1. CISBIC: Sub-project 1: Stephen Muggleton CISBIC, Flowers Building, Imperial College London. www.imperial.ac.uk/cisbic Modeling genotype-phenotype relations in Campylobacter: an update and future plans

2. Overview Machine Learning in Systems Biology CISBIC sub-project 1 Hypotheses being tested Automated experiment selection Conclusions

3. Systems Biology: The CISBIC Vision

4. Machine Learning BLPsPMDPsLogic Programs SCFGsHMMsGrammars Bayes’ netsNeural netsDecision trees MixedProbabilisticLogical

5. Inductive Logic Programming Background knowledge. Incomplete biological network. Examples. Temporal traces of up/down regulation. Hypothesis. Extra network annotation.

6. CISBIC subproject 1 Aim. Model effects of changes to pathogen genome of expression of glycosolated surface molecules involved in triggering of innate immune response of host. Mycobacterium bovisCampylobacter jejuni

7. Initial focus Synthetic pathways for capsule in C. jejuni 38 genes involved. Full set of knock-outs. Functions - 1/3 known,1/3 suspected, 1/3 unknown. Microarray and metabonomic experiments. Polysaccharide capsule

8. Pathway database Prolog database Machine learning Visualisation KEGGBioCyc ONDEX Brendan/papers

9. Hypotheses for capsule pathway (in red) ‏ cj1432c cj1416c / cj1417c / cj1418c

10. Hypotheses predict Cj1416, Cj1417, Cj1418 involved in OMePN synthesis. Wren group has verified this by mutagenesis and structural analysis. Fairly obvious from BLAST analysis. Cj1432, a protein of unknown function, is central to capsule synthesis. Not predictable from amino acid similarity and BLAST analysis.

11. Experiments to test cj1432 hypothesis 1.Immunoassay. 2.Alcian Blue dye staining of Campylobacter. 3.Electron microscopy – direct visual inspection. 4.Complementation – reintroduce cj1432 to chromosome of mutant 5.Structural analysis of capsule glycan. 6.Protein purification and enzyme assays.

12. Hypotheses/experiments E CBA Pre-E Pre-C Pre-B rB rC rD E E10 E9 E11 H4H1 0 0 0 1 1 1 H5 E8 H2H3

13. Conclusions Integration of diverse background knowledge ILP produces readable rules Gap-filling in networks Ongoing NMR/MS experimental testing of hypotheses Cj1432 – potential C. jejuni vaccine