Pedro T. Monteiro

According to our database, Pedro T. Monteiro authored at least 41 papers between 2006 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Iterative Train Scheduling under Disruption with Maximum Satisfiability.

Alexandre Lemos, Filipe Gouveia, Pedro T. Monteiro, Inês Lynce

J. Artif. Intell. Res., 2024

2023

YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis.

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

Nucleic Acids Res., January, 2023

2022

Introducing UniCorT: an iterative university course timetabling tool with MaxSAT.

Alexandre Lemos, Pedro T. Monteiro, Inês Lynce

J. Sched., 2022

Functional Characterization of Transcriptional Regulatory Networks of Yeast Species.

Paulo Dias, Pedro T. Monteiro, Andreia Sofia Teixeira

Proceedings of the Network Science - 7th International Winter Conference, 2022

2021

Disruptions in timetables: a case study at Universidade de Lisboa.

Alexandre Lemos, Pedro T. Monteiro, Inês Lynce

J. Sched., 2021

From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon.

Jorge Oliveira, Miguel Antunes, Cláudia P. Godinho, Miguel C. Teixeira, Isabel Sá-Correia, Pedro T. Monteiro

BMC Bioinform., 2021

Prediction and Boolean logical modelling of synergistic microRNA regulatory networks during reprogramming of male germline pluripotent stem cells.

Praveen Kumar Guttula, Pedro T. Monteiro, Mukesh Kumar Gupta

Biosyst., 2021

2020

YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts.

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

Nucleic Acids Res., 2020

Revision of Boolean Models of Regulatory Networks Using Stable State Observations.

Filipe Gouveia, Inês Lynce, Pedro T. Monteiro

J. Comput. Biol., 2020

A Boolean Logical model for Reprogramming of Testes-derived male Germline Stem Cells into Germline pluripotent stem cells.

Praveen Kumar Guttula, Pedro T. Monteiro, Mukesh Kumar Gupta

Comput. Methods Programs Biomed., 2020

Minimal Perturbation in University Timetabling with Maximum Satisfiability.

Alexandre Lemos, Pedro T. Monteiro, Inês Lynce

Proceedings of the Integration of Constraint Programming, Artificial Intelligence, and Operations Research, 2020

ModRev - Model Revision Tool for Boolean Logical Models of Biological Regulatory Networks.

Filipe Gouveia, Inês Lynce, Pedro T. Monteiro

Proceedings of the Computational Methods in Systems Biology, 2020

2019

Partial Order on the set of Boolean Regulatory Functions.

José E. R. Cury, Pedro T. Monteiro, Claudine Chaouiya

CoRR, 2019

Repairing Boolean logical models from time-series data using Answer Set Programming.

Alexandre Lemos, Inês Lynce, Pedro T. Monteiro

Algorithms Mol. Biol., 2019

Model Revision of Boolean Regulatory Networks at Stable State.

Filipe Gouveia, Inês Lynce, Pedro T. Monteiro

Proceedings of the Bioinformatics Research and Applications - 15th International Symposium, 2019

2018

YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae.

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

Nucleic Acids Res., 2018

Large-Scale Simulations of Bacterial Populations Over Complex Networks.

Andreia Sofia Teixeira, Pedro T. Monteiro, João A. Carriço, Francisco C. Santos, Alexandre P. Francisco

J. Comput. Biol., 2018

EpiLog: A software for the logical modelling of epithelial dynamics.

Pedro L. Varela, Camila V. Ramos, Pedro T. Monteiro, Claudine Chaouiya

F1000Research, 2018

Stable States of Boolean Regulatory Networks Composed Over Hexagonal Grids.

Pedro L. Varela, Inês Lynce, Vasco M. Manquinho, Claudine Chaouiya, Pedro T. Monteiro

Proceedings of SASB 2018, 2018

Model Revision of Logical Regulatory Networks Using Logic-Based Tools.

Filipe Gouveia, Inês Lynce, Pedro T. Monteiro

Proceedings of the Technical Communications of the 34th International Conference on Logic Programming, 2018

2017

The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts.

Pedro Tiago Monteiro, Pedro Pais, Catarina Costa, Sauvagya Manna, Isabel Sá-Correia, Miguel Cacho Teixeira

Nucleic Acids Res., 2017

Using Spark and GraphX to Parallelize Large-Scale Simulations of Bacterial Populations over Host Contact Networks.

Andreia Sofia Teixeira, Pedro T. Monteiro, João A. Carriço, Francisco C. Santos, Alexandre P. Francisco

Proceedings of the Algorithms and Architectures for Parallel Processing, 2017

Logic-Based Encodings for Ricochet Robots.

Filipe Gouveia, Pedro T. Monteiro, Vasco M. Manquinho, Inês Lynce

Proceedings of the Progress in Artificial Intelligence, 2017

2015

Cooperative development of logical modelling standards and tools with CoLoMoTo.

Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomás Helikar, Claudine Chaouiya

Bioinform., 2015

2014

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in <i>Saccharomyces cerevisiae</i>.

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

Nucleic Acids Res., 2014

Quantification of reachable attractors in asynchronous discrete dynamics.

Nuno D. Mendes, Pedro T. Monteiro, Jorge Carneiro, Elisabeth Remy, Claudine Chaouiya

CoRR, 2014

Model Checking Logical Regulatory Networks.

Pedro T. Monteiro, Wassim Abou-Jaoudé, Denis Thieffry, Claudine Chaouiya

Proceedings of the 12th International Workshop on Discrete Event Systems, 2014

2013

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.

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

BMC Syst. Biol., 2013

2012

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods.

Alexandre P. Francisco, Cátia Vaz, Pedro T. Monteiro, José Melo-Cristino, Mário Ramirez, João A. Carriço

BMC Bioinform., 2012

Efficient Verification for Logical Models of Regulatory Networks.

Pedro T. Monteiro, Claudine Chaouiya

Proceedings of the 6th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2012

Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control.

Aurélien Naldi, Pedro T. Monteiro, Claudine Chaouiya

Proceedings of the Computational Methods in Systems Biology, 2012

2011

CTRL: Extension of CTL with regular expressions and fairness operators to verify genetic regulatory networks.

Radu Mateescu, Pedro T. Monteiro, Estelle Dumas, Hidde de Jong

Theor. Comput. Sci., 2011

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in <i>Saccharomyces cerevisiae</i> through a web services interface.

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

Nucleic Acids Res., 2011

2010

Efficient parameter search for qualitative models of regulatory networks using symbolic model checking.

Grégory Batt, Michel Page, Irene Cantone, Gregor Goessler, Pedro T. Monteiro, Hidde de Jong

Bioinform., 2010

Modeling and formal verification of biological regulatory networks: An integrative approach.

Pedro T. Monteiro, Ana T. Freitas, Delphine Ropers, Radu Mateescu, Hidde de Jong

Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2010

2009

A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks.

Pedro T. Monteiro, Estelle Dumas, Bruno Besson, Radu Mateescu, Michel Page, Ana T. Freitas, Hidde de Jong

BMC Bioinform., 2009

2008

YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in <i>Saccharomyces cerevisiae</i>.

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

Nucleic Acids Res., 2008

Temporal logic patterns for querying dynamic models of cellular interaction networks.

Pedro T. Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas, Hidde de Jong

Proceedings of the ECCB'08 Proceedings, 2008

Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks.

Pedro T. Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas, Hidde de Jong

Proceedings of the ECAI 2008, 2008

Computation Tree Regular Logic for Genetic Regulatory Networks.

Radu Mateescu, Pedro T. Monteiro, Estelle Dumas, Hidde de Jong

Proceedings of the Automated Technology for Verification and Analysis, 2008

2006

The YEASTRACT database: a tool for the analysis of transcription regulatory associations in <i>Saccharomyces cerevisiae</i>.

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

Nucleic Acids Res., 2006