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Publications
2011
Stadler L, Hoffmann T, Tomlinson D, Song Q, Lee T, Busby M, Nyathi Y, Gendra E, Tiede C, Flanagan K, Cockell SJ, Wipat A, Harwood C, Wagner S, Knowles M, Davis J, Ko Ferrigno P. (2011). Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and Applications of the SQT variant PEDS (in press).
Alcaraz N, Kucuk H, Weile J, Wipat A, Baumbach J (2011) KeyPathwayMiner - Detecting case-specific biological pathways by using expression data. Int. Math. (in press).
Weile, J., Pocock, M. Cockell, S. J., Lord, P., Dewar, J. M., Holstein, E., Wilkinson, D., Lydall, D., Hallinan, J. S. & Wipat, A. (2011). Customisable views on semantically integrated networks for systems biology. Bioinformatics 27(9): 1299 - 1306.
Misirli, G., Hallinan, J. S., Yu, T., Lawson, J. R., Wimalaratne, S. M., Cooling, M. T. & Wipat, A. (2011). Model annotation for synthetic biology: Automated model to sequence conversion. Bioinformatics. 2011 Apr 1;27(7):973-9.
Addinall SG, Holstein EM, Lawless C, Yu M, Chapman K, Banks AP, Ngo HP, Maringele L, Taschuk M, Young A, Ciesiolka A, Lister AL, Wipat A, Wilkinson DJ, Lydall D. (2011). Quantitative Fitness Analysis Shows That NMD Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects. PLoS Genet. 2011 Apr;7(4):e1001362. Epub 2011 Apr 7.
2010
Fuellen G, Adjaye J, de Grey A, Lepperdinger G, de Magalhães JP, Sühnel J, Wipat A. (2011) Bioinformatics in aging research: a workshop report. Rejuvenation Res. 2010 Dec;13(6):763-7.
Gibson F, Hoogland C, Martinez-Bartolomé S, Medina-Aunon JA, Albar JP, Babnigg G, Wipat A, Hermjakob H, Almeida JS, Stanislaus R, Paton NW, Jones AR. (2010) The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative. Proteomics. Jul 19. PMID: 20677327.
Lister AL, Lord P, Pocock M, Wipat A. (2010). Annotation of SBML models through rule-based semantic integration. J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S3.PMID: 20626923
Hallinan, JS, Misirli, G and Wipat A. (2010). Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits. IEEE Eng Med Biol Soc. 2010:768-774.
Cockell, S. J., Weile, J., Lord, P., Wipat, C., Andriychenko, D., Pocock, M., Wilkinson, D., Young, M. and Wipat., A. (2010). An integrated dataset for in silico drug discovery. J. Integrative Bioinformatics. Mar 25;7(3). doi: 10.2390/biecoll-jib-2010-116.PMID: 20375448
Passos, J., Nelson, G., Wang, C., Richter, T., Simillion, C., Proctor, C. J., Miwa, S., Olijslagers, S., Hallinan, J., Wipat, A., Saretski, G., Rudolph, K. L., Kirkwood, T. B. L. & von Zglinicki, T. (2010). A feedback loop between p21 and reactive oxygen production is necessary for establishment of cell senescence. Molecular Systems Biology 6(347).
M. T. Cooling, Rouilly, V., Misirli, G., Lawson, L., Yu, T., Hallinan, J. and Wipat, A.. (2010). Standard Virtual Biological Parts: A Repository of Modular Modelling Components for Synthetic Biology. Bioinformatics Apr 1;26(7):925-31.
Passos, J. F., Simillion, C., Hallinan, J., Wipat, A. & von Zglinicki, T. (2010). Cellular senescence: Unravelling complexity. Age. 31(4):353 - 363.
2009
A. L. Lister, Pocock, M., Taschuk, M., and Wipat, A. (2009). Saint: a lightweight integration environment for model annotation. Bioinformatics 25(22):3026-3027.
Hallinan, J., Pocock, M., Addinall, S., Lydall, D. A. & Wipat, A. (2009). Clustering incorporating shortest paths identifies relevant modules in functional interaction networks. 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB09).
James, K., Wipat, A. & Hallinan, J. (2009). Integration of full-coverage probabilistic functional networks with relevance to specific biological processes. Data Integration in the Life Sciences (DILS 2009).
Jones, A. R., Lister, A. L., Hermida, L., Wilkinson, P., Eisenacher, K. B., Gibson, F., Lord, P., Pocock, M., Rosenfelder, H., Santoyo-Lopez, J., Wipat, A. and Paton, N. (2009). Modeling and Managing Experimental Data Using FuGE. OMICS: A Journal of Integrative Biology. June 2009, 13(3): 239-25.
2008
Craddock T, Harwood CR, Hallinan J, Wipat A. (2008) e-Science: relieving bottlenecks in large-scale genome analyses. Nature Rev Microbiol. Dec;6(12):948-54. (PMID: 19008893).
Addinall SG, Downey M, Yu M, Zubko M, Dewar J, Leake A, Hallinan J, Shaw O, James K, Wilkinson DJ, Wipat A, Durocher D, Lydall D. (2008) A Genome-wide Suppressor and Enhancer Analysis of cdc13-1 Reveals Varied Cellular Processes Influencing Telomere Capping in Saccharomyces cerevisiae. Genetics. Oct 9. (PMID: 18845848)
Greenall A, Lei G, Swan DC, James K, Wang L, Peters H, Wipat A, Wilkinson DJ, Lydall D.(2008) A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection. Genome Biol. Oct 1;9(10):R146. (PMID: 18828915)
Hallinan, J. & Wipat, A. (2008). Network motifs in context: An exploration of the evolution of oscillatory dynamics in transcriptional networks. Proceedings of the 2008 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB08).
Field, D, et al and Wipat, A. (2008). Towards a richer description of our complete collection of genomes and metagenomes: the "Minimum Information about a Genome Sequence" (MIGS) specification. Nature Biotechnol 26, 541-547.
Gibson F, Anderson L, Babnigg G, Baker M, Berth M, Binz PA, Borthwick A, Cash P, Day BW, Friedman DB, Garland D, Gutstein HB, Hoogland C, Jones NA, Khan A, Klose J, Lamond AI, Lemkin PF, Lilley KS, Minden J, Morris NJ, Paton NW, Pisano MR, Prime JE, Rabilloud T, Stead DA, Taylor CF, Voshol H, Wipat A, Jones AR.(2008). Guidelines for reporting the use of gel electrophoresis in proteomics. Nature Biotechnol. 2008 Aug;26(8):863-4. .
2007
Lister, A.L., Pocock, M. and Wipat, (2007) Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models. Journal of Integrative Bioinformatics 4 (3):1-12
Sun, Y., Wipat, A., Pocock, M., Lee, P. A., Flanagan, K. and Worthington, J. T.(2007). Exploring Microbial Genome Sequences to Identify Protein Families on the Grid, IEEE Transactions on Information Technology in Biomedicine, Volume 11, Issue 4, pp 435-442
Hallinan J, Wipat A. (2007) Motifs and modules in a fractured yeast functional network. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.
Steggles, L. J., Banks, R., Shaw, O. and Wipat, A. (2007). Qualitatively Modelling and Analysing Genetic Regulatory Networks: A Petri Net Approach. Bioinformatics 23(3):336-43.
2006
Steggles, L. J., Banks, R., Shaw, O. and Wipat, A. (2006). Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets. Lecture Notes in Computing Science. In Proceedings of the Computational Methods in Systems Biology. International Conference, CMSB 2006, Trento, Italy, October 18-19, 2006 Priami, C. (ed.) [PDF]
T. Craddock, P. Lord, C. Harwood, and A. Wipat. e-science tools for the genomic scale characterisation of bacterial secreted proteins. In S. J. Cox, editor, Proceedings of the UK e-Science All Hands Meeting (2006), pages 788-795. National e-Science Centre, 2006. [PDF]
Hallinan, J. & Wipat, A. (2006). Clustering and crosstalk in a yeast functional interaction network. (2006) IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. [PDF]
Allenby, N.E.E, Watts, C. A., Homuth, G, Prágai, Z, Wipat, A, Ward, A and C. R. Harwood. (2006) Phosphate Starvation Induces the Sporulation Killing Factor of Bacillus subtilis. J Bacteriol. (2006) July; 188(14): 5299–5303.
2005 and older
Sun, Y., Wipat, A., Pocock, M., Lee, P., Watson, P., Flanagan, K. and Worthington, J. (2005) A Grid-based System for Microbial Genome Comparison and Analysis, In Proceedings of the 5th IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2005), Cardiff, UK, May 9-12 2005 pp. Paper no. 120. IEEE Computer Society 2005.
Allenby, N. E., O'Connor N, Prágai Z, Ward A. C., Wipat A., Harwood C.R.(2005) Genome-Wide Transcriptional Analysis of the Phosphate Starvation Stimulon of Bacillus subtilis. J Bacteriol. 187(23): 8063-8080.
Flanagan, K, Stevens, R., Pocock, M., Lee, P and A. Wipat. (2004). Ontologies for genome comparison and genomic rearrangements Comp. Funct. Genom. 5: 537-544
Wipat, A., Sun, Y., Pocock, M, Lee, P, Watson, P. and Flanagan, K. (2004). Developing Grid-based systems for microbial genome comparisons: The Microbase project. In Proceedings of the UK e-Science All Hands Meeting, Nottingham, UK. Cox, S. J. (ed) pp. 459-466.
Shaw, O., Koelmans, A., Steggles, J. and Wipat, A. (2004). Applying Petri Nets to Systems Biology using XML Technologies. In Proceedings of the Workshop on the Definition, Implementation and Application of a Standard Interchange Format for Petri Nets, Satellite event of the 25th International Conference on Application and Theory of Petri Nets, 2004, Bologna, Italy pages 11-25
Oinn T, Addis M, Ferris J, Marvin D, Greenwood M, Carver T, Wipat A and Li P. (2004) Taverna: Lessons in creating a workflow environment for the life sciences. Special Issue of Concurrency and Computation: Practice and Experience. (Accepted for publication).
Stevens R, McEntire R, Goble C, Greenwood M, Zhao J, Wipat A and Li P. (2004) myGrid and the drug discovery process. BioSilico (Accepted for publication).
Shaw, O. J., Steggles, L..J., Harwood, C. R. and Wipat, A. (2004) SARGE: A tool for creation of putative genetic networks. Bioinformatics 20: 3638-3640.
Oinn T, Addis M, Ferris J, Marvin D, Greenwood M, Carver T, Senger M, Glover K, Wipat A and Li P. (2004) Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics. 20:3045-3054.
Allenby NE, O'Connor N, Pragai Z, Carter NM, Miethke M, Engelmann S, Hecker, M, Wipat A, Ward AC, Harwood CR. (2004). Post-transcriptional regulation of the Bacillus subtilis pst operon encoding a phosphate-specific ABC transporter. Microbiology. 150:2619-28.
Stephens, R., Glover, K., Greenhalgh, C., Jennings, C., Pearce, S., Li, P., Radenkovic, M. and A. Wipat. (2003) Performing in silico experiments on the Grid: A users perspective. In Proceedings of the UK e-Science programme All Hands Conference, 2-4 Sept 2003, Nottingham, UK.
Addis, M., Greenwood, M., Oinn, T., Li, P., Wipat, A., Ferris, J., and Marvin, D. (2003). Experiences with workflow specification and enactment for bioinformatics. In Proceedings of the UK e-Science programme All Hands Conference, 2-4 Sept 2003, Nottingham, UK.
Kobayashi K., Ehrlich S.D., ..Wipat, A. and others (2003) Essential Bacillus subtilis genes. PNAS, 100(8): 4678-83
Luc Moreau, .. Anil Wipat, Chris Wroe and others (2003). On the Use of Agents in a BioInformatics Grid. In Sangsan Lee, Satoshi Sekguchi, Satoshi Matsuoka, and Mitsuhisa Sato, editors, Proceedings of the Third IEEE/ACM CCGRID'2003 Workshop on Agent Based Cluster and Grid Computing, pages 653-661, Tokyo, Japan, May 2003.
Harwood, C.R., Wipat, A and Prágai, Z. (2002) Functional analysis of the Bacillus subtilis genome. Methods in Microbiology 33 337-367
Harwood, C.R., Wipat, A. and Prágai. Z. (2002). Functional analysis of the Bacillus subtilis genome, In, Functional Microbial Genomics (B. Wren, and N. Dorrell), Academic Press, in press.
Harwood, C.R. and Wipat, A. (2002). Bacterial protein synthesis. In, Molecular Medical Microbiology (M Sussman, Ed), Volume 1, pp. 321-338. London: Academic Press
Harwood, C. R. and Wipat, A. (2001). Genome management and analysis: prokaryotes. In, Basic Biotechnology. Eds. C. Ratledge and B. Kristiansen. Cambridge Univerisity Press.
Harwood, C. R., Crawshaw, S. G. and Wipat, A. (2001). From genome to function: systematic analysis of the soil bacterium Bacillus subtilis. Comp. Funct. Genom., 2: 22-24.
Wipat, A and Harwood, C. R. (1999) The Bacillus subtilis genome sequence: the molecular blueprint of a soil bacterium FEMS Microbiology Ecology, 28(1): 1-9
Wipat, A., Brignell, C., Guy, J., Rose, M., Emmerson, P., and C. R. Harwood. (1998). The region of the Bacillus subtilis chromosome between yvsA and yvqA (293°-289°) containing genes involved in metal ion uptake and a putative sigma factor. Microbiology, 144(6): 1593-1600.
Bron, S., Meima, R., -M van Dijl, J., Wipat, A., and Harwood, C. R. (1998). Molecular biology and genetics of Bacillus species., In, Molecular Biology of Industrial Microorganisms. American Society of Microbiology, In Press.
Kunst, F., ..Wipat, A. and others. (1997). The complete genome sequence of the Gram-positive model organism Bacillus subtilis. Nature, 390: 249-256.
Emmerson, P. T., Brignell, C., Wipat, A., Carter N, Pragia Z, Guy, B. J., and Harwood, C. R. (1997). A putative DNA repair operon in B. subtilis comprising a gene encoding a DNA repair polymerase, a mutS homolog and an unidentified ORF. 1997. FASEB journal, 11(9): 2994.
Gothel, S.F., Schmid, R., Wipat, A., Carter, N.M., Emmerson, P.T., Harwood, C.R. and Marahiel. M.A. (1997). An internal FK506-binding domain is the catalytic core of the prolyl isomerase activity associated with the Bacillus subtilis trigger factor. Eur. J. Biochem. 244: 59-65.
Harwood, C.R., and Wipat, A. (1996). Sequencing and functional analysis of the genome of Bacillus subtilis strain 168. FEBS Lett. 389:84-87.
Wipat, A, Carter, N., Brignell, S.C., Guy, B.J., Piper, K., Sanders, J., Emmerson P.T. and Harwood, C.R. (1996). The dnaB to pheA (256° to 240°) region of the Bacillus subtilis chromosome containing genes responsible for stress responses, the utilisation of plant cell walls and primary metabolism. Microbiology 142: 3067-3078.
Gerth, U., Wipat, A., Harwood, C.R., Carter, N., Emmerson, P.T. and Hecker, M. (1996). Sequence and transcriptional analysis of clpX, a class-III heat shock gene of Bacillus subtilis. Gene 181:77-83.
Wipat, A., Wellington, E. M. H. and Saunders, V. A. (1994). Monoclonal antibodies for Sreptomyces lividans and their use for immunomagnetic capture of spores from soil. Microbiology 140:2067-2076.
Saunders, V.A., Wellington, E. M. H. and Wipat, A. (1992). Detection of Streptomyces marker plasmids in soil. In, The release of Genetically-Engineered microorganisms. ed. D.E.S.Stewart-Tull and M.Sussman. Plenum Publishing Corporation, N.York.
Wipat, A., Wellington, E. M. and Saunders, V.A.(1992). Detection systems for streptomycetes. In, Genetic Interactions Between Microorganisms in Natural Environments. ed. E.M.Wellington and M.J.Day. Pergamon Press, Oxford.
Wipat, A., Wellington, E. M. H., and Saunders, V. A.(1991). Streptomyces marker plasmids for monitoring survival and spread of streptomycetes in soil. Applied and Environmental Microbiology 57(11):3322-3330.
Wellington, E. M. H., Cresswell, N., Herron, P. R., Clewlow, L. J., Saunders, V. A. and Wipat, A. (1990). Gene transfer between streptomycetes in soil. In Bacterial Genetics in Natural Environments. ed. J.C.Fry and M.J.Day. Chapman Hall.
Wellington, E. M. H., Saunders, V. A., Cresswell, N and Wipat, A. (1988). Plasmid transfer between streptomycetes in soil p300-305. In, Biology of Actinomycetes 88. ed. Y.Okami, T.Beppu and H.Ogaqara. Japan scientific societies press.
Saunders, V. A., Wipat, A., Cresswell, N. and Wellington, E. M. H.(1988). In, Abstracts Risk Assessment in Agricultural Biotechnology No.10, p5. Davis, California, U.S.A.