Simulating regulatory networks in Escherichia coli by comparative modelling of transcription factors Posdoctoral fellow:
Dr. Bruno Contreras Moreira.
This project is about integrating experimental data related with gene
expression and genomic data through theoretical models in Escherichia
coli, using microarray data, RegulonDB and the Protein Data Bank (PDB).
The goal is to simulate transcriptional regulation systems, in which
transcription factors binding to regulatory regions of genes control
the timing and the intensity of their expression. Our chosen system is
Escherichia coli, a bacteria for which there is a wealth of
experimental data organized in databases such as RegulonDB. This
database contains a repertoire of transcription factors (105 confirmed
experimentally and ~200 predicted), controlling the expression of ~750
open reading frames. We hope to expand the known regulatory network of
E.coli using structural knowledge, prompted by recent progress by
several groups suggesting that this knowledge can be used to predict
what DNA sequences are preferably bound by regulatory proteins.