. STITCH can be accessed at http://stitch.embl.de/...
  38. 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...
  39. 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
    ....
  40. 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...
  41. 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...
  42. 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...
  43. 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...
  44. doi request reprint Metagenomic species profiling using universal phylogenetic marker genes
    Shinichi Sunagawa
    European Molecular Biology Laboratory, Heidelberg, Germany
    Nat Methods 10:1196-9. 2013
    ..An implementation of the method is available at http://www.bork.embl.de/software/mOTU/. ..
  45. 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...
  46. pmc eggNOG v4.0: nested orthology inference across 3686 organisms
    Sean Powell
    European Molecular Biology Laboratory, Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany, University of Zurich and Swiss Institute of Bioinformatics, Institute of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zurich, Switzerland, Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109 5234, USA, Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, C Dr Aiguader 88, 08003 Barcelona, Spain, Universitat Pompeu Fabra UPF, 08003 Barcelona, Spain, CUBE Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3FG, UK, Biotechnology Center, TU Dresden, 01062 Dresden, Germany, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Atlanta
    Nucleic Acids Res 42:D231-9. 2014
    ..Users can access the complete database of orthologous groups via a web interface, as well as through bulk download. ..
  47. 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...
  48. 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...
  49. 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...
  50. 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...
  51. 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
    ....
  52. 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...
  53. 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...
  54. 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...
  55. 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...
  56. 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%)...
  57. 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...
  58. 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...
  59. ncbi request reprint Co-evolution of transcriptional and post-translational cell-cycle regulation
    Lars Juhl Jensen
    European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    Nature 443:594-7. 2006
    ....
  60. 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/..
  61. 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/...
  62. 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..
  63. pmc Deciphering a global network of functionally associated post-translational modifications
    Pablo Minguez
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 8:599. 2012
    ..The global network of co-evolving PTM types implies a complex and intertwined post-translational regulation landscape that is likely to regulate multiple functional states of many if not all eukaryotic proteins...
  64. 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
    ....
  65. 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...
  66. 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...
  67. doi request reprint A quantitative liposome microarray to systematically characterize protein-lipid interactions
    Antoine Emmanuel Saliba
    1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany 2
    Nat Methods 11:47-50. 2014
    ..Here we describe a liposome microarray-based assay (LiMA), a method that measures protein recruitment to membranes in a quantitative, automated, multiplexed and high-throughput manner. ..
  68. 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
    ....
  69. 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/...
  70. pmc Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets
    Jan Rehwinkel
    European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    RNA 11:1530-44. 2005
    ..Thus phenotypic differences observed across species following inhibition of NMD can be largely attributed to changes in the repertoire of regulated genes...
  71. pmc Assessment of metagenomic assembly using simulated next generation sequencing data
    Daniel R Mende
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS ONE 7:e31386. 2012
    ..The metagenomic simulators developed for this research are freely available...
  72. pmc Ancient animal microRNAs and the evolution of tissue identity
    Foteini Christodoulou
    Developmental Biology Unit, European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    Nature 463:1084-8. 2010
    ..Also, they outline a minimum set of cell types and tissues that existed in the protostome-deuterostome ancestor...
  73. 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...
  74. 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)...
  75. pmc A side effect resource to capture phenotypic effects of drugs
    Michael Kuhn
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 6:343. 2010
    ..We illustrate the potential of SIDER with a number of analyses. The resource is freely available for academic research at http://sideeffects.embl.de...
  76. pmc Assessing systems properties of yeast mitochondria through an interaction map of the organelle
    Fabiana Perocchi
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS Genet 2:e170. 2006
    ..Our network thus advances the understanding of the mitochondrial system in yeast and identifies properties of genes underlying human mitochondrial disorders...
  77. doi request reprint Accurate and universal delineation of prokaryotic species
    Daniel R Mende
    European Molecular Biology Laboratory, Heidelberg, Germany
    Nat Methods 10:881-4. 2013
    ..Applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters. Of 314 discrepancies with a widely used taxonomic classification, >62% were resolved by literature support. ..
  78. 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...
  79. 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...
  80. pmc Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding
    Murat Iskar
    Structural and Computational Biology Unit, European Molecular Biology Laboratory EMBL, Heidelberg, Germany
    Mol Syst Biol 9:662. 2013
    ..Taken together, the identified modules reveal the conservation of transcriptional responses towards drugs across cell types and organisms, and improve our understanding of both the molecular basis of drug action and human biology...
  81. 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...
  82. 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...
  83. 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...
  84. 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
    ..Our current implementation relies on two alignment programs (MUSCLE and MAFFT), one refinement program (RASCAL) and one assessment program (NORMD), but other programs could be incorporated at any of the three steps...
  85. pmc Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data
    Jeroen Raes
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 7:473. 2011
    ..Together, our results show that the functional community composition derived from metagenomes is an important quantitative readout for molecular trait-based biogeography and ecology...
  86. 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...
  87. pmc Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability
    Sebastian Korff
    Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
    BMC Cancer 8:329. 2008
    ....
  88. pmc STITCH 4: integration of protein-chemical interactions with user data
    Michael Kuhn
    Biotechnology Center, TU Dresden, 01062 Dresden, Germany, Institute of Molecular Life Sciences, University of Zurich and Swiss Institute of Bioinformatics, Winterthurerstrasse 190, 8057 Zurich, Switzerland, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany and Max Delbrück Centre for Molecular Medicine, Robert Rossle Strasse 10, 13092 Berlin, Germany
    Nucleic Acids Res 42:D401-7. 2014
    ..This improves the performance within protein families, where scores are now transferred only to orthologous proteins, but not to paralogous proteins. STITCH can be accessed with a web-interface, an API and downloadable files. ..
  89. 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/...
  90. 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/...
  91. ncbi request reprint A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development
    Thomas Sandmann
    European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    Dev Cell 10:797-807. 2006
    ..The number and diversity of new direct target genes indicates a much broader role for Mef2, at all stages of myogenesis, than previously anticipated...
  92. 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...
  93. pmc STRING v9.1: protein-protein interaction networks, with increased coverage and integration
    Andrea Franceschini
    Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland
    Nucleic Acids Res 41:D808-15. 2013
    ....