Contact Email: ajones@cs.man.ac.uk Telephone: +44 161 2750646 Address: Room LF8 Kilburn Building School of Computer Science University of Manchester Oxford Road, Manchester M13 9PL, United Kingdom

Research Interests:

• Developing data standards for functional genomics (The FuGE project).
• Databases and software for functional genomics. I am a member of the PEDRo project.
• Proteome standards in collaboration with the PSI.
• Analyses of publicly available proteomics data sets

Publications:

2007

• Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, DeGreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian Jr RK, Laursen K, Oliver SG, Paton NW, Sarkans U, Sansone S, Stoeckert Jr. CJ, Taylor CF, Whetzel PL, White JA, Spellman P and Pizarro A. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics, Nat. Biotechnol. 2007 in community consultation.
• Taylor CF, Paton NW, Lilley KS, Binz P-A, Julian Jr. RK, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch R, Macht M, Mann M, Neubert T, Patterson S, Seymour S, Tsugita A, Xenarios I and Hermjakob H, The Minimum Information About a Proteomics Experiment (MIAPE), Nat. Biotechnol. 2007 in community consultation.
• Gibson F., Anderson L., Babnigg G., Baker M. Berth M., Binz P-A., Borthwick A., Cash P., Day B.W., Friedman D.B., Garland D., Gutstein H.B., Hoogland C., Jones N.A., Jones A.R., Khan A., Klose J., Lamond A.I., Lemkin P.F., Lilley K.S., Minden J., Morris N.J., Paton N.W., Pisano M.R., Prime J.E., Rabilloud T., Stead D.A., Taylor C.F., Voshol H., Wipat A., MIAPE Gel Electrophoresis, Nat. Biotechnol. 2007, in community consultation.
• Siepen JA, Swainston N, Jones AR, Hart SR, Hermjakob H, Jones P, Hubbard SJ. An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ. , Proteome Sci. 2007 5(1):4
• Orchard S, Jones AR, Stephan C, Binz PA The HUPO Pre-Congress Proteomics Standards Initiative Workshop HUPO 5th Annual World Congress Long Beach, CA, USA 28 October-1 November 2006 Proteomics. 2007: Early view
• Orchard S, Taylor CF, Jones P, Montechi-Palazzo L, Binz PA, Jones AR, Pizarro A, Julian RK Jr, Hermjakob H. Entering the Implementation Era A report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA. Proteomics. 2007 Feb;7(3):337-9.

2006

• Jones AR, Pizarro A, Spellman P, Miller M; FuGE Working Group. FuGE: Functional Genomics Experiment Object Model, OMICS: A Journal of Integrative Biology, 2006 10:2 p179-184
• Sansone SA, Rocca-Serra P, Tong W, Fostel J, Morrison N, Jones AR; Rsbi Members. A Strategy Capitalizing on Synergies: The Reporting Structure for Biological Investigation (RSBI) Working Group, OMICS: A Journal of Integrative Biology, 2006 10:2 p164-171
• Orchard S, Apweiler R, Barkovich R, Field D, Garavelli JS, Horn D, Jones A, Jones P, Julian R, McNally R, Nerothin J, Paton N, Pizarro A, Seymour S, Taylor C, Wiemann S, Hermjakob H. Proteomics and Beyond A report on the 3(rd) Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA. Proteomics. 2006 Aug 8;6(16):4439-4443
• Zamboulis L, Fan H, Belhajjame K, Siepen J, Jones A, Martin N, Poulovassilis A, Hubbard S, Embury SM and Paton NW, Data Access and Integration in the ISPIDER Proteomics Grid in Data Integration in the Life Sciences, Third International Workshop, DILS 2006, Hinxton, UK, July 20-22, 2006, Proceedings Series: Lecture Notes in Computer Science , Vol. 4075
• Paton NW, Jones AR, Garwood C, Garwood K and Oliver S, Storing, Searching and Disseminating Experimental Proteomics Data, in Introduction to Systems Biology by Humana Press 2006 (in press)
• Jones A, Faldas A, Foucher A, Hunt E, Tait A, Wastling JM, Turner CM. Visualisation and analysis of proteomic data from the procyclic form of Trypanosoma brucei, Proteomics 2006. 6:1, p259-267

2005

• Jones AR and Paton NW, An analysis of extensible modelling for functional genomics data, BMC Bioinformatics 2005, 6:235.
• Paton NW, Jones A and Oliver SG, Proteomics data representation and management in Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Wiley, 2005.
• The Digital Archiving Consultancy (DAC), The Bioinformatics Research Centre, University of Glasgow (BRC), The National e-Science Centre (NeSC), Large-scale data sharing in the life sciences: Data standards, incentives, barriers and funding models (The "Joint Data Standards Study"), August 2005 (named co-author)
• Jones A, The Development of Data Standards and a Database to Aid Proteomic Research, PhD thesis, submitted for the degree of Doctor of Philosophy in Computing Science at the University of Glasgow.

2004

• Jones A, Hunt E, Wastling JM, Pizarro A, Stoeckert CJ Jr. An Object Model and Database for Functional Genomics, Bioinformatics 20:10, p1583-90.

2003

• Jones A, Wastling J and Hunt E, Proposal for a standard representation of two-dimensional gel electrophoresis data, Comparative and Functional Genomics 2003 4:5, p492-501.

Previous research projects:

• RNA and Protein Abundance Database (RAPAD) at Glasgow
• Supplementary data for Visualisation and analysis of proteomic data from the procyclic form of Trypanosoma brucei