Publications

Books

Book Chapters: 1

2016

- Miguel C. Teixeira and Pedro T. Monteiro and Isabel Sá-Correia, Predicting Gene and Genomic Regulation in Saccharomyces cerevisiae, using the YEASTRACT Database: A Step By Step Guided Analysis, chapter of Yeast Functional Genomics: Methods and Protocols, Jan. 2016, Humana Press [bibTex]

Articles

International Journal Articles: 9

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, 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]

2016

- Wassim Abou-Jaoudé and Pauline Traynard and Pedro T. Monteiro and Julio Saez-Rodriguez and Tomas Helikar and Denis Thieffry and Claudine Chaouiya, Logical modeling and dynamical analysis of cellular networks, article in Frontiers in Genetics vol. 7 pp. 94, May. 2016 [DOI Article link] [bibTex]

International Conferences: 6

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]

2016

- Pedro Varela and Inês Lynce and Vasco Manquinho and Claudine Chaouiya and Pedro T. Monteiro, SAT-based identification of stable states in composed Boolean regulatory networks, presented at International Workshop on Static Analysis and Systems Biology (SASB 2016), Sep. 2016 [bibTex]
- Pedro T. Monteiro and José E.R. Cury and Claudine Chaouiya, On the number and structure of Boolean functions compatible with a regulatory network topology, presented at [Abstract and Presentation at] 10th European Conference on Mathematical and Theoretical Biology (ECMTB), Jul. 2016 [bibTex]
- Sébastien Fueyo and Pedro T. Monteiro and Aurélien Naldi and Elisabeth Remy and Claudine Chaouiya, Reversing Boolean gene regulatory networks, presented at [Abstract and oral presentation at] 10th European Conference on Mathematical and Theoretical Biology (ECMTB), Jul. 2016 [bibTex]

Dissertations

MSc Theses: 2

2016

- Alexandre Lemos advised by Pedro T. Monteiro and Inês Lynce, Inference in Biological Regulatory Networks, MSc Thesis at Instituto Superior Técnico - Universidade de Lisboa, Sep. 2016 [bibTex]
- Sauvagya Manna advised by Pedro T. Monteiro and Miguel Cacho Teixeira, Development of the PathoYeastract database: aiming the study of transcriptional regulation in pathogenic yeasts, MSc Thesis at Instituto Superior Técnico - Universidade de Lisboa, Jul. 2016 [bibTex]

Reports

Technical Reports: 1

2016