my photo  
Pedro T. Monteiro
  Tecnico
INESC-ID
Address: INESC-ID Lisboa, SAT group
Rua Alves Redol 9
P-1000-029 Lisboa
PORTUGAL
Email:
Tel: (+351) 21 3100 320

Index - Teaching - Research - Software

Research Interests

I have been mainly interested on the formal and static analysis 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 belong to http://CoLoMoTo.org (Consortium for Logical Models and Tools), a consortium of research groups interested in logical modelling. The consortium works on the definition of standards for model representation and interchange (especially the SBML qual format), and on the comparison of methods, models and tools.
In this context, I am currently involved on the development of:
- http://ginsim.org, a computer tool for the modeling and simulation of genetic regulatory networks.
- http://epilog-tool.org, a computer tool for the modeling, simulation and visualisation of logical models for epithelial pattern formation.

I collaborate, since their creation, in the continuous maintenance and development of both http://yeastract.com and http://pathoyeastract.org databases, repositories of regulatory associations for Saccharomyces cerevisiae and pathogenic Candida species (currently C. albicans and C. glabrata), respectively.

Finally, I also collaborated on the development of plugins for http://www.phyloviz.net, a data integration and visualization tool for multiple phylogenetic inference methods.

Publications

[ DBLP ] [ gScholar ] [ Pubmed ] [ ResearcherID ]

Journal or Conference articles
  • M.C. Teixeira, P.T. Monteiro, M. Palma, C. Costa, C.P. Godinho, P. Pais, M. Cavalheiro, M. Antunes, A. Lemos, T. Pedreira, I. Sá-Correia (2018)
    YEASTRACT, an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae
    Nucleic Acids Research, accepted
    [ bib ] [ doi:10.1093/nar/gkx842 ] († joint first authorship)

  • F. Gouveia, P.T. Monteiro, V. Manquinho, I. Lynce (2017)
    Logic-Based Encodings for Ricochet Robots
    E. Oliveira, J. Gama, Z. Vale, H. Lopes Cardoso (editors)
    Proc. of the 18th EPIA Conference on Artificial Intelligence (EPIA'17), LNCS 10423, 657-680
    [ bib ] [ doi:10.1007/978-3-319-65340-2_54 ]

  • A.S. Teixeira, P.T. Monteiro, J.A. Carriço, F.C. Santos, A.P. Francisco (2017)
    Using Spark and GraphX to Parallelize Large-Scale Simulations of Bacterial Populations over Host Contact Networks
    in S. Ibrahim, K.-K. Raymond Choo, Z. Yan, W. Pedrycz (editors)
    Proc. of the International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP'17), LNCS 10393, 591-600
    [ bib ] [ doi:10.1007/978-3-319-65482-9_44 ]

  • P.T. Monteiro, P. Pais, C. Costa, S. Manna, I. Sá-Correia, M.C. Teixeira (2017)
    The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts
    Nucleic Acids Research, 45(D1): D597-D603
    [ bib ] [ doi:10.1093/nar/gkw817 ]

  • P.L. Varela, I. Lynce, V. Manquinho, C. Chaouiya, P.T. Monteiro (2017)
    Stable states of Boolean regulatory networks composed over hexagonal grids
    Electronic Notes in Theoretical Computer Science, to appear
    [ bib ]

  • W. Abou-Jaoudé, P. Traynard, P.T. Monteiro, J. Saez-Rodriguez, T. Helikar, D. Thieffry, C. Chaouiya (2016)
    Logical modeling and dynamical analysis of cellular networks
    Frontiers in Genetics, 7:94
    [ bib ] [ doi:10.3389/fgene.2016.00094 ] († joint first authorship)

  • A.S. Teixeira, P.T. Monteiro, M. Ramirez, J.A. Carriço, A.P. Francisco (2015)
    Not seeing the forest for the trees: Size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis
    PLOS ONE, 10(3): e0119315
    [ bib ] [ doi:10.1371/journal.pone.0119315 ]

  • A. Naldi, P.T. Monteiro, C. Müssel, the Consortium for Logical Models and Tools, H.A. Kestler, D. Thieffry, I. Xenarios, J.Saez-Rodriguez, T. Helikar, C. Chaouiya (2015)
    Cooperative development of logical modelling standards and tools with CoLoMoTo
    Bioinformatics, 31(7): 1154-1159
    [ bib ] [ doi:10.1093/bioinformatics/btv013 ] [ bioRxiv doi:10.1101/010504 ]

  • W. Abou-Jaoudé, P.T. Monteiro, A. Naldi, M. Grandclaudon, V. Soumelis, C. Chaouiya, D. Thieffry (2015)
    Model checking to assess T-helper cell plasticity
    Frontiers in Bioengineering and Biotechnology, 2:86
    [ bib ] [ doi:10.3389/fbioe.2014.00086 ] [ bioRxiv doi:10.1101/012641 ] († joint first authorship)

  • N.D. Mendes, P.T. Monteiro, J. Carneiro, E. Remy, C. Chaouiya (2014)
    Quantification of reachable attractors in asynchronous discrete dynamics
    arXiv
    [ arxiv:1411.3539 ] († joint first authorship)

  • P.T. Monteiro, W. Abou-Jaoudé, D. Thieffry, C. Chaouiya (2014)
    Model Checking Logical Regulatory Networks
    in J.-J. Lesage, J.-M. Faure, J.E.R. Cury and B. Lennartson (editors)
    Proc. of the 12th IFAC - IEEE International Workshop on Discrete Event Systems (WODES'14), 170-175
    [ bib ] [ doi:10.3182/20140514-3-FR-4046.00135 ] [ preprint ]

  • M.C. Teixeira, P.T. Monteiro, J. Guerreiro, J.P. Gonçalves, N.P. Mira, S.C. dos Santos, T.R. Cabrito, M. Palma, C. Costa, A.P. Francisco, S.C. Madeira, A.L. Oliveira, A.T. Freitas, I. Sá-Correia (2014)
    The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae
    Nucleic Acids Research, 42(D1): D161-D166
    [ bib ] [ doi:10.1093/nar/gkt1015 ] († joint first authorship) ISI highly cited paper

  • C. Chaouiya, D. Berenguier, S.M. Keating, A. Naldi, M.P. van Iersel, N. Rodriguez, A. Dräger, F. Büchel, T. Cokelaer, B. Kowal, B. Wicks, E. Gonçalves, J. Dorier, M. Page, P.T. Monteiro, A. von Kamp, I. Xenarios, H. de Jong, M. Hucka, S. Klamt, D. Thieffry, N. Le Novère, J. Saez-Rodriguez, T. Helikar (2013)
    SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
    BMC Systems Biology, 7:135
    [ bib ] [ doi:10.1186/1752-0509-7-135 ] BMC highly accessed paper

  • D. Bérenguier, C. Chaouiya, P.T. Monteiro, A. Naldi, E. Remy, D. Thieffry and L. Tichit (2013)
    Dynamical modeling and analysis of large cellular regulatory networks
    Chaos: An Interdisciplinary Journal of Nonlinear Science, 23(2):025114
    [ bib ] [ doi:10.1063/1.4809783 ] Most cited articles in 2014 from Chaos
    Copyright (2013) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The article may be found at: [ pdf ]

  • 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 (editors)
    Proc. of the 10th Intl. Conf. on Computational Methods in Systems Biology (CMSB'12), LNCS 7605, Springer Verlag, 288-306
    [ bib ] [ doi:10.1007/978-3-642-33636-2_17 ]

  • A.P. Francisco, C. Vaz, P.T. Monteiro, J. Melo-Cristino, M. Ramirez and J.A. Carriço (2012)
    PHYLOViZ: Phylogenetic Inference and Data Visualization for Sequence Based Typing Methods
    BMC Bioinformatics, 13:87
    [ bib ] [ doi:10.1186/1471-2105-13-87 ] BMC highly accessed paper

  • P.T. Monteiro and C. Chaouiya (2012)
    Efficient verification for logical models of regulatory networks
    in M.P. Rocha, N. Luscombe, F. Fdez-Riverola and J.M. Corchado Rodriguez (editors)
    Proc. of the 6th Intl. Conf. on Practical Applications on Computational Biology & Bioinformatics (PACBB'12), AISC 154, Springer Berlin / Heidelberg, 259-267
    [ bib ] [ doi:10.1007/978-3-642-28839-5_30 ] PAAMS'12 Award of Scientific Excellence

  • 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
    [ bib ] [ doi:10.1049/iet-syb.2011.0001 ] [ pdf ]

  • P.J. Dias, C.P. Costa, I. Sá-Correia, M.C. Teixeira, P.T. Monteiro, A.L. Oliveira, A.T. Freitas (2011)
    Using systems biology approaches to study a multidrug resistance network
    Proc. of the 1st Portuguese meeting in Bioengineering (ENBENG'11), 1-4
    [ bib ] [ doi:10.1109/ENBENG.2011.6026073 ]

  • 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
    [ bib ] [ doi:10.1016/j.tcs.2010.05.009 ]

  • D. Abdulrehman, P.T. Monteiro, M.C. Teixeira, N.P. Mira, A.B. Lourenço, S.C. dos Santos, T.R. Cabrito, A.P. Francisco, S.C. Madeira, R.S. Aires, A.L. Oliveira, I. Sá-Correia and A.T. Freitas (2011)
    YEASTRACT: Providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface
    Nucleic Acids Research, 39(suppl 1): D136-D140
    [ bib ] [ doi:10.1093/nar/gkq964 ]

  • 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
    [ bib ] [ 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)
    [ bib ] [ 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
    [ bib ] [ 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 S. Cha, J.-Y. Choi, M. Kim, I. Lee and M. Viswanathan (editors)
    Proc. of the 6th Intl. Symposium on Automated Technology for Verification and Analysis (ATVA'08), LNCS 5311, Springer Verlag, 48-63
    [ bib ] [ doi:10.1007/978-3-540-88387-6_6 ]

  • 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)
    [ bib ] [ doi:10.1093/bioinformatics/btn275 ]

  • P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas and H. de Jong (2008)
    Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks
    in M. Ghallab, C.D. Spyropoulos, N. Fakotakis and N. Avouris (editors)
    Proc. of the 18th European Conference on Artificial Intelligence (ECAI'08), IOS Press, Amsterdam, 229-233
    [ bib ] [ doi:10.3233/978-1-58603-891-5-229 ]

  • P.T. Monteiro, N. Mendes, M.C. Teixeira, S. d'Orey, S. Tenreiro, N.P. Mira, H. Pais, A.P. Francisco, A.M. Carvalho, A. Lourenço, I. Sá-Correia, A.L. Oliveira and A.T. Freitas (2008)
    YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae
    Nucleic Acids Research, 36(Database issue): D132-D136
    [ bib ] [ doi:10.1093/nar/gkm976 ]

  • M.C. Teixeira, P. Monteiro, P. Jain, S. Tenreiro, A.R. Fernandes, N.P. Mira, M. Alenquer, A.T. Freitas, A.L. Oliveira and I. Sá-Correia (2006)
    The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae
    Nucleic Acids Research, 34(Database issue): D446-D451
    [ bib ] [ doi:10.1093/nar/gkj013 ] († joint first authorship) ISI highly cited paper

  • P. Monteiro, M.C. Teixeira, P. Jain, S. Tenreiro, A.R. Fernandes, N. Mira, M. Alenquer, A.T. Freitas, A.L. Oliveira and I. Sá-Correia (2005)
    YEASTRACT: a database of transcription regulatory associations in Saccharomyces cerevisiae
    in F.M. Couto, M.J. Silva and P. Fernandes (editors)
    Proc. of Bioinformatics: Knowledge Discovery in Biology (BKDB'05), Lisbon, Portugal, 34-38
    [ bib ] [ pdf ]

  • M.C. Teixeira, P. Monteiro, P. Jain, S. Tenreiro, A.R. Fernandes, N. Mira, M. Alenquer, A.T. Freitas, A.L. Oliveira and Isabel Sá-Correia (2005)
    A Bioinformática e as Bases de Dados: o exemplo de uma Base de Dados para Análise de Mecanismos de Regulação em Levedura
    Boletim de Biotecnologia, 81: 23-31

  • M.C. Teixeira, P. Monteiro, P. Jain, S. Tenreiro, A.R. Fernandes, N.P. Mira, M. Alenquer, A.T. Freitas, A.L. Oliveira and I. Sá-Correia (2005)
    YEASTRACT: a database to search for transcription regulatory associations in Saccharomyces cerevisiae
    Yeast, 22(S1): S191-S195, 16-1
    [ bib ] [ doi:10.1002/yea.1271 ]

  • J. Graça, M. Mourão, O. Anunciação, P. Monteiro, H.S. Pinto and V. Loureiro (2005)
    Ontology building process: the wine domain
    in 5th Conference of the European Federation for Information Technology in Agriculture, Food and Environment (EFITA/WCCA'05), Vila Real, Portugal
    [ bib ] [ pdf ]

 

Book chapters
  • M.C. Teixeira, P.T. Monteiro, I. Sá-Correia (2016)
    Predicting Gene and Genomic Regulation in Saccharomyces cerevisiae, using the YEASTRACT Database: A Step By Step Guided Analysis
    in F. Devaux (editor)
    Yeast Functional Genomics: Methods and Protocols, 1361: 391-404, Humana Press Inc
    [ bib ] [ doi:10.1007/978-1-4939-3079-1_22 ]

  • G. Batt, B. Besson, P.-E. Ciron, H. de Jong, E. Dumas, J. Geiselmann, R. Monte, P.T. Monteiro, M. Page, F. Rechenmann and D. Ropers (2012)
    Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks
    in J. van Helden, A. Toussaint and D. Thieffry (editors)
    Bacterial molecular networks, 804: 439-462, Humana Press Inc
    [ bib ] [ doi:10.1007/978-1-61779-361-5_22 ]

  • V. Baldazzi, P.T. Monteiro, M. Page, D. Ropers, J. Geiselmann, H. de Jong (2011)
    Qualitative analysis of genetic regulatory networks in bacteria
    in W. Dubitzky, J. Southgate and H. Fuss (editors)
    Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology, 111-130, Springer-Verlag, Berlin
    [ bib ] [ doi:10.1007/978-1-4419-7964-3_6 ]

 

Research reports
  • A. Lemos, P.T. Monteiro, I. Lynce (2016)
    Repairing Boolean regulatory networks using Answer Set Programming
    Technical Report n° 5/2016, INESC-ID, Lisboa, Portugal
    [ bib ]

  • A.S. Teixeira, V. Ribeiro, P.T. Monteiro, J.A. Carriço, M. Ramirez, A.P. Francisco (2014)
    Large scale simulation of bacterial population evolution over host contact networks
    Technical Report n° 17/2014, INESC-ID, Lisboa, Portugal
    [ bib ] [ pdf ]

  • P.T. Monteiro, A.P. Francisco, M. Ramirez, J.A. Carriço (2014)
    Topological representation of the within-species evolutionary structure of bacterial populations: the SLV graph
    Technical Report n° 16/2014, INESC-ID, Lisboa, Portugal
    [ bib ] [ pdf ]

  • G. Batt, M. Page, I. Cantone, G. Goessler, P.T. Monteiro and H. de Jong (2010)
    Efficient parameter search for qualitative models of regulatory networks using symbolic model checking
    Research Report RR-7284, May 2010, INRIA Grenoble - Rhone-Alpes, France
    [ bib ] [ pdf ]

  • R. Mateescu, P.T. Monteiro, E. Dumas and H. de Jong (2008)
    Computation Tree Regular Logic for Genetic Regulatory Networks
    Research Report RR-6521, May 2008, INRIA Grenoble - Rhône-Alpes, France
    [ bib ] [ 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
    Research Report RR-6470, Mar 2008, INRIA Grenoble - Rhône-Alpes, France
    [ bib ] [ pdf ]

  • A. Ramalho and P.T. Monteiro (2003)
    Avaliação de métodos computacionais para a detecção de estruturas em genomas
    Technical Report n° 3/2003, INESC-ID, Lisboa, Portugal
    [ bib ]

 

Workshop Publications - i.e. without a DOI
  • P.L. Varela, I. Lynce, V. Manquinho, C. Chaouiya, P.T. Monteiro (2016)
    SAT-based identification of stable states in composed Boolean regulatory networks
    Working notes of the International Workshop on Static Analysis and Systems Biology (SASB 2016), Edinburgh, UK

  • P.L. Varela, I. Lynce, V. Manquinho, C. Chaouiya, P.T. Monteiro (2016)
    SAT-based identification of stable states in composed Boolean regulatory networks
    Working notes of the 8th INForum - Simpósio de Informática (INForum'16), Lisboa, Portugal

  • W. Abou-Jaoudé, M. Grandclaudon, P.T. Monteiro, A. Naldi, C. Chaouiya, V. Soumelis, D. Thieffry (2014)
    Logical modeling of T-helper cell differentiation and plasticity
    Working notes of the Logical Modelling and Analysis of Cellular Networks Workshop (LMACN-ECCB'14), Strasbourg, France

  • P.L. Varela, N.D. Mendes, P.T. Monteiro, A. Fauré, C. Chaouiya (2013)
    EpiLog: a novel tool for the qualitative modelling of epithelial patterning
    Working notes of the 5th INForum - Simpósio de Informática (INForum'13), Évora, Portugal

  • A.S. Teixeira, P.T. Monteiro, J.A. Carriço, M. Ramirez, A. P. Francisco (2013)
    Spanning edge betweenness
    Working notes of the Mining and Learning with Graphs - Knowledge Discovery and Data Mining (MLG-KDD'13), Chicago, US
    [ pdf ]

  • 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 (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, D. Ropers, R. Mateescu, A.T. Freitas and H. de Jong (2008)
    Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks
    in Elizabeth Bradley, Louise Travé-Massuyès, eds., Working notes of the 22nd International Workshop on Qualitative Reasoning (QR'08), 102-7, Boulder, CO, USA

  • 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
    in Jacques van Helden, Yves Moreau, eds., Working notes of the Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM'08), 71-6, Lille, France

  • A. Ramalho and P. Monteiro (2003)
    PoeTA III - Poetry Teaching Agent III
    Working notes of the Workshop of Introduction to Autonomous Agents (WIAA'03), Lisboa, Portugal

 

Theses
  • Dual PhD Thesis, P.T. Monteiro (2010)
    Towards an integrative approach for the modeling and formal verification of biological regulatory networks
    Instituto Superior Técnico - Technical University of Lisbon, Portugal
    Université Claude Bernard Lyon 1, France
    [ pdf ]

  • MSc Thesis, P.T. Monteiro (2005)
    Sistema de gestão da informação associada à regulação da transcrição da Saccharomyces cerevisiae
    Instituto Superior Técnico - Technical University of Lisbon, Portugal
    [ pdf ]

  • Diploma Thesis, A. Ramalho and P. Monteiro (2003)
    Avaliação de métodos computacionais para a detecção de estruturas em genomas
    Instituto Superior Técnico - Technical University of Lisbon, Portugal

 

Posters and Abstracts
  • C. Chaouiya, L. Calzone, T. Helikar, C. Hernandez, P. Monteiro, A. Naldi, D. Thieffry, D Waltemath (2017)
    Standardisation effort from the Consortium for Logical Models and Tools (CoLoMoTo)
    Poster and oral presentation at COMBINE 2017, Milan, Italy

  • T. Pedreira, P.T. Monteiro, M.C. Teixeira, C. Chaouiya (2017)
    Reconstruction and analysis of the global transcriptional regulatory network in yeast
    Poster at 13th Basel Computational Biology Conference ([BC]2'17), Basel, Switzerland

  • Fueyo S., Monteiro P.T., Naldi A., Dorier J., Remy A., Chaouiya C. (2017)
    Reversed dynamics to uncover basins of attraction of asynchronous logical models
    Poster and oral presentation at ISMB/ECCB, Prague, Czech Republic [F1000Posters]

  • C. Ramos, P.L. Varela, P.T. Monteiro, C. Chaouiya (2016)
    Patterning in proliferating epithelia, a modelling approach
    Poster at 17th International Conference on Systems Biology (ICSB'16), Barcelona, Spain

  • C. Ramos, P.L. Varela, P.T. Monteiro, C. Chaouiya (2016)
    Patterning in proliferating epithelia, a modelling approach
    Poster and oral presentation at 8th INForum - Simpósio de Informática (INForum'16), Lisboa, Portugal

  • A. Lemos, P.T. Monteiro, I. Lynce (2016)
    Repairing Boolean regulatory networks using Answer Set Programming
    Poster and oral presentation at 8th INForum - Simpósio de Informática (INForum'16), Lisboa, Portugal

  • Monteiro P.T., Cury J.E.R., Chaouiya C. (2016)
    On the number and structure of Boolean functions compatible with a regulatory network topology
    Abstract and oral presentation at 10th European Conference on Mathematical and Theoretical Biology (ECMTB), Nottingham, UK

  • Fueyo S., Monteiro P.T., Naldi A., Remy A., Chaouiya C. (2016)
    Reversing Boolean gene regulatory networks
    Abstract and oral presentation at 10th European Conference on Mathematical and Theoretical Biology (ECMTB), Nottingham, UK

  • Teixeira A.S., Monteiro P.T., Francisco A.P., Carriço J.A. (2016)
    Large scale simulation of bacterial populations evolution over host contact networks
    Poster at 8th International Conference on Discrete Models of Complex Systems, Aveiro, Portugal

  • Chaves I., Mendes N.D., Vaz C., Miguel C., Monteiro P.T. (2016)
    Plant Experimental Assay Ontology
    Abstract and oral presentation at Plant Biology Europe EPSO/FESPB, Prague, Czech Republic

  • Dias P.J., Machado A., Zhang K., Blake T., Monteiro P.T., Sá-Correia I. (2015)
    Yeast Drug:H+ antiporters: comparative genomic and phylogenetic analyses and design and implementation of a dedicated database
    Poster at Congress of Microbiology and Biotechnology (MicroBiotec'15), Évora, Portugal

  • W. Abou-Jaoudé, M. Grandclaudon, P.T. Monteiro, A. Naldi, C. Chaouiya, V. Soumelis, D. Thieffry (2015)
    Predicting T-helper cell differentiation and plasticity using logical modelling and model-checking
    Poster at 4th European Congress of Immunology (ECI'15), Vienna, Austria

  • Varela P.L., Fauré A., Chaouiya C., P.T. Monteiro (2015)
    A computational framework for the logical modelling of epithelial patterning
    Presentation and poster at 12th Basel Computational Biology Conference ([BC]2'15), Basel, Switzerland

  • W. Abou-Jaoudé, M. Grandclaudon, P.T. Monteiro, A. Naldi, C. Chaouiya, V. Soumelis, D. Thieffry (2015)
    Logical modeling of T-helper cell differentiation and plasticity
    Poster at 6th Young Researchers in Life Sciences Conference (YRLS'15), Paris, France

  • A. Naldi, P.T. Monteiro, D. Thieffry, C. Chaouiya (2014)
    GINsim: a software tool for the modelling and analysis of logical regulatory networks
    Poster at 13th European Conference on Computational Biology (ECCB'14), Strasbourg, France

  • P.L. Varela, P.T. Monteiro, Nuno Mendes, Adrien Fauré, C. Chaouiya (2014)
    EpiLog, a computational tool for the logical modelling of epithelial pattern formation
    Poster at 13th European Conference on Computational Biology (ECCB'14), Strasbourg, France [F1000Posters]

  • N.D. Mendes, P.T. Monteiro, C. Vaz, I. Chaves (2014)
    Towards a Plant Experimental Assay Ontology
    Poster at 10th International Conference on Data Integration in the Life Sciences (DILS'14), Lisbon, Portugal

  • F. Rebelo, I. Chaves, N.D. Mendes, P.T. Monteiro, J. Borbinha (2014)
    A Repository for Biological Data applied to the Woody Plants Domain
    Poster at 10th International Conference on Data Integration in the Life Sciences (DILS'14), Lisbon, Portugal

  • P.T. Monteiro, M.C. Teixeira, A.P. Francisco, I. Sá-Correia (2014)
    YEASTRACT-NET: extracting and visualizing transcription regulatory networks in S. cerevisiae
    Poster and oral presentation at XX Jornadas de leveduras Professor Nicolau van Uden, Lisbon, Portugal

  • A.S. Teixeira, A.P. Francisco, P.T. Monteiro, R. Oliveira, M. Ramirez, J.A. Carriço (2013)
    NetPopSim - a population simulator for microbial allelic profiles for simulating spread and evolution within social networks
    Poster at 10th International Meeting on Microbial Epidemiological Markers (IMMEM), Paris, France

  • P.L. Varela, N.D. Mendes, P.T. Monteiro, A. Fauré, C. Chaouiya (2013)
    Epilog: a software for the logical modelling of epithelial patterning
    Poster at Bioinformatic Open Days'13, Braga, Portugal

  • A.P. Francisco, C. Vaz, P.T. Monteiro, M. Ramirez, J. Carriço (2011)
    Fooled by trees: when simple can be misleading
    Poster at Congresso Nacional MicroBiotec'11, Braga, Portugal

  • P.J. Dias, P.T. Monteiro, A.L. Oliveira, A.T. Freitas, I. Sá-Correia, M.C. Teixeira (2011)
    Insights into the transcription regulatory network controlling the multidrug resistance gene FLR1: a systems biology approach
    Poster at 25th International Conference on Yeast Genetics and Molecular Biology, Olsztyn-Kortowo, Poland

  • P.T. Monteiro, A.T. Freitas, D. Ropers, R. Mateescu, H. de Jong (2010)
    Modeling and formal verification of biological regulatory networks: an integrative approach
    Poster at IEEE International Conference on Bioinformatics & Biomedicine (BIBM'10), Hong Kong, China

  • P.T. Monteiro, P.J. Dias, D. Ropers, A.L. Oliveira, I. Sá-Correia, M.C. Teixeira, A.T. Freitas (2010)
    Computational modeling and analysis of the yeast FLR1 regulatory network in mancozeb-challenged cells
    Poster at 11th International Conference on Systems Biology (ICSB'10), Edinburgh, Scotland, UK

  • G. Batt, M. Page, P. Monteiro, G. Goessler, Hidde de Jong (2010)
    Design of synthetic gene networks: symbolic model checking of PADE models
    Poster at Systems Biology of Microorganisms'10, Paris, France

  • P.T. Monteiro, P.J. Dias, D. Ropers, A.L. Oliveira, A.T. Freitas, I. Sá-Correia, M.C. Teixeira (2009)
    The regulatory network underlying the transcriptional up-regulation of the FLR1 gene in mancozeb stressed yeast cells: qualitative modeling and simulation
    Abstract at Congresso Nacional MicroBiotec'09, Vilamoura, Portugal

  • P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas, H. de Jong (2008)
    Temporal logic patterns for querying dynamic models of cellular interaction networks
    Poster at Forum Português de Biologia Computacional (FPBC'08), Oeiras, Portugal

  • M.C. Teixeira, P.T. Monteiro, N.P. Mira, P.M. Santos, A.T. Freitas, A.L. Oliveira, I. Sá-Correia (2008)
    The YEASTRACT database and its exploitation in Toxicogenomics: the Yeast response to the herbicide 2,4-D
    Poster at Forum Português de Biologia Computacional (FPBC'08), Oeiras, Portugal

  • M.C. Teixeira, P. Monteiro, S. Tenreiro, N.P. Mira, A.B. Lourenço, A.M. Carvalho, N. Mendes, S. d'Orey, H. Pais, A.T. Freitas, A.L. Oliveira and Isabel Sá-Correia (2007)
    Analysis of transcription regulatory associations in Saccharomyces cerevisiae using the YEASTRACT database
    Extended abstract at 3rd Conference on Physiology of Yeasts and Filamentous Fungi, S245: 52, Helsinki, Finland [pdf]

  • P. Monteiro, N. Mendes, M.C. Teixeira, S. d'Orey, S. Tenreiro, N.P. Mira, H. Pais, A.P. Francisco, A.M. Carvalho, A.B. Lourenço, I. Sá-Correia, A.L. Oliveira and A.T. Freitas (2007)
    Analysis of new and known DNA-binding site motifs in Saccharomyces cerevisiae using the YEASTRACT-DISCOVERER tools
    Poster and Extended abstract at Congresso Nacional MicroBiotec'07, Lisboa, Portugal
    Sartorius award - Inovation in Microbiology/Biotechnology

  • M.C. Teixeira, P. Monteiro, S. Tenreiro, N. Mira, A.M. Carvalho, N. Mendes, A. Casimiro, C. Nogueira, C. Oliveira, A.T. Freitas, A.L. Oliveira and I. Sá-Correia (2006)
    Analysis of transcription regulatory associations in Saccharomyces cerevisiae using the YEASTRACT database
    Poster at Yeast Genetics and Molecular Biology Meeting, Book of Abstracts 529A, Princeton, USA [www]

  • M.C. Teixeira, P. Monteiro, S. Tenreiro, N.P. Mira, A.M. Carvalho, N. Mendes, A. Casimiro, C. Nogueira, C. Oliveira, A.T. Freitas, A.L. Oliveira and I. Sá-Correia (2006)
    Analysis of transcription regulatory associations in Saccharomyces cerevisiae using the YEASTRACT database
    Poster at 2nd FEMS Congress of European Microbiologists, Book of Abstracts W12.4-P.COM.3, Madrid, Spain

  • M.C. Teixeira, P. Monteiro, N.P. Mira, S. Tenreiro, A.T. Freitas, A.L. Oliveira and Isabel Sá-Correia (2006)
    The YEASTRACT database: application to the analysis of Saccharomyces cerevisiae genome-wide expression data
    Extended abstract at XVth National Congress of Biochemistry, 1(SA1): 30, Aveiro, Portugal

  • M.C. Teixeira, P. Monteiro, P. Jain, S. Tenreiro, A.R. Fernandes, N.P. Mira, M. Alenquer, A.B. Lourenço, A.T. Freitas, A.L. Oliveira and I. Sá-Correia (2005)
    The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae
    Poster at Congresso Nacional MicroBiotec'05, Book of Abstracts OC28, Póvoa do Varzim, Portugal

  • P. Monteiro, A. Ramalho, A.T. Freitas and A.L. Oliveira (2005)
    DECIDE: A Gene Finding Evaluation Tool
    Poster at Bioinformatics: Knowledge Discovery in Biology BKDB'05