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Andrew Jones

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Oligonucleotide Array Sequence Analysis

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TOP 3
Louise Y C Takeshita; Syed M S Zain; Faviel F Gonzalez-Galarza; Maria Helena T Maia; Derek Middleton; Mushome M Rahman; Eduardo J M Dos Santos; Andrew R Jones
A database for curating the associations between killer cell immunoglobulin-like receptors and diseases in worldwide populations.
Achchuthan Shanmugasundram; Olga Vasieva; Jonathan Wastling; Faviel F Gonzalez-Galarza; Andrew R Jones
Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites.
Sandra Orchard; Juan Antonio Vizcaino; Andrew R Jones; George Nicola; Pierre-Alain Binz; Christoph Borchers; Eric Deutsch; Michael K Gilson; Henning Hermjakob
Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA.

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2013: Louise Y C Takeshita; Syed M S Zain; Faviel F Gonzalez-Galarza; Maria Helena T Maia; Derek Middleton; Mushome M Rahman; Eduardo J M Dos Santos; Andrew R Jones
A database for curating the associations between killer cell immunoglobulin-like receptors and diseases in worldwide populations.
Database : the journal of biological databases and curation 2013;2013():bat021.
2013: Achchuthan Shanmugasundram; Olga Vasieva; Jonathan Wastling; Faviel F Gonzalez-Galarza; Andrew R Jones
Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites.
Nucleic acids research 2013;41(Database issue):D706-13.
2012: Sandra Orchard; Juan Antonio Vizcaino; Andrew R Jones; George Nicola; Pierre-Alain Binz; Christoph Borchers; Eric Deutsch; Michael K Gilson; Henning Hermjakob
Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA.
Proteomics 2012;12(18):2767-72.
2012: Da Qi; Dong Xia; Jenna Kenyani; Katherine Mackay; Robert J Beynon; Philip Brownridge; Faviel F Gonzalez-Galarza; Victoria Harman; Andrew R Jones
A software toolkit and interface for performing stable isotope labeling and top3 quantification using Progenesis LC-MS.
Omics : a journal of integrative biology 2012;16(9):489-95.
2012: Faviel F Gonzalez-Galarza; Henning Hermjakob; Simon Hubbard; Conrad Bessant; Jun Fan; Craig Lawless; Andrew R Jones
A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis.
Omics : a journal of integrative biology 2012;16(9):431-42.
2012: Andrew R Jones
Bioinformatics challenges and solutions in proteomics as quantitative methods mature.
Omics : a journal of integrative biology 2012;16(9):429-30.
2012: Andrew R Jones; Randall Julian; Oliver Kohlbacher; Gerhard Mayer; Angel Pizarro; Florian Reisinger; Brian C Searle; Julian N Selley; Sean L Seymour; James Shofstahl; Jennifer Siepen; Juan Antonio Vizcaino; Eric Deutsch; Martin Eisenacher; Johannes Griss; Henning Hermjakob; Simon Hubbard; Pierre-Alain Binz; Matthew Chambers; David Creasy
The mzIdentML data standard for mass spectrometry-based proteomics results.
Molecular & cellular proteomics : MCP 2012;11(7):M111.014381.
2012: Dong Xia; Simon J Gaskell; Fawaz Ghali; Ronan O'Cualain; Paul F G Sims; Andrew R Jones
Software for analysing ion mobility mass spectrometry data to improve peptide identification.
Proteomics 2012;12(12):1912-6.
2012: Florian Reisinger; Daniel Ríos; Juan Antonio Vizcaíno; Fawaz Ghali; Henning Hermjakob; Ritesh Krishna; Andrew R Jones
jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data.
Proteomics 2012;12(6):790-4.
2012: Ana Alfirevic; Catherine Bell; Giovanna Bretland; Karin Cederbrant; Jane Evely; Neil French; Faviel Gonzalez-Galarza; Andrew R Jones; Maike Lichtenfels; Klara Martinsson; Dean J Naisbitt; B Kevin Park; Vivien Platt; Munir Pirmohamed
In silico analysis of HLA associations with drug-induced liver injury: use of a HLA-genotyped DNA archive from healthy volunteers.
Genome medicine 2012;4(6):51.
2011: Alberto Medina-Aunon; Rosana Navajas; Alberto Paradela; Emilio Salazar; Andrew R Jones; Miguel A López-García; Salvador Martínez-Bartolomé; Juan Pablo Albar
The ProteoRed MIAPE web toolkit: a user-friendly framework to connect and share proteomics standards.
Molecular & cellular proteomics : MCP 2011;10(10):M111.008334.
2011: David C Wedge; Ritesh Krishna; Paul Blackhurst; Jennifer A Siepen; Andrew R Jones; Simon Hubbard
FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines.
Journal of proteome research 2011;10(4):2088-94.
2011: Jenna Kenyani; Alberto Medina-Aunon; Salvador Martínez-Bartolomé; Juan Pablo Albar; Jonathan M Wastling; Andrew R Jones
A DIGE study on the effects of salbutamol on the rat muscle proteome - an exemplar of best practice for data sharing in proteomics.
BMC research notes 2011;4():86.
2010: Andrew R Jones; Kathleen Carroll; David Knight; Kirsty Maclellan; Paula J Domann; Cristina Legido-Quigley; Lihua Huang; Lance Smallshaw; Hamid Mirzaei; James Shofstahl; Norman W Paton
Guidelines for reporting the use of column chromatography in proteomics.
Nature biotechnology 2010;28(7):654.
2010: Andrew R Jones; Allyson L Lister
Managing experimental data using FuGE.
Methods in molecular biology (Clifton, N.J.) 2010;604():333-43.
2010: Andrew R Jones; Simon Hubbard
An introduction to proteome bioinformatics.
Methods in molecular biology (Clifton, N.J.) 2010;604():1-5.
2009: Luisa Montecchi-Palazzi; Samuel Kerrien; Florian Reisinger; Bruno Aranda; Andrew R Jones; Lennart Martens; Henning Hermjakob
The PSI semantic validator: a framework to check MIAPE compliance of proteomics data.
Proteomics 2009;9(22):5112-9.
2009: Sandra Orchard; Eric Deutsch; Pierre-Alain Binz; Andrew R Jones; David Creasy; Luisa Montechi-Palazzi; Garry Corthals; Henning Hermjakob
Annual spring meeting of the Proteomics Standards Initiative.
Proteomics 2009;9(19):4429-32.
2009: Andrew R Jones; Allyson L Lister; Leandro Hermida; Peter Wilkinson; Martin Eisenacher; Khalid Belhajjame; Frank Gibson; Phil Lord; Matthew Pocock; Heiko Rosenfelder; Javier Santoyo-Lopez; Anil Wipat; Norman W Paton
Modeling and managing experimental data using FuGE.
Omics : a journal of integrative biology 2009;13(3):239-51.
2009: Andrew R Jones; Jennifer A Siepen; Simon Hubbard; Norman W Paton
Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines.
Proteomics 2009;9(5):1220-9.
2008: Khalid Belhajjame; Andrew R Jones; Norman W Paton
A toolkit for capturing and sharing FuGE experiments.
Bioinformatics (Oxford, England) 2008;24(22):2647-9.
2007: Andrew R Jones; Michael Miller; Ruedi Aebersold; Rolf Apweiler; Catherine A Ball; Alvis Brazma; James Degreef; Nigel Hardy; Henning Hermjakob; Simon Hubbard; Peter Hussey; Mark Igra; Helen Jenkins; Randall K Julian; Kent Laursen; Stephen G Oliver; Norman W Paton; Susanna-Assunta Sansone; Ugis Sarkans; Christian J Stoeckert; Christopher Taylor; Patricia L Whetzel; Joseph A White; Paul Spellman; Angel Pizarro
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Nature biotechnology 2007;25(10):1127-33.
2007: Sandra Orchard; Luisa Montechi-Palazzi; Eric Deutsch; Pierre-Alain Binz; Andrew R Jones; Norman Paton; Angel Pizarro; David M Creasy; Jérôme Wojcik; Henning Hermjakob
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, France.
Proteomics 2007;7(19):3436-40.
2007: Christopher Taylor; Norman W Paton; Kathryn S Lilley; Pierre-Alain Binz; Randall K Julian; Andrew R Jones; Weimin Zhu; Rolf Apweiler; Ruedi Aebersold; Eric Deutsch; Michael J Dunn; albert heck; Alexander Leitner; Marcus Macht; Matthias Mann; Lennart Martens; Thomas A Neubert; Scott D Patterson; Peipei Ping; Sean L Seymour; Puneet Souda; Akira Tsugita; Joel Vandekerckhove; Thomas M Vondriska; Julian P Whitelegge; Marc R Wilkins; Ioannnis Xenarios; John R Yates; Henning Hermjakob
The minimum information about a proteomics experiment (MIAPE).
Nature biotechnology 2007;25(8):887-93.
2007: King Wai Lau; Andrew R Jones; Neil Swainston; Jennifer A Siepen; Simon Hubbard
Capture and analysis of quantitative proteomic data.
Proteomics 2007;7(16):2787-99.
2007: Sandra Orchard; Andrew R Jones; Christian Stephan; Pierre-Alain Binz
The HUPO pre-congress Proteomics Standards Initiative workshop. HUPO 5th annual World Congress. Long Beach, CA, USA 28 October-1 November 2006.
Proteomics 2007;7(7):1006-8.
2007: Sandra Orchard; Christopher Taylor; Philip Jones; Luisa Montechi-Palazzo; Pierre-Alain Binz; Andrew R Jones; Angel Pizarro; Randall K Julian; Henning Hermjakob
Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA.
Proteomics 2007;7(3):337-9.
2007: Jennifer A Siepen; Neil Swainston; Andrew R Jones; Sarah Hart; Henning Hermjakob; Philip Jones; Simon Hubbard
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ.
Proteome science 2007;5():4.
2006: Andrew R Jones; Angel Pizarro; Paul Spellman; Michael Miller
FuGE: Functional Genomics Experiment Object Model.
Omics : a journal of integrative biology 2006;10(2):179-84.
2006: Susanna-Assunta Sansone; Philippe Rocca-Serra; Weida Tong; Jennifer Fostel; Norman Morrison; Andrew R Jones
A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group.
Omics : a journal of integrative biology 2006;10(2):164-71.
2005: Andrew R Jones; Norman W Paton
An analysis of extensible modelling for functional genomics data.
BMC bioinformatics 2005;6():235.