Jo Dicks

Group Leader in Computational Biology

Curriculum vitae

Editorial

• Editorial Board: Briefings in Bioinformatics (1999 - )
• Book proposal referee: Blackwell Science
• Book referee: Human Genomics
• Journal referee: Bioinformatics, BMC Bioinformatics, BMC Evolutionary Biology, Briefings in Bioinformatics, Genetical Research, IMA Journal of Mathematics Applied in Medicine and Biology, Journal of Mathematical Modelling and Algorithms, Journal of Molecular Biology, Nucleic Acids Research, Plant Molecular Biology, Proceedings of the Royal Society: Biological Sciences, Trends in Biochemical Sciences
• Grant referee: BBSRC, NSF, SEERAD, USDA and Wellcome Trust
• Grant award panel: NSF Young Investigator Awards in Plant Genome Research (2002, 2003)

Panels and committees

• BBSRC Review Panel of UK training in Bioinformatics (1998)
• Advisory Panel on Bioinformatics, International Rice Research Institute (IRRI), The Philippines (1999)
• Plant and Animal Genome Conference Bioinformatics Workshop, Organiser (1999-2003)
• Organising Panel for MSc in Bioinformatics, University of East Anglia (2000, 2006)
• Organising Committee and Lecturer, Bioinformatics course for the Centro Internacional de Altos Estudios Agronomicos Mediterraneos (CIHEAM) (2001)
• External Advisory Panel, School of Computing Sciences, University of East Anglia (2001-2005)
• Discovery Informatics Advisory Committee, BioIndustry Association (BIA) (2002-2006)
• Strategic Advisory Board for BBSRC BioCatalogue project (2008- )

Societies

• Fellow of the Royal Statistical Society (2003-)
• Member of the International Society for Computational Biology

Grant awards (2000 onwards)

• EU FrameWork V (2001-2004) “GENE-MINE – Improved use of germplasm collections with the aid of novel methodologies for integration, analysis and presentation of genetic data sets” (with 9 EU partner organisations, €1.34m total) - €303k JIC
• BBSRC Bioinformatics and E-Science Initiative (2002-2005) “Novel approaches to the analysis of genetic diversity in germplasm collections” (with A. Flavell – University of Dundee, N. Ellis – JIC and D. Marshall – SCRI) - £323k UoD/SCRI
• Generation Challenge Program Year 1 travel funding (2003-4) - $3,540 JIC
• EU ARI project (funded through the Linnaeus Centre for Bioinformatics, Uppsala University, Sweden) (2003-4) “Mathematical modelling of evolutionary processes in crop plants” (with K. Huber and V. Moulton – LCB) - €3,000 JIC
• UK Research Councils program for High-Performance Computing in the Life Sciences (2004-2005) “Parallel computation of statistical methodologies for the study of chromosomal evolution in plants” - approx. £50k JIC
• EU FrameWork VI (2004-2008) “Grain Legumes - New Strategies to Improve Grain Legumes for Food and Feed” (with N. Ellis – JIC plus 52 partner organisations) - £154k JIC
• BBSRC Bioinformatics and E-Science Initiative II (2005-2008) “ComparaGrid – enabling GRID technologies for comparative genomics” (with A. Law – RI and 5 other UK universities/institutes including I. Roberts - IFR) - £161k NRP
• BBSRC GDB (2006-2008) “Bioinformatics tools for plant genetic resources” (with A. Flavell – University of Dundee, N. Ellis & M. Ambrose – JIC and V. Moulton – UEA) - £191k JIC
• BBSRC Crops Science Initiative (2007-2009) “The establishment and application of a forward genetic resource for the development of efficient breeding strategies in grass and the cereals” (with I. King – IGER, J. Snape – JIC and L. Ramsay – SCRI) - £58k JIC
• BBSRC Tools and Resources Development Fund (2008-2009) “Fine-scale phylogeny using a mathematical model of the dynamics of rDNA repeat sequence evolution” (with I. Roberts – IFR) - £76k NRP

Recent presentations (2000 onwards)

• Plant and Animal Genome VIII, San Diego (2000) Invited talk
• Gene Order Dynamics, Comparative Maps and Gene Families (DCAF), Montreal (2000) Selected talk
• Swedish 1st Annual Bioinformatics Meeting, Uppsala (2000) Invited talk
• Plant and Animal Genome IX, San Diego (2001) 2 invited talks
• International Plant Genome Database Workshop, JIC (2001) Organiser and speaker
• Genome Informatics Conference, Hinxton (2001) Selected talk
• Plant and Animal Genome X, San Diego (2002) Invited talk
• Genome Informatics Conference, Hinxton (2002) Selected talk
• University of Kent, Canterbury (2002) Invited seminar
• Stadler Genetics Symposium, Missouri (2003) Invited talk
• Wenner-Gren Foundation International Symposium, Stockholm (2003) Invited talk
• Royal Statistical Society Conference, Diepenbeek (2003) Invited talk
• EUCARPIA Biometrics and Plant Breeding Meeting, La Coruna (2003) Invited talk
• (Break for maternity leave)
• University of East Anglia, Norwich (2006) Invited seminar
• UK Knowledge Discovery and Data mining conference (UKKDD’06), Norwich (2006) Invited talk
• European Bioinformatics Institute, Hinxton (2006) Invited seminar
• (Break for maternity leave)

Recent publications (2000 onwards)

• Dicks J (2000) Plant Genome Databases: From References to Inference Tools. Briefings in Bioinformatics 1 (2): 138-150.
• Dicks J (2000) Graphical Tools for Comparative Genome Analysis. Yeast (Comparative and Functional Genomics) 17 (1): 6-15.
• Dicks J, Anderson M, Cardle L, Cartinhour S, Couchman M, Davenport G, Dickson J, Gale M, Marshall D, May S, McWilliam H, O'Malia A, Ougham H, Trick M, Walsh S and Waugh R (2000) UK CropNet: A Collection of Databases and Bioinformatics Resources for Crop Plant Genomics. Nucleic Acids Research 28:104-107.
• Dicks J (2000) CHROMTREE: Maximum likelihood estimation of chromosomal phylogenies. In Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families (eds. D Sankoff and JH Nadeau), Kluwer Academic Press, Dordrecht pp 333-342.
• Dicks J (2002) Plant Bioinformatics: Current status and future trends. AgBiotechNet4 ABN 080.
• Wesselink J-J, de la Iglesia B, James SA, Dicks JL, Roberts IN and Rayward-Smith VJ (2002) Determining a unique defining DNA sequence for yeast species using hashing techniques. Bioinformatics18(7):1004-1010.
• De la Iglesia B, Wesselink JJ, Rayward-Smith VJ, Dicks J, Roberts IN, Roberts V and Boekhout T (2003) Developing classification techniques from biological databases using simulated annealing, In Metaheuristics: Computer Decision-Making (eds. MGC Resende and JP de Sousa), Kluwer Academic Publishers, pp 347-368.
• Reynolds AP, Dicks JL, Roberts IN, Wesselink J-J, de la Iglesia B, Roberts V, Boekhout T and Rayward-Smith VJ (2003) Algorithms for Identification Key Generation and Optimization with Application to Yeast Identification. In Applications of Evolutionary Computing (eds. G. Raidl et al.), Lecture Notes in Computer Science, Vol 2611, Springer-Verlag, Berlin Heidelberg.
• Savva G, Dicks J and Roberts IN (2003) Current approaches to whole genome phylogenetic analysis. Briefings in Bioinformatics 4 (1): 63 -74. Link to copy in PDF format
• Dicks J and Savva G (2003) Comparative Genomics. In Handbook of Statistical Genetics, Second edition (eds. DJ Balding, MJ Bishop and C Cannings),Wiley Press pp 139-161.
• Davenport G, Ellis THN, Ambrose M and Dicks J (2004) Using bioinformatics to analyse germplasm collections. Euphytica 137(1): 39-54. Link to copy in PDF format
• Savva G, Conn J and Dicks J (2004) Drawing phylogenetic trees in LaTeX and Word. Bioinformatics 20(14): 2322-2323.
• Etherington GJ, Dicks J and Roberts IN (2005) Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination. Bioinformatics 21(3):278-281. Electronic link for copy in PDF format
• Lee JM, Davenport G, Marshall D, Ellis THN, Ambrose MJ, Dicks J, van Hintum TJL and Flavell AJ (2005) GERMINATE: A database for plant genetic resources. Plant Physiology 139: 619-631.
• Etherington GJ, Dicks J and Roberts IN (2006) High throughput sequence analysis reveals hitherto unreported recombination in the genus Norovirus. Virology 345 (1): 88-95.
• Davey R, Savva G, Jing R, Lott M, Ellis THN, Ambrose M, Moulton V, Flavell A, Roberts I and Dicks J (2006) Germplasm collections: Gaining new knowledge from old datasets. Proceedings of the 2nd UK KDD Conference pp 32-38.
• Etherington GJ, Ring SM, Charleston MA, Dicks J, Rayward-Smith VJ and Roberts IN (2006) Tracing the origin, co-phylogeny and demographic growth of the Caliciviruses. Journal of General Virology 87 (5): 1229-1235.
• Davey RP, Savva G, Dicks J and Roberts IN (2007) MPP: A Microarray-To-Phylogeny Pipeline for Analysis of Gene and Marker Content Datasets. Bioinformatics 23 (8): 1023-1025 Link to copy in PDF format
• Dicks J and Savva G (2007) Comparative Genomics. In Handbook of Statistical Genetics, Third edition (eds. DJ Balding, MJ Bishop and C Cannings),Wiley Press pp 160-199.
• Bailey P, Dicks J, Wang T and Martin C (2008) Development of an Interspecies Transcription Factor Function Finder for Plants. Phytochemistry 69: 2417-2425.
• Burdett T, Davey R, Gibson AP, Paterson T, Pocock M, Dicks J, Law AS, Rice P, Roberts IN, Stevens R, and Wipat A. The Fluxion DataPublisher: Publishing Relational Database Data as OWL. (submitted)
• Davey R, Burdett T, Gibson AP, Paterson T, Pocock M, Wipat A, Law AS, Stevens R, Rice P, Dicks J and Roberts IN. Pussycat: a Flexible Semantic Web Browser. (submitted)
• Savva G, Moulton V, Huber K, Roberts IN and Dicks J. A Novel Statistical Measure for Testing Hypotheses of Treelikeness in Genomic Datasets. (submitted)
• Inagaki Y-S, Etherington G, Dokarry M, Field B, Dicks J and Osbourn A. Analysis of genes implicated in triterpene synthesis in rice. (submitted)
• Garvin DF, Mckenzie N, Vogel JP, Mockler TC, Blankenheim ZJ, Wright J, Cheema JJS, Dicks J, Huo N, Hayden DM, Gu Y, Tobias C, Chang JH, Chu A, Trick M, Michael TP, Bevan MW, and Snape JW. A genetic linkage map of the model grass Brachypodium distachyon. (submitted)

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LAST UPDATED: 8th May 2009