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: 4

2017

- 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, to appear on 2017 [bibTex]
- 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 [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]
- Valter Balegas and Cheng Li and Mahsa Najafzadeh and Daniel Porto and Allen Clement and Sergio Duarte and C. Ferreira and Johannes Gehrke and João Leitão and Nuno Preguiça and Rodrigo Rodrigues and Marc Shapiro and Viktor Vafeiadis, Geo-Replication: Fast If Possible, Consistent If Necessary, article in IEEE Data Eng. Bull. vol. 39 (1) pp. 81-92, Mar. 2016, IEEE [bibTex]

International Conferences: 10

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]
- Miguel Neves and Inês Lynce and Vasco Manquinho, Introducing Pareto Minimal Correction Subsets, presented at International Conference on Theory and Applications of Satisfiability Testing (SAT), Aug. 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

- Miguel Neves and Inês Lynce and Vasco Manquinho, Non-Portfolio Approaches for Distributed Maximum Satisfiability, presented at IEEE International Conference on Tools with Artificial Intelligence, Nov. 2016 [DOI Article link] [bibTex]
- Xujie Si and Xin Zhang and Vasco Manquinho and Mikolas Janota and Alexey S. Ignatiev and Mayur Naik, On Incremental Core-Guided MaxSAT Solving, presented at International Conference Principles and Practice of Constraint Programming (CP 2016), Sep. 2016 [DOI Article link] [bibTex]
- 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]
- Valter Balegas and Nuno Preguiça and Sergio Duarte and C. Ferreira and Rodrigo Rodrigues, Making Weak Consistency Great Again, presented at Workshop on Principles and Practice of Consistency for Distributed Data (PaPoC 2016)., Apr. 2016 [bibTex]

Dissertations

MSc Theses: 5

2017

- José Francisco Pires Amaral advised by Vasco Manquinho, Algorithms for Markov Logic Networks, MSc Thesis, Nov. 2017 [bibTex]
- João Pedro Mateus Alexandre advised by Vasco Manquinho, Automatic generation of test cases for MOOCs, MSc Thesis at IST - Universidade de Lisboa, Jul. 2017 [bibTex]
- André Filipe Ribeiro dos Reis advised by Vasco Manquinho and Luis Guerra e Silva, Algorithms for Maximum Satisfiability using GPU, MSc Thesis, Jun. 2017 [bibTex]

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