CISBIC Sub-project 1: Glycomics of Mycobacterium bovis and Campylobacter jejuni

The overall aim of sub-project 1 is to develop models that will allow the prediction the effect of changes to the pathogen genome on expression of glycosylated surface molecules involved in triggering the innate immune response of the host.

Organisms:

  • Campylobacter jejuni
  • Mycobacterium bovis

Funding:

  • BBSRC Research Grant: 

Affiliates:

For more information about the outputs from this project or to discuss data reuse please contact bsshelp@imperial.ac.uk

CISBIC Sub-project 1

Project Members
  • Prof Stephen Muggleton
  • Prof Brendan Wren
  • Prof Michael Sternberg
  • Dr Emily Kay (biology)
  • Dr Victor Lesk (modelling)
  • Alireza Tamaddoni-Nezhad (modelling)
  • Dr Adrian Cootes (modelling)
  • Hiroake Watanabe (modelling)
  • Dr Richard Barton (core facility)
  • Dr Paul Hitchen (core facility)
  • Dr Frances Turner (statistics)
Software
  •  (Lesk)
    The Workbench for Integrative Systems Biology is a portal-based workbench for interdisciplinary systems biology projects
  •  (Cootes)
    Web-based tool for the visualization and interrogation of Campylobacter jejuni glycomics pathway
  •  (Tamaddoni-Nezhad)
    Progol code and interpreter to perform Inductive Logic Programming using a Prolog knowledge base
  • PINALOG (Sternberg)
    PINALOG is a novel approach to align two protein-protein interaction (PPI) networks which combines information available for the proteins in the networks, including sequence, function and network topology
Datasets
  •  (Lesk)
    Prolog clauses representing background knowledge relating to Campylobacter capsule formation
  •  (Turner)
    A comparison of the transcript profiles of mutants in capsule locus genes from Campylobacter jejuni strain 13362 compared to wild type
  •  (Turner)
    Treatment of Campylobacter jejuni wild type strain NCTC 13362 with various infection or environmental mimic perturbations
  •  (Turner)
    Transcriptional profiles of capsule locus mutants compared to wild type Campylobacter jejuni strain NCTC 13362. RNA was extracted after incubation optimized to give maximal capsule expression in the wild type cells
  • Campylobacter mutant capsule NMR (Barton, prepublication)
    Metabolomic characterisations of Campylobacter jejuni mutants as determined by 1H NMR
Publications

Articles:

  • Generation of gene function hypotheses using a logic-based machine learning approach applied to the Campylobacter jejuni glycome (in preparation)
  • Cootes AP, Muggleton SH, Sternberg MJ.
    J Mol Biol. 2007 Jun 15;369(4):1126-39. Epub 2007 Mar 14.
  • Tamaddoni-Nezhad A, Chaleil R, Kakas AC, Sternberg M, Nicholson J, Muggleton S.
    IEEE Eng Med Biol Mag. 2007 Mar-Apr;26(2):37-46.
  • Muggleton SH, Tamaddoni-Nezhad A.
    Machine Learning, 70(2-3):123-133, 2007.
  • Muggleton SH, Tamaddoni-Nezhad A.
    Machine Learning, 76(1):37-72, 2009.
  • Kay E, Lesk VI, Tamaddoni-Nezhad A, Hitchen PG, Dell A, Sternberg MJ, Muggleton S, Wren BW.
    Biochem Soc Trans. 2010 Oct;38(5):1290-3.
  • Muggleton SH, Santos J, Tamaddoni-Nezhad A.
    In Proceedings of the 19th International Conference on Inductive Logic Programming, LNCS 5989, pages 131-148. Springer-Verlag, 2010.
  • Muggleton SH, Santos J, Tamaddoni-Nezhad A.
    In Proceedings of the International Conference on Logic Programming 2008, LNCS 5366, pages 687-692. Springer-Verlag, 2010.
  • Lesk V, Taubert J, Rawlings C, Dunbar S, Muggleton S.
    J Integr Bioinform. 2011 Jun 27;8(2):156. doi: 10.2390/biecoll-jib-2011-156.

Presentations:

  • FASEB Summer Conference on Microbial Polysaccharides, Arizona, USA (Hitchen, 2008)
  • Learning and Inference in Computational Systems Biology, Glasgow, UK (Tamaddoni-Nezhad, 2008)
  • CISBIC International Advisory Board meeting (Muggleton, 2010)
  • Integrative Bioinformatics (Lesk, 2011)
  • KAUST conference on Quantitative Biology (Lesk, 2011)
  • FASEB Summer Conference on Microbial Polysaccharides, Arizona, USA (Hitchen, 2011)

Posters:

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