Toby J Gibson

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. pmc Capturing cooperative interactions with the PSI-MI format
    Kim Van Roey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany, Proteomics Services, EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and UMR 5086 CNRS Université Lyon 1, Institut de Biologie et Chimie des Proteines, 7 passage du Vercors, 69367 Lyon Cedex 07, France
    Database (Oxford) 2013:bat066. 2013
  2. pmc iELM--a web server to explore short linear motif-mediated interactions
    Robert J Weatheritt
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 40:W364-9. 2012
  3. pmc Phospho.ELM: a database of phosphorylation sites--update 2008
    Francesca Diella
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Nucleic Acids Res 36:D240-4. 2008
  4. pmc KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
    Francesca Diella
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Bioinformatics 25:1-5. 2009
  5. pmc Linear motifs confer functional diversity onto splice variants
    Robert J Weatheritt
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
    Nucleic Acids Res 40:7123-31. 2012
  6. pmc The identification of short linear motif-mediated interfaces within the human interactome
    R J Weatheritt
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Bioinformatics 28:976-82. 2012
  7. doi request reprint The transience of transient overexpression
    Toby J Gibson
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Nat Methods 10:715-21. 2013
  8. doi request reprint RACK1 research - ships passing in the night?
    Toby J Gibson
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    FEBS Lett 586:2787-9. 2012
  9. pmc Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?
    Aidan Budd
    European Molecular Biology Laboratory, 69012 Heidelberg, Germany
    Genome Biol 5:R38. 2004
  10. pmc A new protein linear motif benchmark for multiple sequence alignment software
    Emmanuel Perrodou
    Institut de Genetique et de Biologie Moleculaire et Cellulaire, Department of Structural Biology and Genomics, F 67400 Illkirch, France
    BMC Bioinformatics 9:213. 2008

Collaborators

Detail Information

Publications38

  1. pmc Capturing cooperative interactions with the PSI-MI format
    Kim Van Roey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany, Proteomics Services, EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and UMR 5086 CNRS Université Lyon 1, Institut de Biologie et Chimie des Proteines, 7 passage du Vercors, 69367 Lyon Cedex 07, France
    Database (Oxford) 2013:bat066. 2013
    ..This will facilitate the storage, exchange and analysis of cooperative interaction data, which in turn will advance experimental research on this fundamental principle in biology...
  2. pmc iELM--a web server to explore short linear motif-mediated interactions
    Robert J Weatheritt
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 40:W364-9. 2012
    ..ELM resources. A network figure is also presented to aid the interpretation of results. The iELM server supports single protein queries as well as large-scale proteomic submissions and is freely available at http://i.elm.eu.org...
  3. pmc Phospho.ELM: a database of phosphorylation sites--update 2008
    Francesca Diella
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Nucleic Acids Res 36:D240-4. 2008
    ..Phospho.ELM is available on line at: http://phospho.elm.eu.org...
  4. pmc KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
    Francesca Diella
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Bioinformatics 25:1-5. 2009
    ..We noted that the sumoylation site in C/EBP homologues is conserved beyond the canonical consensus sequence for sumoylation. Therefore, we investigated whether this pattern might define a more general protein motif...
  5. pmc Linear motifs confer functional diversity onto splice variants
    Robert J Weatheritt
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
    Nucleic Acids Res 40:7123-31. 2012
    ..This study, therefore, demonstrates that short linear motifs are key components for establishing protein diversity between splice variants...
  6. pmc The identification of short linear motif-mediated interfaces within the human interactome
    R J Weatheritt
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Bioinformatics 28:976-82. 2012
    ..However, these motif classes represent only a small fraction of known SLiMs and outside these examples little effort has been made, either bioinformatically or experimentally, to discover the full complement of motif instances...
  7. doi request reprint The transience of transient overexpression
    Toby J Gibson
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Nat Methods 10:715-21. 2013
    ..To avoid these problems, genome engineering technologies now enable the generation of stable cell lines expressing modified proteins at (almost) native levels. ..
  8. doi request reprint RACK1 research - ships passing in the night?
    Toby J Gibson
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    FEBS Lett 586:2787-9. 2012
    ..It is also a target of intracellular parasites. And yet does this protein have the profile that it should? And why are there two kinds of RACK1 researcher who do not seem to communicate well?..
  9. pmc Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?
    Aidan Budd
    European Molecular Biology Laboratory, 69012 Heidelberg, Germany
    Genome Biol 5:R38. 2004
    ..The protease inhibitor alpha2-macroglobulin provides a major metazoan defense against invasive bacteria, trapping attacking proteases required by parasites for successful invasion...
  10. pmc A new protein linear motif benchmark for multiple sequence alignment software
    Emmanuel Perrodou
    Institut de Genetique et de Biologie Moleculaire et Cellulaire, Department of Structural Biology and Genomics, F 67400 Illkirch, France
    BMC Bioinformatics 9:213. 2008
    ..As a consequence, poor motif alignment quality is hindering efforts to detect new LMs...
  11. doi request reprint Cell regulation: determined to signal discrete cooperation
    Toby J Gibson
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Trends Biochem Sci 34:471-82. 2009
    ..Here, I argue that the true nature of cell signalling and our perceptions of it are in a state of discord. This raises the question: Are our misconceptions detrimental to progress in biomedical science?..
  12. pmc ELM: the status of the 2010 eukaryotic linear motif resource
    Cathryn M Gould
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 38:D167-80. 2010
    ..Using the links, researchers can explore the motifs, proteins, complex structures and associated literature to evaluate whether candidate motifs might be worth experimental investigation...
  13. pmc ELM--the database of eukaryotic linear motifs
    Holger Dinkel
    Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 40:D242-51. 2012
    ..The motif discovery portion of the ELM resource has added conservation, and structural attributes have been incorporated to aid users to discriminate biologically relevant motifs from stochastically occurring non-functional instances...
  14. doi request reprint Attributes of short linear motifs
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Biosyst 8:268-81. 2012
    ..Finally, the most interesting conclusions are examined in regard to their functional consequences...
  15. pmc A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences
    Claudia Chica
    EMBL Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    BMC Bioinformatics 9:229. 2008
    ..It is therefore desirable to efficiently predict linear motifs with some degree of accuracy, yet sequence database searches return results that are not significant...
  16. pmc Phospho.ELM: a database of phosphorylation sites--update 2011
    Holger Dinkel
    SCB Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 39:D261-7. 2011
    ..Finally, special emphasis has been put on linking to external resources such as interaction networks and other databases...
  17. doi request reprint The switches.ELM resource: a compendium of conditional regulatory interaction interfaces
    Kim Van Roey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Sci Signal 6:rs7. 2013
    ..We foresee switches.ELM complementing available resources to extend our knowledge of the molecular mechanisms underlying cell signaling...
  18. pmc Systematic discovery of new recognition peptides mediating protein interaction networks
    Victor Neduva
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS Biol 3:e405. 2005
    ..We estimate that there are dozens or even hundreds of linear motifs yet to be discovered that will give molecular insight into protein networks and greatly illuminate cellular processes...
  19. pmc Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins
    Francesca Diella
    Cellzome AG, Heidelberg, Germany
    BMC Bioinformatics 5:79. 2004
    ..The fast growing number of research reports on protein phosphorylation points to a general need for an accurate database dedicated to phosphorylation to provide easily retrievable information on phosphoproteins...
  20. pmc The eukaryotic linear motif resource ELM: 10 years and counting
    Holger Dinkel
    Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Department of Physiology, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA, Structural Studies Division, MRC, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK, Ruprecht Karls Universitat, 69117 Heidelberg, Germany, School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Co Dublin, Republic of Ireland, Laboratory of Bioinformatics and Biostatistics, Maria Sklodowska Curie Memorial Cancer Center and Institute of Oncology, WK Roentgena 5, 02 781 Warsaw, Poland, Protein Structure Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires Consejo Nacional de Investigaciones Científicas y Técnicas Avenida Patricias Argentinas 435 CP 1405 Buenos Aires, Argentina and Departamento de Química Biológica and IQUIBICEN CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Gúiraldes 2160 CP 1428, Argentina
    Nucleic Acids Res 42:D259-66. 2014
    ..Furthermore, detailed information about motif-mediated interactions has been annotated and made available in standard exchange formats. Where appropriate, links are provided to resources such as switches.elm.eu.org and KEGG pathways. ..
  21. doi request reprint Dimerization and protein binding specificity of the U2AF homology motif of the splicing factor Puf60
    Lorenzo Corsini
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    J Biol Chem 284:630-9. 2009
    ..Our data suggest that the functional cooperativity between U2AF65 and Puf60 may involve simultaneous interactions of the two proteins with SF3b155...
  22. pmc BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases
    Konstantinos Bimpikis
    European Molecular Biology Laboratory, Postfach 10 2209, 69012 Heidelberg, Germany
    Nucleic Acids Res 31:3792-4. 2003
    ..By allowing the user to control SRS from the BLAST output, BLAST2SRS (http://blast2srs.embl.de/) aims to meet this need. This server therefore combines the two ways to search sequence databases: similarity and keyword...
  23. doi request reprint Linear motifs: lost in (pre)translation
    Robert J Weatheritt
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Trends Biochem Sci 37:333-41. 2012
    ....
  24. pmc GlobPlot: Exploring protein sequences for globularity and disorder
    Rune Linding
    European Molecular Biology Laboratory, Biocomputing Unit, D 69117 Heidelberg, Germany
    Nucleic Acids Res 31:3701-8. 2003
    ..GlobPlot has a pipeline interface--GlobPipe--for the advanced user to do whole proteome analysis. GlobPlot can also be used as a generic infrastructure package for graphical displaying of any possible propensity...
  25. pmc Evidence for the concerted evolution between short linear protein motifs and their flanking regions
    Claudia Chica
    Structural and Computational Biology Unit, EMBL Heidelberg, Heidelberg, Germany
    PLoS ONE 4:e6052. 2009
    ..Sometimes linear motifs appear as isolated islands of conservation in multiple sequence alignments. However, they also occur in larger blocks of sequence conservation, suggesting an active role for the neighbouring amino acids...
  26. ncbi request reprint Protein disorder prediction: implications for structural proteomics
    Rune Linding
    EMBL, Biocomputing Unit, Meyerhofstr 1, D 69117 Heidelberg, Germany
    Structure 11:1453-9. 2003
    ..The tool is freely available via a web interface (http://dis.embl.de) and can be downloaded for use in large-scale studies...
  27. ncbi request reprint Understanding eukaryotic linear motifs and their role in cell signaling and regulation
    Francesca Diella
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Front Biosci 13:6580-603. 2008
    ..The discrete deterministic properties implicit to these assemblies suggest that models for cell regulatory networks in systems biology should neither be overly dependent on stochastic nor on smooth deterministic approximations...
  28. doi request reprint Motif switches: decision-making in cell regulation
    Kim Van Roey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Curr Opin Struct Biol 22:378-85. 2012
    ....
  29. pmc Multiple sequence alignment with the Clustal series of programs
    Ramu Chenna
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Nucleic Acids Res 31:3497-500. 2003
    ..Although, Clustal was originally developed to run on a local computer, numerous Web servers have been set up, notably at the EBI (European Bioinformatics Institute) (http://www.ebi.ac.uk/clustalw/)...
  30. doi request reprint Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation
    Sushama Michael
    Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, D 69117, Heidelberg, Germany
    Bioinformatics 24:453-7. 2008
    ..eu.org/), we found that KEN motifs were significantly enriched in human protein entries with cell cycle keywords in the UniProt/Swiss-Prot database-implying that KEN-boxes might be more common than reported...
  31. pmc Malectin: a novel carbohydrate-binding protein of the endoplasmic reticulum and a candidate player in the early steps of protein N-glycosylation
    Thomas Schallus
    European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Mol Biol Cell 19:3404-14. 2008
    ..The localization, structure, and binding specificity of this protein, which we have named malectin, open the way to studies of its role in the genesis, processing and secretion of N-glycosylated proteins...
  32. pmc SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden Württemberg 69117, Germany
    Nucleic Acids Res 40:10628-41. 2012
    ..Finally, the human proteome is analysed to create a set of highly conserved putative motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E...
  33. pmc Drift and conservation of differential exon usage across tissues in primate species
    Alejandro Reyes
    Genome Biology Unit and Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Proc Natl Acad Sci U S A 110:15377-82. 2013
    ..Our findings support the theory that isoform regulation is an important target of evolution in primates, and our method provides a powerful tool for discovering potentially functional tissue-dependent isoforms. ..
  34. doi request reprint EpiC: an open resource for exploring epitopes to aid antibody-based experiments
    Niall J Haslam
    European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
    J Proteome Res 9:3759-63. 2010
    ..It provides the community with a single Web-based portal for the exploration of epitopes on a target protein and connects over the Internet to a wide range of bioinformatic tools ensuring that data being presented are up to date...
  35. pmc Anopheles gambiae SRPN2 facilitates midgut invasion by the malaria parasite Plasmodium berghei
    Kristin Michel
    Department of Biological Sciences, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    EMBO Rep 6:891-7. 2005
    ..gambiae midguts by the rodent malaria parasite Plasmodium berghei. It did not affect ookinete formation, but markedly reduced oocyst numbers, by 97%, as a result of increased ookinete lysis and melanization...
  36. doi request reprint How viruses hijack cell regulation
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Trends Biochem Sci 36:159-69. 2011
    ....
  37. pmc A community standard format for the representation of protein affinity reagents
    David E Gloriam
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Mol Cell Proteomics 9:1-10. 2010
    ..Further information and documentation are available on the PSI-PAR web site...
  38. doi request reprint A careful disorderliness in the proteome: sites for interaction and targets for future therapies
    Robert B Russell
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    FEBS Lett 582:1271-5. 2008
    ..These regions also offer new possibilities into how interactions can be targeted by small molecules...