Publicado em: 12/04/2010

Série de Seminários do Instituto de Informática UFRGS

Série de Seminários do Instituto de Informática UFRGS
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SEXTA-FEIRA, 16 de abril de 2010
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Horário: 12h45min
Duração: 45min
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Local:
Auditório Prof José M. V. de Castilho
Instituto de Informática, UFRGS
Av Bento Gonçalves 9500, Bloco IV
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Palestrante: Dr. Ronnie Alves, Pós-doutorando do INF

Título: Transcriptomic Data Analysis: Theoretical and Practical Aspects
of Gene Expression Analysis.

Gene expression analysis is an essential and polemical task in transcriptomic data analysis. It is essential because it can highlights gene products, gene regulation and function, as well as, gene conservation when more than one study is available for meta-analysis; the polemical side comes from the fact that the results depends on the computational approach employed. Several methods have been proposed but no consensus so far. Most of the discovered patterns do not guarantee biological significance. Actually, it might depend on the “biologist decision”. The bioinformatics’ community called this dilemma as “fishing for significance”. This talk presents theoretical and practical aspects observed in two transcriptomic studies we have been conducting in collaboration with the Institute of Developmental Biology and Cancer at Nice (France).

In the first study, the in-house Otx2 knockout experiment in mouse retina was driven to highlight the function of this homeobox gene in adult mice. Using the previously described self knockout strategy by Fossat et al’06, the mouse Otx2 gene was disrupted in all its domain of expression in adults, i.e. mainly in retina. One striking result of this study is the very limited number of genes identified as affected by the loss of Otx2 expression. In the second study, we present an integrated model using high-throughput transcriptomic data to enable predictions of cellular networks model for one of the most prevalent diseases worldwide, Type 2 diabetes (T2D), formally known as the non-insulin dependent diabetes mellitus. Comprehensive elucidation of the genes regulated through this disorder and their “wiring” will provide a more complete understanding of the overall gene network topology and their role in disease progression.

Short-bio:

Ronnie Alves received his Ph.D in Computer Science (Artificial Intelligence) from the University of Minho at Braga (Portugal) in April/2008, under the supervision of Prof. Dr. Orlando Belo. While pursuing his PhD studies, he also served as a visiting researcher in the Data Mining Group (at DAIS Lab in the University of Illinois at Urbana-Champaign, USA) led by Prof. Dr. Jiawei Han and in the Bioinformatics Research Group (at Pablo de Olavide University – Sevilla,Spain) led by Prof. Dr. Jesus Aguilar-Ruiz. Before getting his Ph.D, he also worked as IT Consultant in several industrial projects (From Retail to Telecommunications) in Brazil and Portugal. He was awarded a post-doctoral fellowship from the French National Center for Scientific Research (CNRS) in the Virtual Biology Group at the Institute of Developmental Biology and Cancer (Nice) from September/2008 to March/2010. Currently, he is Postdoc Researcher in the Institute of Informatics at UFRGS leading the MOBIO project – PNPD’09, CAPES. MOBIO is a bioinformatics project to the development of methods and algorithms for analyzing biochemical data and its applications on pharmacogenomics.