Sub-project 1

• 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)

• Interactive Glycomics Workbench (Lesk)
  The Workbench for Integrative Systems Biology is a portal-based workbench for interdisciplinary systems biology projects
• Metabolomics Network Browser (Cootes)
  Web-based tool for the visualization and interrogation of Campylobacter jejuni glycomics pathway
• Progol (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

• Prolog database (Lesk)
  Prolog clauses representing background knowledge relating to Campylobacter capsule formation
• BµG@Sbase microarray experiment 155 (Turner)
  A comparison of the transcript profiles of mutants in capsule locus genes from Campylobacter jejuni strain 13362 compared to wild type
• BµG@Sbase microarray experiment 158 (Turner)
  Treatment of Campylobacter jejuni wild type strain NCTC 13362 with various infection or environmental mimic perturbations
• BµG@Sbase microarray experiment 159 (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

Articles:

• Generation of gene function hypotheses using a logic-based machine learning approach applied to the Campylobacter jejuni glycome (in preparation)
• The identification of similarities between biological networks: application to the metabolome and interactome
  Cootes AP, Muggleton SH, Sternberg MJ.
  J Mol Biol. 2007 Jun 15;369(4):1126-39. Epub 2007 Mar 14.
• Modeling the effects of toxins in metabolic networks
  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.
• QG/GA: a stochastic search for Progol
  Muggleton SH, Tamaddoni-Nezhad A.
  Machine Learning, 70(2-3):123-133, 2007.
• The lattice structure and refinement operators for the hypothesis space bounded by a bottom clause
  Muggleton SH, Tamaddoni-Nezhad A.
  Machine Learning, 76(1):37-72, 2009.
• Systems analysis of bacterial glycomes
  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.
• ProGolem: A System Based on Relative Minimal Generalisation
  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.
• TopLog: ILP Using a Logic Program Declarative Bias
  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.
• WIBL: Workbench for Integrative Biological Learning
  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:

• CISBIC International Advisory Board meeting (Muggleton, 2010)