Publications

Books

Book Chapters: 1

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]

Articles

International Journal Articles: 17

2020

- Alexandre Lemos and Pedro T. Monteiro and Inês Lynce, Disruptions in Timetables: A Case Study at Universidade de Lisboa, article in Journal of Scheduling, Jun. 2020 [bibTex]
- Gianluca Selvaggio and Sara Canato and Archana Pawar and Pedro T. Monteiro and Patrícia S. Guerreiro and M. Manuela Brás and Florence Janody and Claudine Chaouiya, Hybrid epithelial-mesenchymal phenotypes are controlled by microenvironmental factors, article in Cancer Research vol. 80 (11), Jun. 2020 [DOI Article link] [bibTex]
- Praveen Kumar Guttula and Pedro T. Monteiro and Mukesh Kumar Gupta, A Boolean Logical model for Reprogramming of Testes-derived male Germline Stem Cells into Germline pluripotent stem cells, article in Computer Methods and Programs in Biomedicine vol. 192, Mar. 2020 [DOI Article link] [bibTex]
- Filipe Gouveia and Inês Lynce and Pedro T. Monteiro, Revision of Boolean models of regulatory networks using stable state observations, article in Journal of Computational Biology vol. 27 (2) pp. 144-155, Feb. 2020, Mary Ann Liebert, Inc. [DOI Article link] [bibTex]
- Pedro T. Monteiro and Jorge dos Santos Oliveira and Pedro Pais and Miguel Antunes and Margarida Palma and Mafalda Cavalheiro and Mónica Galocha and Cláudia P Godinho and Luís C Martins and Nuno Bourbon and Marta N Mota and Ricardo A Ribeiro and Romeu Viana and Isabel Sá-Correia and Miguel C Teixeira, YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts, article in Nucleic Acids Research vol. 48 pp. D642-D649, Jan. 2020, Oxford University Press [DOI Article link] [bibTex]

2019

- Pedro Varela and Pedro T. Monteiro and Claudine Chaouiya, Impact of Changing Cell-Cell Communication Network in Models of Epithelial Pattern Formation, article in IFAC-PapersOnLine vol. 52 (26) pp. 38-44, Oct. 2019 [DOI Article link] [bibTex]
- Miguel Neves and Inês Lynce and Vasco Manquinho, Virtual machine consolidation using constraint-based multi-objective optimization, article in Journal of Heuristics vol. 25 (3) pp. 339-375, Jun. 2019 [DOI Article link] [bibTex]
- Alexandre Lemos and Francisco S. Melo and Pedro T. Monteiro and Inês Lynce, Room Usage Optimization in Timetabling: A Case Study at Universidade de Lisboa, article in Operations Research Perspectives vol. 6 pp. 100092, May. 2019 [DOI Article link] [bibTex]
- Wassim Abou-Jaoudé and Pedro T. Monteiro, On Logical Bifurcation Diagrams, article in Journal of Theoretical Biology vol. 466 pp. 39-63, Apr. 2019 [DOI Article link] [bibTex]
- 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, Mar. 2019, F1000 Research, Ltd. [DOI Article link] [bibTex]
- Alexandre Lemos and Inês Lynce and Pedro T. Monteiro, Repairing Boolean logical models from time-series data using Answer Set Programming, article in Algorithms for Molecular Biology vol. 14 pp. 9, Mar. 2019 [DOI Article link] [bibTex]

2018

- 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 Sofia 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]

International Conferences: 12

2020

- Pedro Miguel Orvalho Marques da Silva and Miguel Neves and Miguel Ventura and Ruben Carlos Gonçalves Martins and Vasco Manquinho, SQUARES : A SQL Synthesizer Using Query Reverse Engineering, presented at International Conference on Very Large Databases, Jul. 2020 [bibTex]
- José Fragoso Santos and Petar Maksimovic and Sacha-Elie Ayoun and Philippa Gardner, Gillian, Part I: A Multi-language Platform for Symbolic Execution, presented at ACM SIGPLAN Conference on Programming Language Design and Implementation (PLDI), Apr. 2020 [DOI Article link] [bibTex] [PDF]

2019

- Andreia Guerreiro and Miguel Neves and Inês Lynce and José Rui Figueira and Vasco Manquinho, Constraint-Based Techniques in Stochastic Local Search MaxSAT Solving, presented at 25th International Conference Principles and Practice of Constraint Programming, CP 2019, Oct. 2019 [DOI Article link] [bibTex]
- Pedro Miguel Orvalho Marques da Silva and Miguel Neves and Miguel Ventura and Ruben Carlos Gonçalves Martins and Vasco Manquinho, Encodings for Enumeration-Based Program Synthesis, presented at 25th International Conference on Principles and Practice of Constraint Programming, CP 2019, Oct. 2019 [DOI Article link] [bibTex]
- Miguel Neves and Inês Lynce and Vasco Manquinho, Integrating Constraint Reasoning in Multi-Objective Evolutionary Algorithms, presented at 28th International Joint Conference on Artificial Intelligence, IJCAI 2019, May. 2019 [bibTex]
- Filipe Gouveia and Inês Lynce and Pedro T. Monteiro, Model revision of Boolean regulatory networks at stable state, presented at International Symposium on Bioinformatics Research and Applications, May. 2019 [DOI Article link] [bibTex]
- Miguel Neves and Nuno Machado and Inês Lynce and Vasco Manquinho, Concurrency Debugging with MaxSMT, presented at Thirty-Third AAAI Conference on Artificial Intelligence, AAAI 19, Jan. 2019 [bibTex]

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]
- Miguel Neves and Inês Lynce and Vasco Manquinho, Multi-Objective Optimization Through Pareto Minimal Correction Subsets, presented at Twenty-Seventh International Joint Conference on Artificial Intelligence, IJCAI 2018, Jul. 2018 [bibTex]
- Miguel Neves and Inês Lynce and Vasco Manquinho, Stratification for Constraint-Based Multi-Objective Combinatorial Optimization, presented at Twenty-Seventh International Joint Conference on Artificial Intelligence, IJCAI 2018, Jul. 2018 [bibTex]
- 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, AAAI 18, Feb. 2018 [bibTex]

Dissertations

PhD Theses: 1

2019

- Miguel Neves advised by Vasco Manquinho and Inês Lynce, Constraint-Based Multi-Objective Combinatorial Optimization, PhD Thesis at IST - Universidade de Lisboa, Jun. 2019 [bibTex]

MSc Theses: 4

2018

- Magda Carolina Araújo Resende advised by Helena Galhardas and Inês Lynce, DeepSea: Web-based database, MSc Thesis at Instituto Superior Técnico, Univ. de Lisboa, Nov. 2018 [bibTex]
- João Miguel Sousa Varandas advised by Vasco Manquinho, Solving the treevdith and pathwidth in graphs using MaxSat, MSc Thesis, Oct. 2018 [bibTex]
- 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]

Internships: 1

2018

- Ricardo Miguel Bacala Brancas advised by David Martins de Matos, 64-bit ABI for small Compilers, short term traineeship, Jun. 2018 [bibTex]