Wellcome Trust Genome Campus

Summary

Organization: Wellcome Trust Genome Campus
Country: UK

Top Publications

  1. doi Analysing proteomics identifications in the context of functional and structural protein annotation: integrating annotation using PICR, DAS, and BioMart
    Philip Jones
    European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
    Methods Mol Biol 696:107-21. 2011
  2. ncbi The generation of new protein functions by the combination of domains
    Matthew Bashton
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom
    Structure 15:85-99. 2007
  3. pmc New developments in the InterPro database
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute Hinxton, Cambridge, UK
    Nucleic Acids Res 35:D224-8. 2007
  4. ncbi The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data
    Henning Hermjakob
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Proteomics 6:34-8. 2006
  5. pmc Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins
    Shiri Freilich
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
    Genome Biol 7:R89. 2006
  6. pmc AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation
    Vincent Le Texier
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 7:169. 2006
  7. ncbi Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 6:738-41. 2006
  8. ncbi Nomenclature for factors of the HLA system, update April 2005
    Steven G E Marsh
    Anthony Nolan Research Institute, Royal Free Hospital, London, UK
    Hum Immunol 66:1019-21. 2005
  9. ncbi Distributed modules for text annotation and IE applied to the biomedical domain
    Harald Kirsch
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Int J Med Inform 75:496-500. 2006
  10. ncbi Second proteomics standards initiative spring workshop
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Expert Rev Proteomics 2:287-9. 2005

Research Grants

  1. The Nomenclature of Human Genes
    Ewan Birney; Fiscal Year: 2007
  2. The UniProt protein sequence and function knowledgebase
    Rolf Apweiler; Fiscal Year: 2007

Detail Information

Publications62

  1. doi Analysing proteomics identifications in the context of functional and structural protein annotation: integrating annotation using PICR, DAS, and BioMart
    Philip Jones
    European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
    Methods Mol Biol 696:107-21. 2011
    ....
  2. ncbi The generation of new protein functions by the combination of domains
    Matthew Bashton
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom
    Structure 15:85-99. 2007
    ....
  3. pmc New developments in the InterPro database
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute Hinxton, Cambridge, UK
    Nucleic Acids Res 35:D224-8. 2007
    ..ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). The InterProScan search tool is now also available via a web service at http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html...
  4. ncbi The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data
    Henning Hermjakob
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Proteomics 6:34-8. 2006
    ..In this article we provide an overview of PSI organisational structure, activities, and current results, as well as ways to get involved in the broad-based, open PSI process...
  5. pmc Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins
    Shiri Freilich
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
    Genome Biol 7:R89. 2006
    ..We explored the relationship between duplication events, the time at which they took place, and both the expression breadth of the duplicated genes and the cumulative expression breadth of the gene family to which they belong...
  6. pmc AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation
    Vincent Le Texier
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 7:169. 2006
    ..We now extend these pipelines and integrate the resultant data sets to facilitate an integrated view of the contributions from splicing and polyadenylation in the formation of transcript variants...
  7. ncbi Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 6:738-41. 2006
    ..Common to all these efforts is the field of protein modifications, and work has been initiated to establish an ontology in this field that can be used by both workers in the field of proteomics and the wider scientific community...
  8. ncbi Nomenclature for factors of the HLA system, update April 2005
    Steven G E Marsh
    Anthony Nolan Research Institute, Royal Free Hospital, London, UK
    Hum Immunol 66:1019-21. 2005
  9. ncbi Distributed modules for text annotation and IE applied to the biomedical domain
    Harald Kirsch
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Int J Med Inform 75:496-500. 2006
    ..The server and the underlying software are available to the public...
  10. ncbi Second proteomics standards initiative spring workshop
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Expert Rev Proteomics 2:287-9. 2005
  11. ncbi Predicting protein function from sequence and structural data
    James D Watson
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Curr Opin Struct Biol 15:275-84. 2005
    ..Several automated servers that integrate evidence from multiple sources have been released this year and particular improvements have been seen with methods utilizing the Gene Ontology functional annotation schema...
  12. ncbi Nomenclature for Factors of the HLA System, 2004
    Steven G E Marsh
    Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, Hampstead, London NW3 2QG, United Kingdom
    Hum Immunol 66:571-636. 2005
  13. ncbi Dasty and UniProt DAS: a perfect pair for protein feature visualization
    Philip Jones
    EMBL Outstation European Bioinformatics Institute EBI, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 21:3198-9. 2005
    ....
  14. ncbi Nomenclature for factors of the HLA system, update November 2004
    S G E Marsh
    Int J Immunogenet 32:161. 2005
  15. ncbi Publication Committee meeting. HUPO 5th annual World Congress. Long Beach, CA, USA 30 October 2006
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Proteomics 7:1009-11. 2007
    ..Discussions centred on how best to structure interactions between journals, databases and researchers to improve accessibility to data, and facilitate comparisons between datasets...
  16. pmc Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study
    Gabriella Rustici
    EMBL Outstation Hinxton, European Bioinformatics Institute, Cambridge CB10 1SD, UK
    Genome Biol 8:R73. 2007
    ..All cells must adjust to environmental fluctuations in metal levels, because levels that are too low or too high can be detrimental. Here we explore the conservation of metal homoeostasis in two distantly related yeasts...
  17. ncbi The minimum information required for reporting a molecular interaction experiment (MIMIx)
    Sandra Orchard
    European Molecular Biology Laboratory EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
    Nat Biotechnol 25:894-8. 2007
    ....
  18. doi The structures and physicochemical properties of organic cofactors in biocatalysis
    Julia D Fischer
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    J Mol Biol 403:803-24. 2010
    ..Finally, we show that the molecular functions of the cofactors not only may duplicate reactions performed by inorganic metal cofactors and amino acids, the cell's other catalytic tools, but also provide novel chemistries for catalysis...
  19. pmc Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
    William McLaren
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Bioinformatics 26:2069-70. 2010
    ..In Ensembl, a web-based tool (the SNP Effect Predictor) and API interface can now functionally annotate variants in all Ensembl and Ensembl Genomes supported species...
  20. pmc EBImage--an R package for image processing with applications to cellular phenotypes
    Gregoire Pau
    EMBL European Bioinformatics Institute, Cambridge, UK
    Bioinformatics 26:979-81. 2010
    ..This allows the automation of such tasks using the R programming language and use of existing tools in the R environment for signal processing, statistical modeling, machine learning and data visualization...
  21. pmc PaperMaker: validation of biomedical scientific publications
    D Rebholz-Schuhmann
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 26:982-4. 2010
    ..The automatic analysis of scientific literature can support authors in writing their manuscripts...
  22. doi Microarray data quality control improves the detection of differentially expressed genes
    Audrey Kauffmann
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
    Genomics 95:138-42. 2010
    ..Using array weights is similarly effective, but its applicability is more limited. The quality metrics presented here are implemented in the Bioconductor package arrayQualityMetrics...
  23. doi Highly divergent gene expression programs can lead to similar chordate larval body plans
    Daniel Sobral
    Institut de Biologie du Developpement de Marseille Luminy IBDML, UMR6216, CNRS, Universite de la Mediterranee, Campus de Luminy, Case 907, F 13288 Marseille Cedex 09, France
    Curr Biol 19:2014-9. 2009
    ..Thus, a broad divergence in gene expression profiles is compatible with the conservation of similar body plans across large evolutionary distances...
  24. pmc Ensembl's 10th year
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D557-62. 2010
    ....
  25. doi WSsas: a web service for the annotation of functional residues through structural homologues
    David Talavera
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 25:1192-4. 2009
    ..In addition, WSsas can supply information about the relevant functional atoms. The web service definition (WSDL) file and a Perl client are freely available at http://www.ebi.ac.uk/thornton-srv/databases/WSsas/...
  26. pmc Advanced genomic data mining
    Xose M Fernandez-Suarez
    European Bioinformatics Institute, Ensembl Group, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Comput Biol 4:e1000121. 2008
  27. doi In silico characterization of proteins: UniProt, InterPro and Integr8
    Nicola Jane Mulder
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Mol Biotechnol 38:165-77. 2008
    ..This article reviews the tools and resources available on the web for single and large-scale protein characterization and whole proteome analysis...
  28. doi Nomenclature for factors of the HLA system, update November 2007
    Steven G E Marsh
    Anthony Nolan Research Institute, Royal Free Hospital, London NW3 2QG, UK
    Tissue Antigens 71:260-1. 2008
  29. pmc MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology
    Camille Laibe
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Syst Biol 1:58. 2007
    ..In order to enable interoperability of this annotation, the community has to agree on a set of standard URIs, corresponding to recognised data types. MIRIAM Resources are being developed to support the use of those URIs...
  30. pmc Graphs in molecular biology
    Wolfgang Huber
    European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge CB10 1SD, UK
    BMC Bioinformatics 8:S8. 2007
    ..We discuss software that is available through the Bioconductor project and present a simple example application to the integration of a protein-protein interaction and a co-expression network...
  31. ncbi Nomenclature for factors of the HLA System, update December 2004
    Steven G E Marsh
    Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
    Hum Immunol 66:329-30. 2005
  32. pmc InterPro, progress and status in 2005
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 33:D201-5. 2005
    ..The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro)...
  33. ncbi Microarray data representation, annotation and storage
    Alvis Brazma
    EMBL Outstation Hinxton, European Bioinformatics Institute, Cambridge, UK
    Adv Biochem Eng Biotechnol 77:113-39. 2002
    ..We describe two data models--a simpler one called ArrayExpressB and the complete model ArrayExpressC, and discuss some implementation issues. For latest developments see http: wwwebi.ac.uk/arrayexpress..
  34. ncbi Databases and tools for browsing genomes
    Ewan Birney
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
    Annu Rev Genomics Hum Genet 3:293-310. 2002
    ..This article reviews the database systems and tools for analysis that have so far been developed to address this...
  35. ncbi Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory
    Robert E Steward
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    Proteins 48:178-91. 2002
    ..These results will contribute to predicting the arrangement of beta-strands in beta-pleated sheets and protein topology...
  36. ncbi Nomenclature for factors of the HLA system, update February 2002
    Steven G E Marsh
    Anthony Nolan Research Institute Royal Free Hospital Pond Street London NW3 2QG United Kingdom
    Tissue Antigens 59:237-8. 2002
  37. ncbi Nomenclature for factors of the HLA system, update December 2001
    Steven G E Marsh
    Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
    Tissue Antigens 59:172-3. 2002
  38. ncbi Nomenclature for factors of the HLA system, update August 2001
    Steven G Marsh
    Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London NW3 1QG, UK
    Tissue Antigens 59:73-4. 2002
  39. ncbi Minimum information about a microarray experiment (MIAME)-toward standards for microarray data
    A Brazma
    European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nat Genet 29:365-71. 2001
    ..With respect to MIAME, we concentrate on defining the content and structure of the necessary information rather than the technical format for capturing it...
  40. ncbi Regulatory sequence analysis: application to the interpretation of gene expression
    J Vilo
    European Bioinformatics Institute EBI, EMBL Outstation Hinxton, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
    Eur Neuropsychopharmacol 11:399-411. 2001
    ..This article surveys some of the analysis methods and studies for such a computational discovery approach for yeast Saccharomyces cerevisiae...
  41. ncbi A collection of well characterised integral membrane proteins
    S Moller
    European Bioinformatics Institute, Cambridge, UK
    Bioinformatics 16:1159-60. 2000
    ..A collection of transmembrane proteins with annotated transmembrane regions, for which good experimental evidence exist, was created as a test or training set for algorithms to predict transmembrane regions in proteins...
  42. pmc A clean data set of EST-confirmed splice sites from Homo sapiens and standards for clean-up procedures
    T A Thanaraj
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 27:2627-37. 1999
    ..A set of nucleotide regions that can be used to generate a control set of false splice sites that have a high confidence of being non-functional are also reported...
  43. ncbi Removing redundancy in SWISS-PROT and TrEMBL
    C O'Donovan
    EMBL Outstation the European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 15:258-9. 1999
    ..We developed a strategy to identify the redundancy present within and between SWISS-PROT and TrEMBL and its subsequent removal...
  44. ncbi W2H: WWW interface to the GCG sequence analysis package
    M Senger
    DKFZ German Cancer Research Center, Department of Molecular Biophysics, Im Neuenheimer Feld 280, D 69120 Heidelberg, Germany
    Bioinformatics 14:452-7. 1998
    ..Because Web browsers like Netscape are much more common on those platforms, we decided to develop W2H, a WWW interface to the GCG Sequence Analysis Software Package with nearly the same functionality as the X-windows interface WPI...
  45. pmc The EMBL nucleotide sequence database
    G Stoesser
    EMBL Outstation The European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 26:8-15. 1998
    ..EBI's network services allow access to the most up-to-date data collection via Internet and World Wide Web interface, providing database searching and sequence similarity facilities plus access to a large number of additional databases...
  46. ncbi Data mining the protein data bank: residue interactions
    T J Oldfield
    Accelrys Inc, Department of Chemistry, University of York, Heslington, York, Yorkshire, United Kingdom
    Proteins 49:510-28. 2002
    ..The first allows a weighted RMSD search between a template set of coordinates and a list of PDB files, and the second allows the labeling of a protein with the template results from mining to aid in the classification of this protein...
  47. pmc The EMBL Nucleotide Sequence Database: major new developments
    Guenter Stoesser
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 31:17-22. 2003
    ..All resources can be accessed via the EBI home page at http://www.ebi.ac.uk...
  48. ncbi Nomenclature for factors of the HLA system, update September 2002
    S G E Marsh
    Anthony Nolan Research Institute, Royal Free Hospital, London, UK
    Eur J Immunogenet 30:93-4. 2003
  49. ncbi Statistical pattern recognition for macromolecular crystallographers
    Richard J Morris
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England
    Acta Crystallogr D Biol Crystallogr 60:2133-43. 2004
    ..An overview of the most common pattern-recognition approaches is given and some popular model-building packages are briefly reviewed within this context...
  50. ncbi The ArrayExpress gene expression database: a software engineering and implementation perspective
    Ugis Sarkans
    EMBL Outstation Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 21:1495-501. 2005
    ..Our experience will be both relevant and useful for most bioinformaticians involved in developing information systems for a wide range of high-throughput technologies...
  51. ncbi Robustness of metabolic map reconstruction
    Dag G Ahren
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
    J Bioinform Comput Biol 2:589-93. 2004
    ..We also discuss the implications of the results on reference genome projects as well as other large-scale sequencing data...
  52. ncbi Nomenclature for factors of the HLA system, update June 2004
    S G E Marsh
    Anthony Nolan Research Institute, Royal Free Hospital, London, UK
    Eur J Immunogenet 31:199-200. 2004
  53. ncbi Nomenclature for factors of the HLA system, update January 2004
    Steven G E Marsh
    Anthony Nolan Research Institute, Royal Free Hospital, Londaon, UK
    Tissue Antigens 63:619-20. 2004
  54. ncbi Common interchange standards for proteomics data: Public availability of tools and schema
    Sandra Orchard
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 4:490-1. 2004
    ..A draft XML interchange format for mass spectrometry data has been written and is currently undergoing evaluation whilst work is ongoing to develop a proteomics data integration model, MIAPE...
  55. ncbi Nomenclature for factors of the HLA system, update June 2003
    S G E Marsh
    Anthony Nolan Research Institute, Royal Free Hospital, London NW3 2QG, United Kingdom
    Tissue Antigens 62:337-8. 2003
  56. ncbi Pandit: a database of protein and associated nucleotide domains with inferred trees
    Simon Whelan
    Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
    Bioinformatics 19:1556-63. 2003
    ..The large quantity of data may provide inspiration for new models and methodology to study sequence evolution and may allow general statements about the relative effect of different molecular processes on evolution...
  57. ncbi Nomenclature for factors of the HLA system, update February 2003
    Steven G E Marsh
    Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
    Tissue Antigens 62:89-90. 2003
  58. ncbi Killer-cell immunoglobulin-like receptor (KIR) nomenclature report, 2002
    S G E Marsh
    Anthony Nolan Research Institute, Royal Free Hospital, London, UK
    Tissue Antigens 62:79-86. 2003
  59. pmc Mouse proteome analysis
    Alexander Kanapin
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Genome Res 13:1335-44. 2003
    ..The analysis of the membrane organization within the transcriptome of multiple eukaryotes provides valuable statistics about the distribution of secretory and transmembrane proteins..
  60. ncbi Nomenclature for factors of the HLA system, updated November 2002
    Steven G E Marsh
    Hum Immunol 64:385-6. 2003
  61. ncbi Nomenclature for factors of the HLA system, update October 2002
    S G E Marsh
    Anthony Nolan Research Institute, Royal Free Hospital, London, UK
    Eur J Immunogenet 30:95. 2003
  62. pmc Protein secondary structural types are differentially coded on messenger RNA
    T A Thanaraj
    European Molecular Biology Laboratory, Heidelberg, Germany
    Protein Sci 5:1973-83. 1996
    ..The observed absence of such strong positive selection for codons in non-highly expressed genes is compatible with existing theories that mutation pressure may well dominate codon selection in non-highly expressed genes...

Research Grants4

  1. The Nomenclature of Human Genes
    Ewan Birney; Fiscal Year: 2007
    ....
  2. The UniProt protein sequence and function knowledgebase
    Rolf Apweiler; Fiscal Year: 2007
    ....