Probabilistic retrieval and visualization of biologically relevant microarray experiments
Helsinki University of Technology –
As ArrayExpress and other repositories of genome-
wide experiments are reaching a mature size, it is becoming more
meaningful to search for related experiments, given a particular
study. We introduce methods that allow for the search to be
based upon measurement data, instead of the more customary
annotation data. The goal is to retrieve experiments in which the
same biological processes are activated. This can be due either
to experiments targeting the same biological question, or to as-yet
unknown relationships. We use a combination of existing and new probabilistic
machine learning techniques to extract information about the
biological processes differentially activated in each experiment, to
retrieve earlier experiments where the same processes are activated,
and to visualize and interpret the retrieval results. Case studies on a
subset of ArrayExpress show that, with a sufﬁcient amount of data,
our method indeed ﬁnds experiments relevant to particular biological
questions. Results can be interpreted in terms of biological processes
using the visualization techniques.
Date: 2009-Apr-15 Time: 16:00:00 Room: 336
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.