Publications

Books

Book Chapters: 1

2022

- Pedro Pais and Jorge dos Santos Oliveira and Romeu Viana and Inês V. Costa and Isabel Sá-Correia and Pedro T. Monteiro and Miguel C. Teixeira, Prediction of Gene and Genomic Regulation in Candida Species, Using the PathoYeastract Database: A Comparative Genomics Approach, chapter of Yeast Functional Genomics. Methods in Molecular Biology, May. 2022, Humana [bibTex]

Articles

International Journal Articles: 18

2022

- Alexandre Lemos and Pedro T. Monteiro and Inês Lynce, Introducing UniCorT: A University Course Timetabling Tool, article in Journal of Scheduling, to appear on 2022, Springer [DOI Article link] [bibTex]
- Tiago Brito and Pedro Lopes and Nuno Santos and José Fragoso Santos, Wasmati: An Efficient Static Vulnerability Scanner for WebAssembly, article in Computers & Security pp. 102745, to appear on 2022, Elsevier [Article] [DOI Article link] [bibTex]
- Emanuel Gonçalves, DNA methylation fingerprint of hepatocellular carcinoma from tissue and liquid biopsies, article in Scientific Reports, Jul. 2022 [DOI Article link] [bibTex]
- Thomas Tiam-Lee and Rui Miguel Carrasqueiro Henriques and Vasco Manquinho, Associative Analysis of Inefficiencies and Station Activity Levels in Emergency Response, article in International Journal of Geo-Information, Jun. 2022 [bibTex]
- Leonor Pimenta de Oliveira e Silva and Magda Carolina Araújo Resende and Helena Galhardas and Vasco Manquinho and Inês Lynce, DeepData: Machine Learning in the Marine Ecosystems, article in Expert Systems With Applications, Jun. 2022 [bibTex]
- Thomas Tiam-Lee and Rui Miguel Carrasqueiro Henriques, Route choice estimation in rail transit systems using smart card data: handling vehicle schedule and walking time uncertainties, article in European Transport and Research Review (ETRR), Jun. 2022 [bibTex]
- Tiago Miguel Correia de Almeida and Vasco Manquinho, Constraint-based Electoral Districting Using a New Compactness Measure: an application to Portugal, article in Computers and Operations Research, May. 2022, Elsevier [bibTex]
- Emanuel Gonçalves, A suspension technique for efficient large-scale cancer organoid culturing and perturbation screens, article in Scientific Reports vol. 12, Apr. 2022 [Article] [DOI Article link] [bibTex]
- John Zobolas and Pedro T. Monteiro and Martin Kuiper and Asmund Flobak, Boolean function metrics can assist modelers to check and choose logical rules, article in Journal of Theoretical Biology vol. 538 pp. 111025, Apr. 2022, Elsevier [DOI Article link] [bibTex]

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]
- 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]
- Julie Porteous and João F. Ferreira and Alan Lindsay and Marc Cavazza, Automated narrative planning model extension, article in Autonomous Agents and Multi-Agent Systems vol. 35 (19) pp. 1-29, May. 2021, Springer [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]
- Alexandre Lemos and Pedro T. Monteiro and Inês Lynce, Disruptions in Timetables: A Case Study at Universidade de Lisboa, article in Journal of Scheduling vol. 24 (1) pp. 35-48, Feb. 2021 [bibTex]

International Conferences: 24

2022

- Miguel Trinca and João F. Ferreira and Rui Abreu, A Preliminary Study on Generating Well-Formed Q# Quantum Programs for Fuzz Testing, presented at 2nd International Workshop on Artificial Intelligence in Software Testing (AIST'22), to appear on 2022 [bibTex] [PDF]
- Ricardo Pereira and João F. Ferreira and Alexandra Mendes and Rui Abreu, Extending EcoAndroid with Automated Detection of Resource Leaks, presented at 9th IEEE/ACM International Conference on Mobile Software Engineering and Systems 2022, to appear on 2022 [bibTex]
- Miguel Bettencourt Moniz Cabral and Mikolas Janota and Vasco Manquinho, SAT-based Leximax Optimisation Algorithms, presented at International Conference on Theory and Applications of Satisfiability Testing (SAT), to appear on 2022 [bibTex]
- Miguel Grilo and João Campos and João F. Ferreira and José Bacelar Almeida and Alexandra Mendes, Verified Password Generation from Password Composition Policies, presented at 17th International Conference on integrated Formal Methods (iFM), to appear on 2022 [bibTex] [PDF]
- João F. Ferreira, GLITCH: Automated Polyglot Security Smell Detection in Infrastructure as Code, presented at 37th IEEE/ACM International Conference on Automated Software Engineering (ASE), Jul. 2022 [bibTex]
- Carolina Carreira, Studying Users' Willingness to Use a Formally Verified Password Manager, presented at PhD Symposium at the 17th International Conference on integrated Formal Methods (iFM), Jun. 2022 [bibTex] [PDF]
- Thomas Tiam-Lee and Rui Miguel Carrasqueiro Henriques and José Costa and Vasco Manquinho and Helena Galhardas, Consolidation of massive medical emergency events with heterogeneous situational context data sources, presented at 6th International workshop on Data Analytics solutions for Real-LIfe APplications @ EDBT/ICDT 2022, Mar. 2022 [bibTex] [PDF]
- David António Cóias Calhas and Vasco Manquinho and Inês Lynce, Automatic Generation of Neural Architecture Search Spaces, presented at AAAI-2022 Workshop on Combining Learning and Reasoning: Programming Languages, Formalisms, and Representations (CLeaR), Feb. 2022 [bibTex]
- Paulo Dias and Pedro T. Monteiro and Andreia Sofia Teixeira, Functional characterization of transcriptional regulatory networks of yeast species, presented at International School and Conference on Network Science (NetSciX'22), Feb. 2022 [DOI Article link] [bibTex]

2021

- Ana Sofia Gonçalves Ribeiro and João F. Ferreira and Alexandra Mendes, EcoAndroid: An Android Studio Plugin for Developing Energy-Efficient Java Mobile Applications, presented at 2021 IEEE 21st International Conference on Software Quality, Reliability and Security (QRS), Dec. 2021 [DOI Article link] [bibTex] [PDF]
- Eduardo Geraldo and José Fragoso Santos and João Costa Seco, Hybrid Information Flow Control for Low-Level Code, presented at Software Engineering and Formal Methods, Dec. 2021 [DOI Article link] [bibTex] [PDF]
- Ricardo Martins and Rui Abreu and Manuel Lopes and João Nadkarni, Supervised Learning for Test Suit Selection in Continuous Integration, presented at 2021 IEEE International Conference on Software Testing, Verification and Validation Workshops (ICSTW), to appear on 2021 [DOI Article link] [bibTex]
- Rui Lima and João F. Ferreira and Alexandra Mendes, Automatic Repair of Java Code with Timing Side-Channel Vulnerabilities, presented at International Workshop on Refactoring (IWoR 21), Nov. 2021 [bibTex]
- Margarida Ferreira and Akshay Narayan and Justine Sherry and Inês Lynce and Ruben Carlos Gonçalves Martins, Counterfeiting Congestion Control Algorithms, presented at HotNets '21: The 20th ACM Workshop on Hot Topics in Networks, Nov. 2021 [DOI Article link] [bibTex]
- Carolina Carreira and João F. Ferreira and Alexandra Mendes and Nicolas Christin, Exploring Usable Security to Improve the Impact of Formal Verification: A Research Agenda, presented at 1st International Workshop on Applicable Formal Methods (appFM), Nov. 2021 [bibTex] [PDF]
- Mikolas Janota and António José dos Reis Morgado and José Fragoso Santos and Vasco Manquinho, The Seesaw Algorithm: Function Optimization Using Implicit Hitting Sets, presented at 27th International Conference on Principles and Practice of Constraint Programming, Oct. 2021 [DOI Article link] [bibTex] [PDF]
- 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]
- Sacha Elie-Ayoun and Petar Maksimovic and José Fragoso Santos and Philippa Gardner, Gillian, Part II: Real-World Verification for JavaScript and C, presented at Computer Aided Verification, Jul. 2021 [DOI Article link] [bibTex] [PDF]
- 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]
- Margarida Ferreira and Miguel Neves and Miguel Ventura and Inês Lynce and Ruben Carlos Gonçalves Martins, FOREST: An Interactive Multi-tree Synthesizer for Regular Expressions, presented at 27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2021, Mar. 2021 [DOI Article link] [bibTex]

National Conferences: 1

2022

- Fábio Cruz and Pedro T. Monteiro and Andreia Sofia Teixeira, Community detection for the characterization of transcriptional regulatory networks of yeast species, presented at INForum, Sep. 2022 [bibTex]

Dissertations

PhD Theses: 2

2021

- Filipe Gouveia advised by Pedro T. Monteiro and Inês Lynce, Model Revision of Boolean Logical Models of Biological Regulatory Networks, PhD Thesis at Instituto Superior Técnico, Sep. 2021 [bibTex]
- Alexandre Lemos advised by Inês Lynce and Pedro T. Monteiro, Solving Scheduling Problems under Disruptions, PhD Thesis at Instituto Superior Técnico, Jul. 2021 [bibTex]

MSc Theses: 11

2021

- Carolina Parada advised by Pedro T. Monteiro and Miguel C. Teixeira, A Metabolic-Regulatory Genome-Scale Integration forSaccharomyces cerevisiae: Predicting Targets forIncreased Ethanol Production, MSc Thesis at Instituto Superior Técnico, Dec. 2021 [bibTex]
- Paulo Dias advised by Pedro T. Monteiro and Sofia Teixeira, Network motifs in multi-graphs, MSc Thesis at IST, Dec. 2021 [bibTex]
- Catarina Julião Relvas Pires advised by Vasco Manquinho and Inês Lynce, Automatic Chart Interpretation, MSc Thesis at IST, Nov. 2021 [bibTex]
- Miguel Bettencourt Moniz Cabral advised by Mikolas Janota and Vasco Manquinho, Boolean Leximax Optimisation using Iterative SAT Solving, MSc Thesis at IST, U. Lisboa, Nov. 2021 [bibTex]
- Joana Maria Leal Coutinho advised by Inês Lynce and Miguel Neves, Next-Gen Pure Function Synthesis in OutSystems, MSc Thesis, Nov. 2021 [bibTex]
- Carolina Carreira advised by João F. Ferreira and Alexandra Mendes, On Usable Security and Verified Password Managers, MSc Thesis at Instituto Superior Técnico, University of Lisbon, Nov. 2021 [bibTex]
- Viviana de Brito Bernardo advised by Inês Lynce and Miguel Neves, Sketch-Driven SQL Synthesis, MSc Thesis, Nov. 2021 [bibTex]
- 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]

as Editors

Edited Proceedings: 1

2021

- João F. Ferreira and Alexandra Mendes and Claudio Menghi, editors, Formal Methods Teaching: 4th International Workshop and Tutorial, FMTea 2021, Virtual Event, November 21, 2021, Proceedings, LNCS 13122, Nov. 2021, Springer [bibTex]