Dicks Computational Biology Group

Address:
Department of Computational and Systems Biology,
John Innes Centre, Norwich Research Park,
Colney, Norwich, NR4 7UH, UK.

Telephone:
+44(0) 1603 450597 (direct)
+44(0) 1603 450000 (switchboard)

Fax:
+44(0) 1603 450595 (direct)
+44(0) 1603 450045 (JIC reception)

Journal Papers and Book Chapters (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.
• Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, Barton DB, Bailes E, Nguyen AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R, Louis EJ (2009) Population genomics of domestic and wild yeasts. Nature 2009 Feb 11 (Epub ahead of print) doi:10.1038/nature07743
• James SA, O'Kelly MJ, Carter DM, Davey RP, van Oudenaarden A, Roberts IN (2009) Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing. Genome Research 2009 Feb 17 (Epub ahead of print) doi:10.1101/gr.084517.108
• 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)

Conference Abstracts (2000 onwards)

• Bradnam K, Cardle L, Cartinhour S, Couchman M, Davenport G, Devos K, Dicks J, Gale M, Huang L, Marshall D, May S, McWilliam H, Ougham H, Trick M and Waugh R(2000) UK CropNet 99. Plant and Animal Genome VIII, San Diego
• Conn J, James S, Roberts I and Dicks J (2000) A software environment for the analysis of Saccharomyces species. Genomes 2000, Paris
• Conn J, James S, Roberts I and Dicks J (2000) A software environment for the analysis of Saccharomyces species. Yeast, Arnheim
• May S, Bradnam K, Cardle L, Cartinhour S, Couchman M, Davenport G, Devos K, Dicks J, Gale M, Huang L, Marshall D, McWilliam H, Ougham H, Trick M and Waugh R (2000) UK CropNet 99 - The second phase. Journal of Experimental Botany 51 (March Supplement), pp22-23
• Davenport G and Dicks J (2001) Comparative genome analysis within the grasses using ARCADE. Plant and Animal Genome IX, San Diego
• Davenport G, Dicks J, Bradnam K, Cardle L, Cartinhour S, Couchman M, Devos K, Gale M, Huang L, Marshall D, May S, McWilliam H, Ougham H, Trick M and Waugh R. (2001) UK CropNet: Integrating and analysing data from distributed sources. Plant and Animal Genome IX, San Diego
• Ellis THN, Knox MR, Vershinin AV, Dicks J, Pearce SR and Flavell AJ (2001) Untangling transposition histories in pea. Plant and Animal Genome IX, San Diego
• Conn JJ, Dicks JL and Roberts IN (2001) An integrated environment for the comparison of genomes. Genome Informatics, Hinxton
• Davenport G and Dicks J (2001) A Real-Time Comparative Display Environment (ARCADE) Genome Informatics, Hinxton
• Dicks J (2001) CHROMTREE: Deducing evolutionary histories using large-scale genomic data. Genome Informatics, Hinxton
• Dicks JL and Edwards JH (2002) The application of ACEDB to comparative mapping in animals and plants. Plant, Animal and Microbe Genome X, San Diego
• Couchman M, Davenport G and Dicks J (2002) A real-time comparative analysis display environment (ARCADE). Genome Informatics, Hinxton
• Dixon DS, Davenport G, van Hintum TJL, Weems D, Dicks J and Bevis W (2002) A generic model for an object orientated interface to a relational database and its application to genebank data. Genome Informatics, Hinxton
• Conn J, Dicks JL and Roberts IN (2002) Genome Explorer - For Comparative Genome Analysis. Proceedings of Objects in Bioinformatics and Cheminformatics 2002, Washington DC
• Dicks JL, Thierry-Mieg J, Nicholas FW, Edwards JH, Ferguson-Smith MA and Yang F (2002) An extension of ACEDB to the Oxford Grid and OMIA. 49th Annual Meeting of Genetics Society of Australia and Comparative Genomics: 7th Australasian Gene Mapping Workshop, Sydney
• Couchman M, Davenport G and Dicks J (2003) A Real-time comparative analysis display environment (ARCADE) Plant and Animal Genome XI, San Diego
• Dixon DS, Davenport G, van Hintum TJL, Weems D, Dicks J and Bevis W (2003) A generic model for an object orientated interface to a relational database and its application to genebank data. Plant and Animal Genome XI, San Diego
• Etherington G, Roberts I, Dicks J and Rayward-Smith V (2003) EVA: Examining foodborne virus evolution using the Enteric Virus Analysis tool. 11th International Conference on Intelligent Systems for Molecular Biology, Brisbane
• Lee JM, Flavell A, Marshall D, Davenport G, Dicks J, Ellis N and Ambrose M (2004) GERMINATE - A relational database management system for plant data. Plant and Animal Genome XII, San Diego
• Davey RP, Roberts IN, Dicks JL and Rayward-Smith VJ (2004) A Java microarray-to-phylogeny pipeline for gene content analysis. 12th International Conference on Intelligent Systems for Molecular Biology, Glasgow
• Lee J, Davenport G, Marshall D, Ellis THN, Ambrose MJ, Dicks J, van Hintum TJL and Flavell AJ (2004) GERMINATE: A plant data management system. 12th International Conference on Intelligent Systems for Molecular Biology, Glasgow
• Lee J, Davenport G, Marshall D, Ellis THN, Ambrose MJ, Dicks J, van Hintum TJL and Flavell AJ (2005) GERMINATE: A plant data management system. Plant and Animal Genome XIII, San Diego
• Davey R, Lacey G, MacKenzie D, Defernez M, Mellon F, Huber K, Moulton V, Dicks J and Robert IN (2005) Comparative metabolomics of Saccharomyces yeasts. Systems Biology: From molecules & modelling to cells, Gosau, Austria.
• Lee JM, Marshall D, McLaren CG, Ambrose MJ, Dicks J, Ellis THN, Barnard V, Nwankwo D, Waugh R and Flavell AJ (2006) An update on the GERMINATE project, database and tools available. Plant and Animal Genome XIV, San Diego
• Flavell AJ, Jing R, Bolshakov VN, Knox MR, Lee JM, Vershinin AV, Dicks J, Davey R, Ambrose M and Ellis THN (2006) Genotyping a germplasm collection – The genetic diversity of Pisum. Plant and Animal Genome XIV, San Diego
• Battacharjee M, Boys R, Burdett T, Davey R, Dicks J, Gibson A, Lord P, Marshall D, Paterson T, Pocock M, Rice P, Roberts I, Stevens R, Walsh S, Watson P, Wilkinson D, Wipat A and Law A (2006) ComparaGRID – enabling technologies for comparative genomics. Genome Informatics, Hinxton.
• Davey R, Savva G, Dicks J and Roberts I (2006) From microarray to phylogeny using gene content and tagged marker datasets. Genome Informatics, Hinxton.
• Flavell AJ, Jing R, Bolshakov VN, Knox MR, Lee JM, Dicks J, Davey R, Ambrose M and Ellis THN (2007) The genetic diversity of Pisum revealed by retrotransposon-based marker analysis and gene intron sequencing. Plant & Animal Genome XV, San Diego.
• Marshall DF, Waugh R, Dicks J, Nwankwo D, Ellis N, Shaw P, Barnard V, Ambrose M and Flavell AJ (2007) New developments in the GERMINATE project. Plant & Animal Genome XV, San Diego.
• Cheema JJS, Ellis THN and Dicks J (2008) Exploring genome wide genetic linkage manifolds. Genome Informatics, Hinxton.
• Cheema JJS and Dicks J (2009) A new manifold learning approach for analysis and visualisation of differential gene expression. 17th International Conference on Intelligent Systems for Molecular Biology, Stockholm.
• Pocock, M, Burdett T, Davey R, Paterson T, Law AS, Gibson AP, Stevens R, Rice P, Dicks J, Roberts IN and Wipat A (2009) Runcible: Integrating ontologies using a rule-based mapping engine. 17th International Conference on Intelligent Systems for Molecular Biology, Stockholm.

Designed by Virginia Barnard
LAST UPDATED: 8th May 2009