Care was taken to form groups balanced in terms of the students' educational background. This encouraged students to help one another.

All students

Pedro Monteiro

Having a background such as Computer Science, the PhD Program in Computational Biology gives me the possibility to make the brigde to Biology, beeing an unique oportunity to get a broader perspective of all the areas involved and to develop my skills in the field. (2005-12-01)

Resumé

I obtained a BSc and a MSc in Information Systems and Computer Engineering from Instituto Superior Técnico, where I developed the Yeastract.com database (a repository of regulatory associations for Saccharomyces cerevisiae). I continue to collaborate in its regular maintenance and development.

In 2005, I joined the PhD Program in Computational Biology. After attending the first year classes at the Instituto Gulbenkian de Ciência, I got the opportunity to work on my thesis at the IBIS group at INRIA Grenoble Rhone-Alpes, under the supervision of Hidde de Jong (INRIA Grenoble - Rhône-Alpes), Ana T. Freitas (INESC-ID Lisboa) and Radu Mateescu (INRIA Grenoble - Rhône-Alpes). I worked mainly on the analysis and validation of qualitative models of biological regulatory networks. In particular, through the use of formal verification techniques like model checking and temporal logic, for the exploration of interesting dynamical behaviours of qualitative biological models. I obtained a Dual PhD in May 2010 from Instituto Superior Técnico and Université Claude Bernard Lyon 1.

After completing my PhD I worked as a postdoctoral researcher at the Molecular Microbiology and Infection Unit at the Instituto de Medicina Molecular studying the topological structure of the evolutionary relationships within bacterial populations.

In April 2011, I returned to the Instituto Gulbenkian de Ciência, as a postdoctoral researcher at the Network Modelling group, working on the definition of diagnostics for the semi-automatic revision of biological models.

PhD Project

Supervisor: Hidde de Jong

Cosupervisors:

Radu Mateescu
Ana Teresa Freitas

Laboratory: IBIS, INRIA Grenoble Rhône-Alpes, France

University: Instituto Superior Técnico & Université Claude Bernard Lyon 1

Thesis

Towards an integrative approach for the modeling and formal verification of biological regulatory networks. Université Claude Bernard, Lyon 1, and Instituto Superior Técnico, Universidade Técnica de Lisboa (2010) pp.141. [pdf]

Publications

R. Mateescu, P.T. Monteiro, E. Dumas and H. de Jong. CTRL: Extension of CTL with Regular Expressions and Fairness Operators to Verify Genetic Regulatory Networks. Theoretical Computer Science (2011) 412, 2854-2883.

G. Batt, M. Page, I. Cantone, G. Goessler, P. Monteiro and H. de Jong. Efficient parameter search for qualitative models of regulatory networks using symbolic model checking. Bioinformatics (2010) 26(18), i603-i610.

M.C. Teixeira, P.J. Dias, P.T. Monteiro, A. Sala, A.L. Oliveira, A.T. Freitas and I. Sá-Correia. Refining current knowledge on the yeast FLR1 regulatory network by combined experimental and computational approaches. Molecular BioSystems (2010) 6(12), 2471-2481.

G. Batt, B. Besson, H. de Jong, E. Dumas, J. Geiselmann, P.T. Monteiro, M. Page and D. Ropers. Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks. Bacterial molecular networks (2009) , .

V. Baldazzi, P.T. Monteiro, M. Page, D. Ropers, J. Geiselmann, H. de Jong. Qualitative analysis of genetic regulatory networks in bacteria. Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology (2009) , .

P.T. Monteiro, E. Dumas, B. Besson, R. Mateescu, M. Page, A.T. Freitas and H. de Jong. A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks. BMC Bioinformatics (2009) 10, 450.

R. Mateescu, P.T. Monteiro, E. Dumas and H. de Jong. Computation Tree Regular Logic for Genetic Regulatory Networks. Proceedings of the 6th International Symposium on Automated Technology for Verification and Analysis (ATVA'08) (2008) LNCS 5311, 48-63.

P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas and H. de Jong . Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks. Proceedings of the 18th European Conference on Artificial Intelligence (ECAI'08) (2008) , 229-233.

P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas and H. de Jong. Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks. Bioinformatics (2008) 24(16), i227-i233.