Cladosporum fulvum is a fungus infecting crops. In a recent study, a tomato expressing a fungal resistance gene and a receptor recognizing pathogen-secreted proteins was infected, and during the so-called hypersensitive response both RNA expression was measured over time using microarrays . Moreover, metabolomics data was measured on the same samples.
In this project, the goal is to go beyond the initial analyses performed in . In particular, we would like to learn more on the dynamics of the hypersensitive response by inferring regulatory networks (e.g. ), incorporating as much prior knowledge as possible.
 D.W. Etalo et al. (2013) System-wide hypersensitive response-associated transcriptome and metabolome reprogramming in tomato. Plant Physiology 162:1599-1617.  C. Roven and H.J. Bussemaker (2003) REDUCE: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data. Nucleic Acids Research 31(13):3487-90.
Used skills: Programming, statistics
Requirements: INF-22306 Programming in Python, SSB-30306Molecular systems biology, BIF-30806 Advanced bioinformatics