The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. - Miguel C. Teixeira; Pedro T. Monteiro 001; 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)

Computation Tree Regular Logic for Genetic Regulatory Networks. - Radu Mateescu 001; Pedro T. Monteiro 001; Estelle Dumas; Hidde de Jong (ATVA, 2008)

Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks. - Pedro T. Monteiro 001; Delphine Ropers; Radu Mateescu 001; Ana T. Freitas; Hidde de Jong (ECAI, 2008)

Temporal logic patterns for querying dynamic models of cellular interaction networks. - Pedro T. Monteiro 001; Delphine Ropers; Radu Mateescu 001; Ana T. Freitas; Hidde de Jong (ECCB, 2008)

YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. - Pedro T. Monteiro 001; 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; et al. (Nucleic Acids Res., 2008)

A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks. - Pedro T. Monteiro 001; Estelle Dumas; Bruno Besson; Radu Mateescu 001; Michel Page; Ana T. Freitas; Hidde de Jong (BMC Bioinform., 2009)

Modeling and formal verification of biological regulatory networks: An integrative approach. - Pedro T. Monteiro 001; Ana T. Freitas; Delphine Ropers; Radu Mateescu 001; Hidde de Jong (BIBM Workshops, 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 001; Hidde de Jong (Bioinform., 2010)

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. - Dário Abdulrehman; Pedro T. Monteiro 001; 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; et al. (Nucleic Acids Res., 2011)

CTRL: Extension of CTL with regular expressions and fairness operators to verify genetic regulatory networks. - Radu Mateescu 001; Pedro T. Monteiro 001; Estelle Dumas; Hidde de Jong (Theor. Comput. Sci., 2011)

Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control. - Aurélien Naldi; Pedro T. Monteiro 001; Claudine Chaouiya (CMSB, 2012)

Efficient Verification for Logical Models of Regulatory Networks. - Pedro T. Monteiro 001; Claudine Chaouiya (PACBB, 2012)

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. - Alexandre P. Francisco; Cátia Vaz; Pedro T. Monteiro 001; José Melo-Cristino; Mário Ramirez; João A. Carriço (BMC Bioinform., 2012)

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 001; Andreas Dräger; Finja Büchel; Thomas Cokelaer; Bryan M. Kowal; Benjamin Wicks; Emanuel J. V. Gonçalves; et al. (BMC Syst. Biol., 2013)

Model Checking Logical Regulatory Networks. - Pedro T. Monteiro 001; Wassim Abou-Jaoudé; Denis Thieffry; Claudine Chaouiya (WODES, 2014)

Quantification of reachable attractors in asynchronous discrete dynamics. - Nuno D. Mendes; Pedro T. Monteiro 001; Jorge Carneiro; Elisabeth Remy; Claudine Chaouiya (CoRR, 2014)

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. - Miguel Cacho Teixeira; Pedro Tiago Monteiro 001; 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; et al. (Nucleic Acids Res., 2014)

Cooperative development of logical modelling standards and tools with CoLoMoTo. - Aurélien Naldi; Pedro T. Monteiro 001; Christoph Müssel; Hans A. Kestler; Denis Thieffry; Ioannis Xenarios; Julio Saez-Rodriguez; Tomás Helikar; Claudine Chaouiya (Bioinform., 2015)

Logic-Based Encodings for Ricochet Robots. - Filipe Gouveia; Pedro T. Monteiro 001; Vasco Manquinho; Inês Lynce (EPIA, 2017)

Using Spark and GraphX to Parallelize Large-Scale Simulations of Bacterial Populations over Host Contact Networks. - Andreia Sofia Teixeira; Pedro T. Monteiro 001; João A. Carriço; Francisco C. Santos; Alexandre P. Francisco (ICA3PP, 2017)

The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts. - Pedro Tiago Monteiro 001; Pedro Pais; Catarina Costa; Sauvagya Manna; Isabel Sá-Correia; Miguel Cacho Teixeira (Nucleic Acids Res., 2017)

Model Revision of Logical Regulatory Networks Using Logic-Based Tools. - Filipe Gouveia; Inês Lynce; Pedro T. Monteiro 001 (ICLP (Technical Communications), 2018)

Stable States of Boolean Regulatory Networks Composed Over Hexagonal Grids. - Pedro L. Varela; Inês Lynce; Vasco Manquinho; Claudine Chaouiya; Pedro T. Monteiro 001 (SASB, 2018)

EpiLog: A software for the logical modelling of epithelial dynamics. - Pedro L. Varela; Camila V. Ramos; Pedro T. Monteiro 001; Claudine Chaouiya (F1000Research, 2018)

Large-Scale Simulations of Bacterial Populations Over Complex Networks. - Andreia Sofia Teixeira; Pedro T. Monteiro 001; João A. Carriço; Francisco C. Santos; Alexandre P. Francisco (J. Comput. Biol., 2018)

YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae. - Miguel C. Teixeira; Pedro T. Monteiro 001; Margarida Palma; Catarina Costa; Cláudia P. Godinho; Pedro Pais; Mafalda Cavalheiro; Miguel Antunes; Alexandre Lemos; Tiago Pedreira; Isabel Sá-Correia (Nucleic Acids Res., 2018)

Model Revision of Boolean Regulatory Networks at Stable State. - Filipe Gouveia; Inês Lynce; Pedro T. Monteiro 001 (ISBRA, 2019)

Repairing Boolean logical models from time-series data using Answer Set Programming. - Alexandre Lemos; Inês Lynce; Pedro T. Monteiro 001 (Algorithms Mol. Biol., 2019)

Partial Order on the set of Boolean Regulatory Functions. - José E. R. Cury; Pedro T. Monteiro 001; Claudine Chaouiya (CoRR, 2019)

ModRev - Model Revision Tool for Boolean Logical Models of Biological Regulatory Networks. - Filipe Gouveia; Inês Lynce; Pedro T. Monteiro 001 (CMSB, 2020)

Minimal Perturbation in University Timetabling with Maximum Satisfiability. - Alexandre Lemos; Pedro T. Monteiro 001; Inês Lynce (CPAIOR, 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 001; Mukesh Kumar Gupta (Comput. Methods Programs Biomed., 2020)

Revision of Boolean Models of Regulatory Networks Using Stable State Observations. - Filipe Gouveia; Inês Lynce; Pedro T. Monteiro 001 (J. Comput. Biol., 2020)

YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts. - Pedro T. Monteiro 001; 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; et al. (Nucleic Acids Res., 2020)

Prediction and Boolean logical modelling of synergistic microRNA regulatory networks during reprogramming of male germline pluripotent stem cells. - Praveen Kumar Guttula; Pedro T. Monteiro 001; Mukesh Kumar Gupta (Biosyst., 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 001 (BMC Bioinform., 2021)

Disruptions in timetables: a case study at Universidade de Lisboa. - Alexandre Lemos; Pedro T. Monteiro 001; Inês Lynce (J. Sched., 2021)

Functional Characterization of Transcriptional Regulatory Networks of Yeast Species. - Paulo Dias; Pedro T. Monteiro 001; Andreia Sofia Teixeira (NetSci-X, 2022)

Introducing UniCorT: an iterative university course timetabling tool with MaxSAT. - Alexandre Lemos; Pedro T. Monteiro 001; Inês Lynce (J. Sched., 2022)

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; et al. (Nucleic Acids Res., 2023)

Logical Modelling, Some Recent Methodological Advances Illustrated. - Claudine Chaouiya; Pedro T. Monteiro 001; Elisabeth Remy (AUTOMATA, 2024)

Context-Aware Deep Forecasting: Principles for the Nation-Wide Management of Blood Products. - Miguel Dauphinet; Rui Henriques; Pedro T. Monteiro 001 (EPIA (3), 2024)

Immediate Neighbours of Monotone Boolean Functions. - José E. R. Cury; Patrícia Tenera Roxo; Vasco Manquinho; Claudine Chaouiya; Pedro T. Monteiro 001 (CoRR, 2024)

Iterative Train Scheduling under Disruption with Maximum Satisfiability. - Alexandre Lemos; Filipe Gouveia; Pedro T. Monteiro 001; Inês Lynce (J. Artif. Intell. Res., 2024)

Computation of Immediate Neighbours of Monotone Boolean Functions. - José E. R. Cury; Patrícia Tenera Roxo; Vasco Manquinho; Claudine Chaouiya; Pedro T. Monteiro 001 (CMSB, 2025)