Motif representation and discovery
Alexandra M. Carvalho,
An important part of gene regulation is mediated by specific proteins, called transcription factors (TF), which influence the transcription of a particular gene by binding to specific sites on DNA sequences, called transcription factor binding sites (TFBS). Such binding sites are relatively short stretches of DNA, normally 5 to 25 nucleotides long. A commonly used representation of TFBS is a position specific scoring matrices (PSSM) which assumes independence of nucleotides in
the binding sites. Recently, some works argued in the direction of non-additivity in protein-DNA interactions making a way for more complex models to appear which account for nucleotide interactions. We propose to model TFBS representing nucleotide interactions with consistent k-graph Bayesian networks (where k represents the maximum number of interactions between nucleotides) jointly with a set of features, directly scored from each base sequence, which appear to be relevant for TFBS characterization. The model is flexible to incorporate any set of features scored from base sequences. We consider discriminative learning of such models since it
outperforms generative learning in the context of classification with a large set of features.
Date: 2010-Jan-08 Time: 14:30:00 Room: 04
For more information:
Workshop “Metabolism and mathematical models: Two for a tango” – 2nd Edition
Title: Workshop Metabolism and mathematical models: Two for a tango – 2nd Edition
Dates: October 25-26, 2022
Location: This workshop will be held in a virtual way
The topic of this workshop is metabolism in general, with a special focus, although not exclusive, on parasitology. Besides an exploration of the biological, biochemical and biomedical aspects, the workshop will also aim at presenting some of the mathematical modelling, algorithmic theory and software development that have become crucial to explore such aspects.
This workshop is being organised in the context of two projects, both with the Inria European Team Erable. One of the projects involves a partnership with the University of São Paulo (USP), in São Paulo, Brazil, more specifically the Institute of Mathematics and Statistics (IME) and the Institute of Biomedical Sciences – Inria Associated Team Capoeira – and the other involves the Inesc-ID/IST in Portugal, ETH in Zürich and EMBL in Heidelberg – H2020 Twinning Project Olissipo.
The workshop is open to all members of these two projects but also, importantly, to the community in general.
The program and more details are available here.