Evaluating differential gene expression using RNA-sequencing data: a case study in host-pathogen interaction upon Listeria monocytogenes infection
Joana Cruz,
Departamento de Engenharia Informática –
Abstract:
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
For more information:
- http://kdbio.inesc-id.pt/cms/
- lsr@kdbio.inesc-id.pt
- (+351) 21 31 00272
Upcoming Events
INESC Brussels HUB Winter Meeting 2023

This edition of the HUB Winter Meeting will be co-organised with Science Business and will take place on the 30 and 31 January, in Lisbon, at Instituto Superior Técnico, Department of Computer Science and Engineering.
Please see below a summary of the agenda, this will be updated on the INESC Brussels HUB website regularly (confirmed speakers and other relevant info). Places for onsite participation are limited so registration is mandatory. Online participants will be sent a ZOOM link for each specific session on the 27th January.
INESC Brussels HUB website: https://hub.inesc.pt/
Monday, 30 January
a) Digital Europe Programme & Chips Act: state of play and possibilities for INESC.
9h to 10h30 GMT
(Exclusive for INESC researchers and administrators).
b) Science Business: how can INESC tap into Science Business network, activities and communications tools.
(Exclusive for INESC researchers and administrators).
c) Networking Lunch (for all onsite participants).
d) Roundtable: From rhetoric to reality – Embedding international strategy in the DNA of research organisations.
(Closed-door, roundtable workshop, Chatham House rules, open to INESC researchers and administrators, external participants by invitation only).
e) Networking Dinner
(By invitation only – INESC researchers participating onsite in the event are elegible to join).
Tuesday, 31 January
f) Workshop: How they did it? Strategic positioning for structural success in Horizon Europe: a discussion of best practices.
(Exclusive for INESC researchers, administrators and international invited speakers).
g) The public consultation on European R&I Programmes: Towards FP10.
(Closed-door, roundtable workshop, Chatham House rules, open to INESC researchers and administrators, external participants by invitation only).
h) Networking Lunch (for all onsite participants).
i) Management Committee meeting (Directors and POB members)
The HUB Winter Meeting aims at bringing together researchers and administrators from the 5 INESC institutes, affiliated higher education institutions in Portugal and abroad, with key European and global players, to:
– Discuss key research and innovation issues at EU level.
– Inform institutional policy and strategy.
– Exchange best-practices about R&I management, career development and policy positioning.
– Promote, discuss and deliver vision, visibility, networking and impactful communication.
– Create, identify and deepen partnerships and collaboration opportunities for collaborative R&I.