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Pedro T. Monteiro

P.T. Monteiro I am currently an Assistant Professor at INESC-ID / Instituto Superior Técnico - Universidade de Lisboa.

I continue to collaborate with the Network Modelling group as a Visiting Researcher of the Instituto Gulbenkian de Ciência.

Current webpage: http://pedromonteiro.org

Research interests:

Since my PhD, I have been mainly interested 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 am currently working on the definition of diagnostics for the semi-automatic revision of biological models.

Selected publications (until 2012):

  • A. Naldi, P.T. Monteiro and C. Chaouiya (2012)
    Efficient handling of large signalling-regulatory networks by focusing on their core control
    in D. Gilbert and M. Heiner, eds., Proc. of the 10th Intl. Conf. on Computational Methods in Systems Biology (CMSB'12), LNCS 7605, Springer Verlag, 288-306
    [ doi:10.1007/978-3-642-33636-2_17 ]

  • C. Chaouiya, A. Naldi, L. Spinelli, P.T. Monteiro, D. Berenguier, L. Grieco, A. Mbodj, S. Collombet, A. Niarakis, L. Tichit, E. Remy, D. Thieffry (2012)
    Logical modelling of cellular decision processes with GINsim
    Working notes of the Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM'12), Rennes, France

  • P.T. Monteiro and C. Chaouiya (2012)
    Efficient verification for logical models of regulatory networks
    in Rocha et al., eds., Proc. of the 5th Intl. Conf. on Practical Applications on Computational Biology & Bioinformatics (PACBB'12), AISC 154, Springer Berlin / Heidelberg, 259-267
    [ doi:10.1007/978-3-642-28839-5_30 ] PAAMS'12 Award of Scientific Excellence

  • P.T. Monteiro and C. Chaouiya (2011)
    Logical modelling of biological regulatory networks: turning automatic verification effective
    Working notes of the 3rd INForum - Simpósio de Informática (INForum'11), Coimbra, Portugal

  • P.T. Monteiro, P.J. Dias, D. Ropers, A.L. Oliveira, I. Sá-Correia, M.C. Teixeira and A.T. Freitas (2011)
    Qualitative modeling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae
    IET Systems Biology, 5(5): 308-316
    [ doi:10.1049/iet-syb.2011.0001 ]

  • R. Mateescu, P.T. Monteiro, E. Dumas and H. de Jong (2011)
    CTRL: Extension of CTL with Regular Expressions and Fairness Operators to Verify Genetic Regulatory Networks
    Theoretical Computer Science, 412(26): 2854-2883
    [ doi:10.1016/j.tcs.2010.05.009 ]

  • M.C. Teixeira, P.J. Dias, P.T. Monteiro, A. Sala, A.L. Oliveira, A.T. Freitas and I. Sá-Correia (2010)
    Refining current knowledge on the yeast FLR1 regulatory network by combined experimental and computational approaches
    Molecular BioSystems, 6(12), 2471-81
    [ doi:10.1039/C004881J ]

  • G. Batt, M. Page, I. Cantone, G. Goessler, P. Monteiro and H. de Jong (2010)
    Efficient parameter search for qualitative models of regulatory networks using symbolic model checking
    Bioinformatics, 26(18), i603-i610
    Presented at European Conference on Computational Biology (ECCB'10)
    [ doi:10.1093/bioinformatics/btq387 ]

  • P.T. Monteiro, E. Dumas, B. Besson, R. Mateescu, M. Page, A.T. Freitas and H. de Jong (2009)
    A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks
    BMC Bioinformatics, 10:450
    [ doi:10.1186/1471-2105-10-450 ]

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

  • P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas and H. de Jong (2008)
    Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks
    Bioinformatics, 24(16): i227-i233
    Presented at European Conference on Computational Biology (ECCB'08)
    [ doi:10.1093/bioinformatics/btn275 ]