Publications

Books

Book Chapters: 2

2018

- Inês Lynce and Vasco Manquinho and Ruben Carlos Gonçalves Martins, Parallel Maximum Satisfiability, chapter of Handbook of Parallel Constraint Reasoning, May. 2018, Springer [bibTex]

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: 11

2018

- 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

- Joao-Marques-Silva and Mikolas Janota and Carlos Mencia, Minimal sets on propositional formulae. Problems and reductions , article in , Nov. 2017 [DOI Article link] [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, 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]
- Mikolas Janota and William Klieber and Joao Marques-Silva and Edmund Clarke, Solving QBF with Counterexample Guided Refinement , article in Artificial Intelligence vol. 234 pp. 1-25, May. 2016 [DOI Article link] [bibTex]
- Mikolas Janota and Joao Marques-Silva, On the Query Complexity of Selecting Minimal Sets for Monotone Predicates , article in vol. 233 pp. 73-83, Apr. 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: 14

2018

- Mikolas Janota, Towards Generalization in QBF Solving via Machine Learning , presented at Thirty-Second AAAI Conference on Artificial Intelligence , Apr. 2018 [bibTex]
- Miguel Neves and Inês Lynce and Vasco Manquinho, Enhancing Constraint-Based Multi-Objective Combinatorial Optimization, presented at AAAI Conference on Artificial Intelligence, Feb. 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]
- Mikolas Janota and Joao-Marques-Silva, An Achilles' Heel of Term-Resolution, presented at EPIA Conference on Artificial Intelligence, Aug. 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]
- Mikolas Janota, On Q-Resolution and CDCL QBF Solving , presented at Theory and Applications of Satisfiability Testing – SAT 2016, Jun. 2016 [DOI Article link] [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: 7

2018

- Rubén Filipe Martins Marques advised by Vasco Manquinho and Inês Lynce, Algorithms for Leakage Detection System, MSc Thesis at IST, May. 2018 [bibTex]
- Amândio de Jesus Cordeiro Almada advised by Vasco Manquinho and Inês Lynce, Optimization algorithms in forest planning models, MSc Thesis, Apr. 2018 [bibTex]

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