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Pedro T. Monteiro 0001

Pedro Tiago Monteiro 0001

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affiliation: University of Lisbon, Instituto Superior Técnico, Portugal
affiliation: INESC-ID, Lisbon, Portugal

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2020 – today

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2024
[j23]
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Alexandre Lemos, Filipe Gouveia, Pedro T. Monteiro, Inês Lynce:
Iterative Train Scheduling under Disruption with Maximum Satisfiability. J. Artif. Intell. Res. 79: 1047-1090 (2024)
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Claudine Chaouiya, Pedro T. Monteiro, Elisabeth Remy:
Logical Modelling, Some Recent Methodological Advances Illustrated. AUTOMATA 2024: 3-22
[c16]
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Miguel Dauphinet, Rui Henriques, Pedro T. Monteiro:
Context-Aware Deep Forecasting: Principles for the Nation-Wide Management of Blood Products. EPIA (3) 2024: 359-372
[i4]
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  - journals/corr/abs-2407-01337
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José E. R. Cury, Patrícia Tenera Roxo, Vasco Manquinho, Claudine Chaouiya, Pedro T. Monteiro:
Immediate Neighbours of Monotone Boolean Functions. CoRR abs/2407.01337 (2024)
2023
[j22]
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Miguel Cacho Teixeira, Romeu Viana, Margarida Palma, Jorge Oliveira, Mónica Galocha, Marta Neves Mota, Diogo Couceiro, Maria Galhardas Pereira, Miguel Antunes, Inês V. Costa, Pedro Pais, Carolina Parada, Claudine Chaouiya, Isabel Sá-Correia, Pedro Tiago Monteiro:
YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis. Nucleic Acids Res. 51(D1): 785-791 (2023)
2022
[j21]
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Alexandre Lemos, Pedro T. Monteiro, Inês Lynce:
Introducing UniCorT: an iterative university course timetabling tool with MaxSAT. J. Sched. 25(4): 371-390 (2022)
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Paulo Dias, Pedro T. Monteiro, Andreia Sofia Teixeira:
Functional Characterization of Transcriptional Regulatory Networks of Yeast Species. NetSci-X 2022: 140-154
2021
[j20]
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Praveen Kumar Guttula, Pedro T. Monteiro, Mukesh Kumar Gupta:
Prediction and Boolean logical modelling of synergistic microRNA regulatory networks during reprogramming of male germline pluripotent stem cells. Biosyst. 207: 104453 (2021)
[j19]
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Jorge Oliveira, Miguel Antunes, Cláudia P. Godinho, Miguel C. Teixeira, Isabel Sá-Correia, Pedro T. Monteiro:
From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon. BMC Bioinform. 22(1): 399 (2021)
[j18]
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Alexandre Lemos, Pedro T. Monteiro, Inês Lynce:
Disruptions in timetables: a case study at Universidade de Lisboa. J. Sched. 24(1): 35-48 (2021)
2020
[j17]
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Praveen Kumar Guttula, Pedro T. Monteiro, Mukesh Kumar Gupta:
A Boolean Logical model for Reprogramming of Testes-derived male Germline Stem Cells into Germline pluripotent stem cells. Comput. Methods Programs Biomed. 192: 105473 (2020)
[j16]
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Filipe Gouveia, Inês Lynce, Pedro T. Monteiro:
Revision of Boolean Models of Regulatory Networks Using Stable State Observations. J. Comput. Biol. 27(2): 144-155 (2020)
[j15]
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Pedro T. Monteiro, Jorge Oliveira, Pedro Pais, Miguel Antunes, Margarida Palma, Mafalda Cavalheiro, Mónica Galocha, Cláudia P. Godinho, Luís C. Martins, Nuno Bourbon, Marta Neves Mota, Ricardo A. Ribeiro, Romeu Viana, Isabel Sá-Correia, Miguel C. Teixeira:
YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts. Nucleic Acids Res. 48(Database-Issue): D642-D649 (2020)
[c14]
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Filipe Gouveia, Inês Lynce, Pedro T. Monteiro:
ModRev - Model Revision Tool for Boolean Logical Models of Biological Regulatory Networks. CMSB 2020: 339-348
[c13]
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Alexandre Lemos, Pedro T. Monteiro, Inês Lynce:
Minimal Perturbation in University Timetabling with Maximum Satisfiability. CPAIOR 2020: 317-333

2010 – 2019

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2019
[j14]
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Alexandre Lemos, Inês Lynce, Pedro T. Monteiro:
Repairing Boolean logical models from time-series data using Answer Set Programming. Algorithms Mol. Biol. 14(1): 9:1-9:16 (2019)
[c12]
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Filipe Gouveia, Inês Lynce, Pedro T. Monteiro:
Model Revision of Boolean Regulatory Networks at Stable State. ISBRA 2019: 100-112
[i3]
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José E. R. Cury, Pedro T. Monteiro, Claudine Chaouiya:
Partial Order on the set of Boolean Regulatory Functions. CoRR abs/1901.07623 (2019)
2018
[j13]
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Andreia Sofia Teixeira, Pedro T. Monteiro, João A. Carriço, Francisco C. Santos, Alexandre P. Francisco:
Large-Scale Simulations of Bacterial Populations Over Complex Networks. J. Comput. Biol. 25(8): 850-861 (2018)
[j12]
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Miguel C. Teixeira, Pedro T. Monteiro, Margarida Palma, Catarina Costa, Cláudia P. Godinho, Pedro Pais, Mafalda Cavalheiro, Miguel Antunes, Alexandre Lemos, Tiago Pedreira, Isabel Sá-Correia:
YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae. Nucleic Acids Res. 46(Database-Issue): D348-D353 (2018)
[c11]
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Filipe Gouveia, Inês Lynce, Pedro T. Monteiro:
Model Revision of Logical Regulatory Networks Using Logic-Based Tools. ICLP (Technical Communications) 2018: 23:1-23:10
[c10]
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  - journals/entcs/VarelaLMCM18
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Pedro L. Varela, Inês Lynce, Vasco Manquinho, Claudine Chaouiya, Pedro T. Monteiro:
Stable States of Boolean Regulatory Networks Composed Over Hexagonal Grids. SASB 2018: 113-130
[i2]
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Pedro L. Varela, Camila V. Ramos, Pedro T. Monteiro, Claudine Chaouiya:
EpiLog: A software for the logical modelling of epithelial dynamics. F1000Research 7: 1145 (2018)
2017
[j11]
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Pedro Tiago Monteiro, Pedro Pais, Catarina Costa, Sauvagya Manna, Isabel Sá-Correia, Miguel Cacho Teixeira:
The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts. Nucleic Acids Res. 45(Database-Issue): D597-D603 (2017)
[c9]
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Filipe Gouveia, Pedro T. Monteiro, Vasco Manquinho, Inês Lynce:
Logic-Based Encodings for Ricochet Robots. EPIA 2017: 657-669
[c8]
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Andreia Sofia Teixeira, Pedro T. Monteiro, João A. Carriço, Francisco C. Santos, Alexandre P. Francisco:
Using Spark and GraphX to Parallelize Large-Scale Simulations of Bacterial Populations over Host Contact Networks. ICA3PP 2017: 591-600
2015
[j10]
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Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomás Helikar, Claudine Chaouiya:
Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinform. 31(7): 1154-1159 (2015)
2014
[j9]
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Miguel Cacho Teixeira, Pedro Tiago Monteiro, Joana Fernandes Guerreiro, Joana Pinho Gonçalves, Nuno Pereira Mira, Sandra Costa dos Santos, Tânia Rodrigues Cabrito, Margarida Palma, Catarina Costa, Alexandre Paulo Francisco, Sara Cordeiro Madeira, Arlindo Limede Oliveira, Ana Teresa Freitas, Isabel Sá-Correia:
The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic Acids Res. 42(Database-Issue): 161-166 (2014)
[c7]
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Pedro T. Monteiro, Wassim Abou-Jaoudé, Denis Thieffry, Claudine Chaouiya:
Model Checking Logical Regulatory Networks. WODES 2014: 170-175
[i1]
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Nuno D. Mendes, Pedro T. Monteiro, Jorge Carneiro, Elisabeth Remy, Claudine Chaouiya:
Quantification of reachable attractors in asynchronous discrete dynamics. CoRR abs/1411.3539 (2014)
2013
[j8]
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Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan M. Kowal, Benjamin Wicks, Emanuel J. V. Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomás Helikar:
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol. 7: 135 (2013)
2012
[j7]
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Alexandre P. Francisco, Cátia Vaz, Pedro T. Monteiro, José Melo-Cristino, Mário Ramirez, João A. Carriço:
PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. BMC Bioinform. 13: 87 (2012)
[c6]
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Aurélien Naldi, Pedro T. Monteiro, Claudine Chaouiya:
Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control. CMSB 2012: 288-306
[c5]
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Pedro T. Monteiro, Claudine Chaouiya:
Efficient Verification for Logical Models of Regulatory Networks. PACBB 2012: 259-267
2011
[j6]
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  - journals/nar/AbdulrehmanMTMLSCFMAOSF11
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Dário Abdulrehman, Pedro T. Monteiro, Miguel C. Teixeira, Nuno P. Mira, Artur B. Lourenço, Sandra Costa dos Santos, Tânia Rodrigues Cabrito, Alexandre P. Francisco, Sara C. Madeira, Ricardo Santos Aires, Arlindo L. Oliveira, Isabel Sá-Correia, Ana T. Freitas:
YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. Nucleic Acids Res. 39(Database-Issue): 136-140 (2011)
[j5]
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Radu Mateescu, Pedro T. Monteiro, Estelle Dumas, Hidde de Jong:
CTRL: Extension of CTL with regular expressions and fairness operators to verify genetic regulatory networks. Theor. Comput. Sci. 412(26): 2854-2883 (2011)
2010
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Grégory Batt, Michel Page, Irene Cantone, Gregor Goessler, Pedro T. Monteiro, Hidde de Jong:
Efficient parameter search for qualitative models of regulatory networks using symbolic model checking. Bioinform. 26(18) (2010)
[c4]
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Pedro T. Monteiro, Ana T. Freitas, Delphine Ropers, Radu Mateescu, Hidde de Jong:
Modeling and formal verification of biological regulatory networks: An integrative approach. BIBM Workshops 2010: 812-813

2000 – 2009

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2009
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Pedro T. Monteiro, Estelle Dumas, Bruno Besson, Radu Mateescu, Michel Page, Ana T. Freitas, Hidde de Jong:
A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks. BMC Bioinform. 10: 450 (2009)
2008
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Pedro T. Monteiro, Nuno D. Mendes, Miguel C. Teixeira, Sofia d'Orey, Sandra Tenreiro, Nuno P. Mira, Hélio Pais, Alexandre P. Francisco, Alexandra M. Carvalho, Artur B. Lourenço, Isabel Sá-Correia, Arlindo L. Oliveira, Ana T. Freitas:
YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res. 36(Database-Issue): 132-136 (2008)
[c3]
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Radu Mateescu, Pedro T. Monteiro, Estelle Dumas, Hidde de Jong:
Computation Tree Regular Logic for Genetic Regulatory Networks. ATVA 2008: 48-63
[c2]
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Pedro T. Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas, Hidde de Jong:
Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks. ECAI 2008: 229-233
[c1]
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Pedro T. Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas, Hidde de Jong:
Temporal logic patterns for querying dynamic models of cellular interaction networks. ECCB 2008: 227-233
2006
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Miguel C. Teixeira, Pedro T. Monteiro, Pooja Jain, Sandra Tenreiro, Alexandra R. Fernandes, Nuno P. Mira, Marta Alenquer, Ana T. Freitas, Arlindo L. Oliveira, Isabel Sá-Correia:
The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res. 34(Database-Issue): 446-451 (2006)

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