Genomes and Genes
Andrew R Jones
Affiliation: University of Manchester
- An analysis of extensible modelling for functional genomics dataAndrew R Jones
School of Computer Science, University of Manchester, Manchester, UK
BMC Bioinformatics 6:235. 2005..Extensions to data formats are important because the experimental methodologies tend to be fairly diverse and rapidly evolving, which hinders the creation of formats that will be stable over time...
- Visualisation and analysis of proteomic data from the procyclic form of Trypanosoma bruceiAndrew Jones
Department of Computing Science, University of Glasgow, Glasgow, Scotland, UK
Proteomics 6:259-67. 2006..gla.ac.uk/functionalgenomics). Using specific proteins as examples, we demonstrate how the visualisation software and the database query facilities can be used...
- FuGE: Functional Genomics Experiment Object ModelAndrew R Jones
School of Computer Science, University of Manchester, Manchester, United Kingdom
OMICS 10:179-84. 2006....
- An update on data standards for gel electrophoresisAndrew R Jones
School of Computer Science and the Faculty of Life Sciences, University of Manchester, Manchester, UK
Proteomics 7:35-40. 2007..We present a tutorial on how such resources can be used and how the community should get involved with the on-going projects. Finally, we present a roadmap for future developments in this area...
- The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomicsAndrew R Jones
School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
Nat Biotechnol 25:1127-33. 2007..Such advances are important for transparent data management and mining in functional genomics and systems biology...
- A toolkit for capturing and sharing FuGE experimentsKhalid Belhajjame
School of Computer Science, University of Manchester, Oxford Road, Manchester, UK
Bioinformatics 24:2647-9. 2008..FuGE applications commonly include components that capture, store and search experiment descriptions, where the requirements of different applications have much in common...
- FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search enginesDavid C Wedge
Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
J Proteome Res 10:2088-94. 2011....
- Capture and analysis of quantitative proteomic dataKing Wai Lau
Faculty of Life Sciences, University of Manchester, Manchester, UK
Proteomics 7:2787-99. 2007..These issues will be discussed, along with those relating to deposition of quantitative data. At present, mature data standards for quantitative proteomics are not yet available, although formats are beginning to emerge...
- The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotationDong Xia
Department of Pre clinical Veterinary Science, Faculty of Veterinary Science, University of Liverpool, Liverpool L69 7ZJ, UK
Genome Biol 9:R116. 2008....
- A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working groupSusanna Assunta Sansone
EMBL EBI, European Nutrigenomics Organisation NuGO, Hinxton, Cambridge, United Kingdom
OMICS 10:164-71. 2006....
- The HUPO pre-congress Proteomics Standards Initiative workshop. HUPO 5th annual World Congress. Long Beach, CA, USA 28 October-1 November 2006Sandra Orchard
EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
Proteomics 7:1006-8. 2007..This should be achieved by early in 2007...
- Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, FranceSandra Orchard
EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Proteomics 7:3436-40. 2007..Finally the Molecular Interaction group discussed the development of a molecular interaction scoring system with accompanying gold standard data test sets...
- Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USASandra Orchard
EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Proteomics 7:337-9. 2007..In parallel with this, minimum reporting requirement have been developed and are now maturing to the point where they have been submitted for journal publication after prolonged exposure to community-input via the PSI website...
- Guidelines for reporting the use of gel electrophoresis in proteomicsFrank Gibson
Nat Biotechnol 26:863-4. 2008
- The minimum information about a proteomics experiment (MIAPE)Chris F Taylor
The HUPO Proteomics Standards Initiative, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
Nat Biotechnol 25:887-93. 2007....