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

2023

- Sofia Reis and Rui Abreu, A Systematic Literature Review of Static Application Security Testing Tools, article in , to appear on 2023 [bibTex]
- Andreia Guerreiro and Joao Cortes and Daniel Vanderpooten and Cristina Bazgan and Inês Lynce and Vasco Manquinho and José Rui Figueira, Exact and Approximate Determination of the Pareto Front Using Minimal Correction Subsets, article in Computers and Operations Research, to appear on 2023 [bibTex]
- Matthew A.Coelho and Sarah Cooper and Magdalena E. Strauss and Emre Karakoc and Shriram Bhosle and Emanuel Gonçalves and Gabriele Picco and Thomas Burgold and Chiara M. Cattaneo and Vivien Veninga and Sarah Consonni and Cansu Dinçer and Sara F. Vieira and Freddy Gibson and Syd Barthorpe and Claire Hardy and Joel Rein and Mark Thomas and John Marioni and Emile E. Voest and Andrew Bassett and Mathew J. Garnett, Base editing screens map mutations affecting interferon-γ signaling in cancer, article in Cancer Cell, Jan. 2023 [Article] [DOI Article link] [bibTex]
- Miguel C. Teixeira and Romeu Viana and Margarida Palma and Jorge dos Santos Oliveira and Mónica Galocha and Marta Neves Mota and Diogo Couceiro and Maria Galhardas Pereira and Miguel Antunes and Inês V Costa and Pedro Pais and Carolina Parada and Claudine Chaouiya and Isabel Sá-Correia and Pedro T. Monteiro, YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis, article in Nucleic Acids Research vol. 51 pp. D785–D791, Jan. 2023, Oxford University Press [DOI Article link] [bibTex]

2022

- Sérgio Guerreiro and João F. Ferreira and Tiago Fonseca and Miguel Correia, Integrating an academic management system with blockchain: A case study, article in Blockchain: Research and Applications vol. 3 (4), Dec. 2022, Elsevier [bibTex]
- 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]
- Tiago Brito and Pedro Lopes and Nuno Santos and José Fragoso Santos, Wasmati: An Efficient Static Vulnerability Scanner for WebAssembly, article in Computers & Security, to appear on 2022 [bibTex]
- João Palet and Vasco Manquinho and Rui Miguel Carrasqueiro Henriques, Multiple-Input Neural Networks for Time Series Forecasting Incorporating Historical and Prospective Context, article in Data Mining and Knowledge Discovery, Nov. 2022 [bibTex]
- Steve Dunne and João F. Ferreira and Alexandra Mendes and Campbell Ritchie and Bill Stoddart and Frank Zeyda, bGSL: An Imperative Language for Specification and Refinement of Backtracking Programs, article in Journal of Logical and Algebraic Methods in Programming vol. 130, Sep. 2022 [DOI Article link] [Supplementary Material] [bibTex]
- Emanuel Gonçalves and Rebecca C Poulos and Zhaoxiang Cai and Syd Barthorpe and Srikanth S Manda and Natasha Lucas and Alexandra Beck and Daniel Bucio-Noble and Michael Dausmann and Caitlin Hall and Michael Hecker and Jennifer Koh and Howard Lightfoot and Sadia Mahboob and Iman Mali and James Morris and Laura Richardson and Akila J Seneviratne and Rebecca Shepherd and Erin Sykes and Frances Thomas and Sara Valentini and Steven G Williams and Yangxiu Wu and Dylan Xavier and Karen L MacKenzie and Peter G Hains and Brett Tully and Phillip J Robinson and Qing Zhong and Mathew J Garnett and Roger R Reddel, Pan-cancer proteomic map of 949 human cell lines, article in Cancer Cell vol. 40 pp. 835-849, Aug. 2022 [DOI Article link] [bibTex]
- Emanuel Gonçalves and Maria Gonçalves-Reis and José B Pereira-Leal and Joana Cardoso, 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]
- Stacey Price and Shriram Bhosle and Emanuel Gonçalves and Xiaodun Li and Dylan P. McClurg and Syd Barthorpe and Alex Beck and Caitlin Hall and Howard Lightfoot and Luke Farrow and Rizwan Ansari and David A. Jackson and Laura Allen and Kirsty Roberts and Charlotte Beaver and Hayley E. Francies and Mathew J. Garnett, 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]

International Conferences: 25

2023

- Sofia Reis and Rui Abreu and Corina Pasareanu, Are security commit messages informative? Not enough!, presented at International Conference on Evaluation and Assessment in Software Engineering, to appear on 2023 [bibTex]
- Sofia Reis and Hakan Erdogmus and Rui Abreu and Corina Pasareanu, Best Practices when Writing Security Commit Messages: Are we there yet?, to appear on 2023 [bibTex]
- João Tiago Aparicio and Thomas Tiam-Lee and Carlos J. Costa, Explaining Wikipedia page similarity using network science, presented at World Conference on Information Systems and Technologies, to appear on 2023 [bibTex]
- João Tiago Aparicio and Thomas Tiam-Lee and Carlos J. Costa, Polarization and similarly of news in Portugal and the Philippines, presented at World Conference on Information Systems and Technologies, to appear on 2023 [bibTex]
- Mafalda Ferreira and Tiago Brito and José Fragoso Santos and Nuno Santos, RuleKeeper: GDPR-Aware Personal Data Compliance for Web Frameworks, presented at Proceedings of 44th IEEE Symposium on Security and Privacy (S&P), to appear on 2023 [bibTex]
- Sofia Reis and Corina Pasareanu and Rui Abreu and Hakan Erdogmus, SECOMlint: A linter for Security Commit Messages, to appear on 2023 [bibTex] [PDF] [Video]
- Eduard Pinconschi and Sofia Reis and Chi Zhang and Rui Abreu and Hakan Erdogmus and Corina Pasareanu and Limin Jia, Tenet: A Flexible Framework for Machine-Learning-based Vulnerability Detection, presented at International Conference on AI Engineering (CAIN) – Software Engineering for AI (Co-located with the International Conference in Software Engineering), to appear on 2023 [bibTex] [PDF]
- Pedro Orvalho and Jelle Piepenbrock and Mikolas Janota and Vasco Manquinho, Graph Neural Networks For Mapping Variables Between Programs, presented at European Conference on Artificial Intelligence (ECAI), Jul. 2023 [bibTex]
- Pedro Orvalho and Vasco Manquinho and Ruben Martins, UpMax: User partitioning for MaxSAT, presented at International Conference on Theory and Applications of Satisfiability Testing, SAT 2023, Jul. 2023 [bibTex]
- Fábio Cruz and Pedro T. Monteiro and Andreia Sofia Teixeira, Community structure in transcriptional regulatory networks of yeast species, presented at International Conference on ​Complex Networks (CompleNet), Apr. 2023 [bibTex]
- Joao Cortes and Inês Lynce and Vasco Manquinho, New Core-Guided and Hitting Set Algorithms for Multi-Objective Combinatorial Optimization, presented at Tools and Algorithms for Construction and Analysis of Systems (TACAS), Apr. 2023 [bibTex]

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]
- Filipe Marques and José Fragoso Santos and Nuno Santos and Pedro Adão, Concolic Execution for WebAssembly, presented at Proceedings of European Conference on Object-Oriented Programming (ECOOP), to appear on 2022 [bibTex]
- 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]
- Sofia Reis and Rui Abreu and Hakan Erdogmus and Corina Pasareanu, SECOM: Towards a convention for security commit messages, presented at International Conference on Mining Software Repositories (MSR), to appear on 2022 [DOI Article link] [bibTex] [PDF]
- 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]
- Sofia Reis and Rui Abreu and Marcelo D'Amorim and Daniel Antunes Bustorff Fortunato, Leveraging Practitioners’ Feedback to Improve a Security Linter, presented at 37th IEEE/ACM International Conference on Automated Software Engineering, Nov. 2022 [bibTex] [PDF]
- Pedro Orvalho and Mikolas Janota and Vasco Manquinho, MultIPAs : Applying Program Transformations to Introductory Programming Assignments for Data Augmentation, presented at 30th Joint European Software Engineering Conference and Symposium on the Foundations of Software Engineering (ESEC/FSE) (ESEC/FSE 2022), Nov. 2022 [bibTex]
- Filipe Marques and António Morgado and José Fragoso Santos and Mikolas Janota, TestSelector: Automatic Test Suite Selection for Student Projects, presented at Runtime Verification, Sep. 2022 [DOI Article link] [bibTex]
- Nuno Saavedra and 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] [PDF]
- 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]

National Conferences: 2

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]
- João Castanheira and Andreia Sofia Teixeira and Sara C. Madeira and Pedro T. Monteiro, Predicting blood donor return in Portugal: the role of demographics, presented at 13th INForum - Simpósio de Informática (INForum'22), Sep. 2022 [bibTex]

Dissertations

MSc Theses: 8

2022

- José Diogo Castro advised by Pedro T. Monteiro and Rui Miguel Carrasqueiro Henriques, Descriptive and predictive modelling of blood activity in Portugal, MSc Thesis, Dec. 2022 [bibTex]
- André Nunes Silva advised by João F. Ferreira and Martin Monperrus, KTH Royal Institute of Technology, A Comparative Study of Self-Supervised Learning Techniques for Functional Program Repair, MSc Thesis at Instituto Superior Técnico, Universidade de Lisboa, Nov. 2022 [bibTex]
- Miguel Trinca advised by João F. Ferreira and Rui Abreu, A Study on Generating Q# Quantum Programs using a Sequence-To-Sequence Machine Learning model, MSc Thesis, Nov. 2022 [bibTex]
- Pedro Nunes advised by Inês Lynce and Miguel Ângelo da Terra Neves, Data Formatting Synthesis by Example, MSc Thesis at Instituto Superior Técnico, Nov. 2022 [bibTex]
- Pedro Carrott advised by João F. Ferreira, Formal Specification and Verification of the Lazy JellyFish Skip List: A Case Study in Iris on the Verification of Concurrent Maps with Version Control, MSc Thesis at Instituto Superior Técnico, Universidade de Lisboa, Nov. 2022 [bibTex]
- Nuno Saavedra advised by João F. Ferreira, GLITCH: Polyglot Code Smell Detection for Infrastructure as Code, MSc Thesis at Instituto Superior Técnico, Universidade de Lisboa, Nov. 2022 [bibTex]
- Andreia Pereira advised by Inês Lynce and Alexandre Duarte de Almeida Lemos, Incremental Synthesis of OutSystems Logic, MSc Thesis at Instituto Superior Técnico, Nov. 2022 [bibTex]
- Tomás Inácio advised by Pedro T. Monteiro and Inês Lynce, Optimization models for IPST blood collection, MSc Thesis at Instituto Superior Técnico, Nov. 2022 [bibTex]

Internships: 1

2022

- Thomas Tiam-Lee advised by Rui Miguel Carrasqueiro Henriques and Vasco Manquinho, Descriptive and predictive analysis of spatiotemporal data in urban domain, short term traineeship, Jun. 2022 [bibTex]

Technologies

International Patents: 1

2022

- Emanuel Gonçalves, Dna methylation biomarkers for hepatocellular carcinoma, Patent Nº 20222435661, May. 2022, Ophiomics [bibTex]