Evaluating differential gene expression using RNA-sequencing data: a case study in host-pathogen interaction upon Listeria monocytogenes infection
Departamento de Engenharia Informática –
Unlike the genome, the cell transcriptome is dynamic and specific for a given cell developmental stage or physiological condition. Understanding the transcriptome is essential for interpreting the functional elements of the genome and revealing the molecular constituents of cells. Recently, developments of high-throughput DNA sequencing methodologies have provided a new method to sequence RNA at unprecedented high resolutions. This method is termed RNA-Seq and has been emerging as the preferred technology for both characterization and quantification of the cell transcripts.
Bearing this in mind, in this thesis I propose a bioinformatics pipeline to compare two RNA-Seq samples. This pipeline permits biological insight into the analysed samples, by extracting the main biological processes that are differentially active among the samples in analysis. Subsequent to this pipeline, I developed a novel methodology to inspect the activation of a given cellular pathway in a time-course RNA-Seq dataset.
The evaluation of a Listeria monocytogenes RNA-Seq dataset with the developed tools testified its proper functioning. It was possible to identify global changes in the human host transcriptome and associate these changes to different stages of the Listeria monocytogenes infection lifecycle.
Date: 2013-Nov-28 Time: 14:30:00 Room: 336
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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.