Publications

Articles

International Journal Articles: 8

2018

- Pedro Varela and Camila Ramos and Pedro T. Monteiro and Claudine Chaouiya, EpiLog: A software for the logical modelling of epithelial dynamics, article in F1000Research vol. 7 pp. 1145, Jul. 2018, F1000 Research, Ltd. [DOI Article link] [bibTex]
- Nuno D. Mendes and Rui Miguel Carrasqueiro Henriques and Elisabeth Remy and Jorge Carneiro and Pedro T. Monteiro and Claudine Chaouiya, Estimating attractor reachability in asynchronous logical models, article in Frontiers in Physiology vol. 9 pp. 1161, Jul. 2018 [DOI Article link] [bibTex]
- Aurélien Naldi and Celine Hernandez and Wassim Abou-Jaoudé and Pedro T. Monteiro and Claudine Chaouiya and Denis Thieffry, Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0, article in Frontiers in Physiology vol. 9 pp. 646, Jun. 2018 [DOI Article link] [bibTex]
- Aurélien Naldi and Celine Hernandez and Nicolas Levy and Gautier Stoll and Pedro T. Monteiro and Claudine Chaouiya and Tomas Helikar and Andrei Zinovyev and Laurence Calzone and Sarah Cohen-Boulakia and Denis Thieffry and Loïc Paulevé, The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks, article in Frontiers in Physiology vol. 9 pp. 680, Jun. 2018 [DOI Article link] [bibTex]
- Andreia Teixeira and Pedro T. Monteiro and João A. Carriço and Francisco C. Santos and A. P. Francisco, Large-Scale Simulations of Bacterial Populations over Complex Networks, article in Journal of Computational Biology, May. 2018 [bibTex]
- Pedro Varela and Inês Lynce and Vasco Manquinho and Claudine Chaouiya and Pedro T. Monteiro, Stable states of Boolean regulatory networks composed over hexagonal grids, article in Electronic Notes in Theoretical Computer Science vol. 335 pp. 113-130, Apr. 2018 [DOI Article link] [bibTex]
- Miguel C. Teixeira and Pedro T. Monteiro and Margarida Palma and Catarina Costa and Claudia P. Godinho and Pedro Pais and Mafalda Cavalheiro and Miguel Antunes and Alexandre Lemos and Tiago Godinho de Ornelas Pedreira and Isabel Sá-Correia, YEASTRACT, an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae, article in Nucleic Acids Research vol. 46 pp. D348-D353, Jan. 2018, Oxford University Press [DOI Article link] [bibTex]

2017

- Pedro T. Monteiro and Pedro Pais and Catarina Costa and Sauvagya Manna and Isabel Sá-Correia and Miguel C. Teixeira, The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts, article in Nucleic Acids Research vol. 45 pp. D597-D603, Jan. 2017, Oxford University Press [DOI Article link] [bibTex]

International Conferences: 4

2018

- Filipe Gouveia and Inês Lynce and Pedro T. Monteiro, Model Revision of Logical Regulatory Networks Using Logic-Based Tools, presented at Technical Communications of the 34th International Conference on Logic Programming, ICLP 2018, Jul. 2018 [bibTex]

2017

- Filipe Gouveia and Pedro T. Monteiro and Vasco Manquinho and Inês Lynce, Logic-Based Encodings for Ricochet Robots, presented at EPIA Conference on Artificial Intelligence (EPIA'17), Sep. 2017 [DOI Article link] [bibTex]
- Andreia Teixeira and Pedro T. Monteiro and João Carriço and Francisco C. Santos and A. P. Francisco, Using Spark and GraphX to Parallelize Large-Scale Simulations of Bacterial Populations over Host Contact Networks, presented at International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP'17), Sep. 2017 [DOI Article link] [bibTex]
- Andreia Teixeira and Pedro T. Monteiro and João Carriço and Francisco C. Santos and A. P. Francisco, Using Spark and MapReduce to Parallelize Large Scale Simulations Over Host Contact Networks, Jul. 2017 [bibTex]