Publications

Articles

International Journal Articles: 16

2021

- Andreia Guerreiro and Vasco Manquinho and José Rui Figueira, Exact Hypervolume Subset Selection Through Incremental Computations, article in Computers & Operations Research vol. 136 pp. 15, Dec. 2021, Elsevier [DOI Article link] [bibTex]
- Emanuel Gonçalves and Christian Frezza, Genome and metabolome: chance and necessity, article in Genome Biology, Sep. 2021, Springer Nature [DOI Article link] [bibTex] [PDF]
- Praveen Kumar Guttula and Pedro T. Monteiro and Mukesh Kumar Guptaa, Prediction and Boolean logical modelling of synergistic microRNA regulatory networks during reprogramming of male germline pluripotent stem cells, article in Biosystems vol. 207, Sep. 2021, Elsevier [DOI Article link] [bibTex]
- Claudia P. Godinho and Margarida Palma and Jorge dos Santos Oliveira and Marta N. Mota and Miguel Antunes and Miguel C. Teixeira and Pedro T. Monteiro and Isabel Sá-Correia, The N.C.Yeastract and CommunityYeastract databases to study gene and genomic transcription regulation in non-conventional yeasts, article in FEMS Yeast Research, Aug. 2021 [DOI Article link] [bibTex]
- Jorge dos Santos Oliveira and Miguel Antunes and Cláudia P. Godinho and Miguel C. Teixeira and Isabel Sá-Correia and Pedro T. Monteiro, From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon, article in BMC Bioinformatics, Jul. 2021, accepted [bibTex]
- Alexandre Lemos and Pedro T. Monteiro and Inês Lynce, Introducing UniCorT: A University Course Timetabling Tool, article in Journal of Scheduling, Jul. 2021, Springer [DOI Article link] [bibTex]
- Andreia Guerreiro and Carlos M. Fonseca and Luís Paquete, The Hypervolume Indicator: Computational Problems and Algorithms, article in Computing Surveys vol. 54 (6) pp. 42, Jul. 2021, ACM [DOI Article link] [bibTex]
- Pedro Pais and Jorge dos Santos Oliveira and Vanda Almeida and Melike Yilmaz and Pedro T. Monteiro and Miguel C. Teixeira, Transcriptome-wide differences between Saccharomyces cerevisiae and Saccharomyces cerevisiae var. boulardii: clues on host survival and probiotic activity based on promoter sequence variability, article in Genomics vol. 113 (2), Mar. 2021 [DOI Article link] [bibTex]

2020

- Abubakar Zakari and Sai Peck Lee and Rui Abreu and Babiker Hussien Ahmed, Multiple fault localization of software programs: A systematic literature review, article in Information and Software Technology vol. 124, to appear on 2020, Elsevier BV [DOI Article link] [bibTex] [PDF]
- Ana Salta and Rui Prada and Francisco S. Melo, A Game AI Competition to foster Collaborative AI research and development, article in IEEE Transactions on Games pp. 1-12, Sep. 2020, IEEE [DOI Article link] [bibTex]
- Pedro T. Monteiro and Tiago Godinho de Ornelas Pedreira and Monica Galocha and Miguel C. Teixeira and Claudine Chaouiya, Assessing regulatory features of the current transcriptional network of Saccharomyces cerevisiae, article in Scientific Reports, Sep. 2020, Nature [DOI Article link] [bibTex]
- 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]

International Conferences: 19

2021

- Thomas Tiam-Lee and Rui Miguel Carrasqueiro Henriques, Where are the Passengers? Individual Passenger Route Choice Estimation from Gate Information in Urban Rail Transit Systems, presented at European Transport Conference (ETC), Sep. 2021 [bibTex]
- Mikolas Janota and António José dos Reis Morgado and José Santos and Vasco Manquinho, The Seesaw Algorithm: Function Optimization using Implicit Hitting Sets, presented at International Conference on Principles and Practice of Constraint Programming, Aug. 2021 [bibTex]
- Changjian Zhang and Ryan Wagner and Pedro Miguel Orvalho and David Garlan and Vasco Manquinho and Ruben Martins and Eunsuk Kang, AlloyMax: Bringing Maximum Satisfaction toRelational Specifications, presented at ACM Joint European Software Engineering Conference and Symposium on the Foundations of Software Engineering (ESEC/FSE), Jun. 2021 [bibTex]
- Miguel Cabral and Mikolas Janota and Vasco Manquinho, How to Approximate Leximax-optimal Solutions, presented at Pragmatics of SAT 2021, Jun. 2021 [bibTex]
- Ansong Ni and Daniel Rosa Ramos and Aidan Yang and Inês Lynce and Vasco Manquinho and Ruben Martins and Claire Le Goues, SOAR: A Synthesis Approach for Data Science API Refactoring, presented at International Conference on Software Engineering (ICSE), May. 2021 [bibTex] [Video]
- Leonor Pimenta de Oliveira e Silva and Helena Galhardas and Vasco Manquinho and Rui Miguel Carrasqueiro Henriques, UNIANO: robust and efficient anomaly consensus in time series sensitive to cross-correlated anomaly profiles, presented at SIAM International Conference on Data Mining, Apr. 2021 [bibTex]

2020

- Daniel Rosa Ramos and Jorge Pereira and Inês Lynce and Vasco Manquinho and Ruben Carlos Gonçalves Martins, UnchartIt: An Interactive Framework for Program Recovery from Charts, presented at IEEE/ACM International Conference on Automated Software Engineering, Oct. 2020 [bibTex]
- Alexandre Lemos and Pedro T. Monteiro and Inês Lynce, Minimal Perturbation in University Timetabling with Maximum Satisfiability, presented at 17th Intl. Conf. on Constraint Programming, Artificial Intelligence, and Operations Research (CPAIOR'20), Sep. 2020 [DOI Article link] [bibTex]
- Filipe Gouveia and Inês Lynce and Pedro T. Monteiro, ModRev - Model Revision tool for Boolean logical models of biological regulatory networks, presented at 18th Intl. Conf. on Computational Methods in Systems Biology (CMSB'20), Sep. 2020 [DOI Article link] [bibTex]
- David Filipe Borges Perreira and João F. Ferreira and Alexandra Mendes, Evaluating the Accuracy of Password Strength Meters using Off-The-Shelf Guessing Attacks, presented at 2020 IEEE International Symposium on Software Reliability Engineering Workshops (ISSREW) – 5th International Workshop on Reliability and Security Data Analysis (RSDA), Aug. 2020 [bibTex] [PDF]
- Inês Lynce and Pedro T. Monteiro, ITC 2019: University Course Timetabling with MaxSAT, presented at Proceedings of the 13th International Conference on the Practice and Theory of Automated Timetabling - PATAT 2021:, Aug. 2020 [bibTex]
- Mikolas Janota and António José dos Reis Morgado, SAT-Based Encodings for Optimal Decision Trees with Explicit Paths., presented at Theory and Applications of Satisfiability Testing - {SAT} 2020, Jul. 2020 [DOI Article link] [bibTex]
- Saul Johnson and João F. Ferreira and Alexandra Mendes and Julien Cordry, Skeptic: Automatic, Justified and Privacy-Preserving Password Composition Policy Selection, presented at 15th ACM ASIA Conference on Computer and Communications Security, Jul. 2020 [bibTex] [PDF]
- João F. Ferreira and António Pedro Cruz Monteiro and Thomas Durieux and Rui Abreu, SmartBugs: A Framework to Analyze Solidity Smart Contracts, presented at 35th IEEE/ACM International Conference on Automated Software Engineering, Tool Demo Track, Jul. 2020 [bibTex] [PDF]
- Pedro Miguel Orvalho 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] [Video]
- Gabriela Sampaio and José Santos and Petar Maksimovic and Philippa Gardner, A Trusted Infrastructure for Symbolic Analysis of Event-Driven Web Applications, presented at European Conference on Object-Oriented Programming (ECOOP 2020), Jun. 2020 [bibTex] [PDF]
- 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]
- Julie Porteous and João F. Ferreira and Alan Lindsay and Marc Cavazza, Extending Narrative Planning Domains with Linguistic Resources, presented at International Conference on Autonomous Agents and Multi-Agent Systems (AAMAS 2020), Jan. 2020 [bibTex] [PDF]
- Rui Abreu and Marcelo D'Amorim and Carlos Mello, Visual Sketching: From Image Sketches to Code, presented at The 42th International Conference on Software Engineering (ICSE'20), Jan. 2020 [bibTex] [PDF]

Dissertations

MSc Theses: 6

2021

- Marcos António Pires Ferreira dos Santos advised by Mikolas Janota and Vasco Manquinho, Automated Computational Complexity Estimation, MSc Thesis at IST - Universidade de Lisboa, Jan. 2021 [bibTex]
- Tiago Miguel Correia de Almeida advised by Vasco Manquinho, Evaluating Redistricting of Electoral Areas, MSc Thesis at IST - U. Lisboa, Jan. 2021 [bibTex]
- Catarina Pina de Almeida Coelho advised by Inês Lynce and Miguel Neves, Pure Function Synthesis in the OutSystems Plataform, MSc Thesis at Instituto Superior Técnico, Jan. 2021 [bibTex]
- Miguel António dos Santos Machado Tavares advised by Vasco Manquinho and Miguel Angelo Terra Neves, Stochastic Multi-Objective Combinatorial Optimization Algorithms, MSc Thesis, Jan. 2021 [bibTex]

2020

- Ricardo Brancas advised by Vasco Manquinho and Miguel Neves, CUBES: A New Dimension in Query Synthesis From Examples, MSc Thesis at IST - Universidade de Lisboa, Nov. 2020 [bibTex]
- Margarida Ferreira advised by Inês Lynce and Miguel Neves, FOREST: An interactive multi-tree synthesizer for regular expressions, MSc Thesis at Instituto Superior Técnico, Nov. 2020 [bibTex]

as Editors

Other Publications: 1

2020

- Andreia Guerreiro and Carlos M. Fonseca, editors, Evolutionary Multiobjective Optimization, EURO Working Group Multicriteria Decision Aiding 3, Nov. 2020 [bibTex]