Modelling yeast gene expression regulation

From the Manchester Bio-Modelling Network

The BioModelling Network organised a meeting for researchers who are working on or are interested in modelling yeast gene expression and its regulation.

Thanks to everyone who joined our meeting. Just to summarize the round, and facilitate further interaction, below please find a little summary of what we wrote down (might be incomplete or even wrong).

Dieter Weichart: MCISB Project Manager, points out that MCISB currently is more interested in protein levels, will not produce data on mRNA expression, but tries to "observe" other projects in this direction.

Chris Knight: Life Sciences, Evolution of regulatory networks, will produce data on tiling arrays to see where adaptive mutations occur, and will do some modelling of these networks lateron.

Olusegun Oshota and Ben Small, DTC Systems Biology: Measure protein expression of isoforms of glycolytic enzymes under different conditions using GFP-tagged proteins to model and understand isoform regulation.

Andy Sharrocks, Life Sciences, showed several relatively complicated network motifs of gene regulation in the G2/M transition of the yeast cell cycle which need some modelling - Pedro pointed to Bela Novak's and John Tyson's earlier work which however focusses more on the protein level. It was suggested that we may invite Bela Novak to our systems biology seminars in MIB.

Jean-Marc Schwartz, Life Science, starts to work on extreme pathway analysis of gene regualtion, which can analyze boolean/integer representation of gene regulatory networks - we might organise a seminar about this method.

Kevin Sharp works on integrating ChIP-Chip data and array data to infer network structure.

Joseph Dada, MIB, works on tools for simulation with Pedro.

Pedro Mendes, MIB, is interested in transcriptional regulations after oxidative stress in yeast and is building a detailed kinetic model of it.

Steve Wilkinson, MIB, works on hierarchical regulation analysis of starvation processes in yeast, where currently enzyme activities over time are measured, but transcriptomics data will be gathered lateron.

Nils Bluethgen, MIB, interested in signalling and gene expression, looking at signalling/gene expression feedback loops, and making a model (as part of a group-wide activity) of yeast glycolysis gene regulation.

Action points

• Try to get Bela Novak for a seminar
• Organise a seminar on extreme pathways analysis of metabolic and regulatory networks