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Journal Papers


  1. Supporting Hypothesis Generation: Identification of Functionally Relevant Pathways in Chronic Trichuriasis Induced Colitis.
    Paul Fisher, Scott Levison, Joanne Pennock, Andrew Brass and Robert Stevens
    Nucleic Acids Research - in preparation

  2. Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection.
    Harry Noyes, Andy Brass, Isaiah Obara, Susan Anderson, Alan Archibald, Dan Bradley, Paul Fisher, Abigail Freeman, John Gibson, Michael Gicheru, Laurence Hall, Olivier Hanotte, Helen Hulme, Declan McKeever, Caitriona Murray, Sung Jong Oh, Catriona Tate, Ken Smith, Miika Tapio, John Wambugu, Diana Williams, Morris Agaba, Stephen Kemp
    Proceedings of the National Academy of Sciences (PNAS). Accepted for Publication - April 2011
    Web version currently unavailable

  3. Genetic analysis of chronic Trichuriasis reveals QTL overlap with Cdcs1 and a novel gene cluster important to colitis.
    Scott E. Levison, Paul Fisher, Jenny Hankinson, Anne Barton, Steve Eyre, William E. Ollier, John T. McLaughlin, Andy Brass, Richard K. Grencis, Joanne L. Pennock.
    Gastroenterology - in submission
    Web version currently unavailable


  1. Further developments towards a genome-scale metabolic model of yeast Paul D Dobson, Kieran Smallbone, Daniel Jameson, Evangelos Simeonidis, Karin Lanthaler, Pnar Pir, Chuan Lu, Neil Swainston, Warwick B Dunn, Paul Fisher, Duncan Hull, Marie Brown, Olusegun Oshota, Natalie J Stanford, Douglas B Kell, Ross D King, Stephen G Oliver, Robert D Stevens and Pedro Mendes
    BMC Systems Biology. 2010;4:145
    Web version - Link

  2. Colonic transcriptional profiling in resistance and susceptibility to Trichuriasis: phenotyping a chronic colitis and lessons for iatrogenic helminthosis Levison, S. E., McLaughlin, J. T., Zeef, L. A. H., Fisher, P., Grencis, R. K., Pennock, J. L.
    Inflammatory Bowel Diseases. 2010
    Web version - Link

  3. Towards Open Science: The myExperiment approach.
    De Roure D, Goble C, Aleksejevs S, Bechhofer S, Bhagat J, Cruickshank D, Fisher P, Hull D, Michaelides D, Newman D et. al.,
    Concurrency and Computation: Practice and Experience 2009, Accepted 31st March 2010
    Web version - Link


  1. A Systematic Approach to Understanding Bacterial Responses to Oxygen Using Taverna and Webservices. Maleki-Dizaji S., Rolfe M., Fisher P., Holcombe M. 13th International Conference on Biomedical Engineering. 2009: 77-80.
    Web version- Link

  2. Benchmarking Workflow Discovery: A Case Study From Bioinformatics.
    Goderis, A., Fisher, P., Gibson, A., Tanoh, F., Wolstencroft, K., De Roure, D., Goble, C.
    Concurrency and Computation: Practice and Experience 2009.
    Web version- Link


  1. A systematic, data-driven approach to the combined analysis of microarray and QTL data.
    Rennie, C., Hulme, H., Fisher, P., Halp, L., Agaba, M., Noyes, H., Kemp, S., Brass, A.
    Developments in biologicals 2008, 132:293-299.
    Web version- Link


  1. A Systematic Strategy for Large-Scale Analysis of Genotype-Phenotype Correlations: Identification of candidate genes involved in African Trypanosomiasis. Fisher, P., Hedeler, C., Wolstencroft, K., Hulme, H., Noyes, H., Kemp, S., Stevens, R., Brass, A. Nucleic Acids Res. 2007;35(16):5625-33. 2007 Aug 20
    Web version- Link

  2. A systematic strategy for the discovery of candidate genes responsible for phenotypic variation. Fisher, P., Hedeler, C., Wolstencroft, K., Hulme, H., Noyes, H., Kemp, S., Stevens, R., Brass, A. BMC Bioinformatics 2007, 8(Suppl 8):P7 (20 November 2007)
    Web version- Link

Book Chapters

  1. A systematic strategy for the discovery of candidate genes responsible for phenotypic variation.
    Fisher, P., Noyes, H., Kemp, S., Stevens, R., Brass, A.
    Methods in molecular biology (Clifton, NJ) 2009, 573:329-345.

  2. Traversing the bioinformatics landscape.
    Stevens, R., Fisher, P., Zhao, J., Goble, C., Brass, A.
    Data Mining Techniques in Grid Computing Environments.
    Edited by Dubitzky W: John Wiley and Sons; 2008: 141-164.

Additional Material

  1. Carole Goble: Democratizing Informatics for the ‘Long Tail’ Scientist
    BioITWorld - March 31st 2011
    An interview with Prof. Carole Goble, in which my research is discussed as a 'personal favourite' of how to utilise scientific workflows for advancing research discoveries in Biology.
    Link to Article

  2. The Taverna Project – a workbench for bioinformatics design
    Bitsizebio Webinar on Taverna
    A video about the Tavena Workflow Workbench, and its role in scientific research
    Link to video

  3. Should researchers share data?
    JISC Inform, Issue 26, Autumn 2009
    A scientific debate on whether researchers should share their data. I provided the 'YES' argument to this debate.
    Link to PDF

  4. A little sharing goes a long way
    The Data revolution; Times Higher Education: JISC; 26th November 2009 (pages 8 to 11)
    An article on the sharing of data and experimental methods. Insert on page 11 discusses my work on African Trypanosomiasis using wokrlfows and myExperiment (under 'Animal Health').
    Link to Web based article

  5. Bioinformatics : eIUS e-Infrastructure Case Study
    A YouTube video about the role of e-Science in assiting scientific research
    Link to video

  6. Sharing Science in the World of Web 2.0
    NeSC News, Issue 69, May 2009
    Page 3 contains a picture of me giving a demo of myExperiment and Taverna (Top right picture)
    Link to PDF

  7. Research intelligence - Log on to a global laboratory
    Zoe Corbyn
    Times Higher Education (THE): 1st January (2009)
    An article I contributed to, about Web 2.0 research tools and my experiences of using them for my research
    Link to article

  8. Acute inflammation and cholesterol: from African cows to Man
    HIGHLIGHTS from the UK e-Science Programme: Issue 2 (2007)
    A small article (page 1) on the success of using e-Science to further research; related to work carried out during my PhD
    Link to PDF

  9. The new networking nexus
    Virginia Gewin
    Nature Special Report: Nature, Volume 451, Issue 21 (2008)
    An article (page 1025 - building a critical mass section) mentioning my research on African Trypanosomiasis using workflows
    Link to article

  10. Interview with Carole Goble
    Marga van Zundert
    Interface Issue 1 (2008) - NBIC
    An article/interview with Prof. Carole Goble, noting my work as a classic case of workflow use in bioinformatics (Page 7)
    Link to PDF

  11. myExperiment and Taverna - a great success at ISMB!
    OMII-UK NEWS (December 2008)
    An article noting the success of Taverna and myExperiment at ISMB in 2008 (Page 2 - contains a photo of me with various myGrid and myExperiment team members)
    Link to PDF