Identification
Personal identification
- Full name
- Emanuel José Vieira Gonçalves
Citation names
- Gonçalves, Emanuel
Author identifiers
- Ciência ID
- DC10-778A-73A8
- ORCID iD
- 0000-0002-9967-5205
- Google Scholar ID
- gyEs3B0AAAAJ
- Scopus Author Id
- 55389922800
Email addresses
- emanuel.v.goncalves@tecnico.ulisboa.pt (Professional)
Websites
- https://twitter.com/emanuelvgo (Social media)
- https://www.linkedin.com/in/emanuel-goncalves-37374b188/ (Social media)
- http://web.tecnico.ulisboa.pt/emanuel.v.goncalves/ (Professional)
Knowledge fields
- Exact Sciences - Computer and Information Sciences - Bioinformatics
Languages
Language | Speaking | Reading | Writing | Listening | Peer-review |
---|---|---|---|---|---|
Portuguese (Mother tongue) | |||||
English | Proficiency (C2) | Proficiency (C2) | Proficiency (C2) | Proficiency (C2) | Proficiency (C2) |
Education
Degree | Classification | |
---|---|---|
2017/04
Concluded
|
Systems Biology (Doctor of Philosophy)
Major in Biological Science at European Bioinformatics Institute
University of Cambridge, United Kingdom
"Modelling regulatory interactions between metabolism and signalling" (THESIS/DISSERTATION)
|
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2012/09
Concluded
|
Bioinformática (Mestrado)
Universidade do Minho, Portugal
"Integration of logic modelling and network visualization tools" (THESIS/DISSERTATION)
|
|
2010/09
Concluded
|
Engenharia Informática (Licenciatura)
Universidade do Minho, Portugal
|
Affiliation
Science
Category Host institution |
Employer | |
---|---|---|
2021/09/01 - Current | Principal Investigator (Research) | Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal |
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal | ||
2020/10/01 - 2022/11/01 | Visiting Researcher (Research) | Wellcome Sanger Institute, United Kingdom |
2017/05/01 - 2019/09/30 | Postdoc (Research) | Wellcome Sanger Institute, United Kingdom |
Wellcome Sanger Institute, United Kingdom | ||
2016/10/01 - 2017/04/01 | Postdoc (Research) | European Bioinformatics Institute, United Kingdom |
European Bioinformatics Institute, United Kingdom | ||
2012/01/10 - 2016/09/30 | Contracted Researcher (Research) | European Bioinformatics Institute, United Kingdom |
European Bioinformatics Institute, United Kingdom | ||
2015/09/01 - 2015/12/31 | Visiting Researcher (Research) | Eidgenössische Technische Hochschule Zürich Institut für Molekulare Systembiologie, Switzerland |
Eidgenössische Technische Hochschule Zürich Institut für Molekulare Systembiologie, Switzerland | ||
2012/01/01 - 2012/09/30 | Visiting Researcher (Research) | European Bioinformatics Institute, United Kingdom |
European Bioinformatics Institute, United Kingdom | ||
2011/10 - 2011/12 | Researcher (Research) | Universidade do Minho, Portugal |
Universidade do Minho Centro de Engenharia Biológica, Portugal |
Teaching in Higher Education
Category Host institution |
Employer | |
---|---|---|
2021/09/01 - Current | Assistant Professor (University Teacher) | Universidade de Lisboa Instituto Superior Técnico, Portugal |
Universidade de Lisboa Instituto Superior Técnico, Portugal |
Others
Category Host institution |
Employer | |
---|---|---|
2020/10/01 - 2021/08/31 | Senior Data Scientist | Ophiomics, Portugal |
Ophiomics, Portugal |
Projects
Grant
Designation | Funders | |
---|---|---|
2011/10/01 - 2021/12/31 | ToMEGIM: Computational Tools for Metabolic Engineering using Genome-scale Integrated Models
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/115176/PT
Research Fellow
|
Universidade do Algarve Faculdade de Ciências e Tecnologia |
2012/10/01 - 2016/09/30 | BioPreDyn
PhD Student Fellow
|
Contract
Designation | Funders | |
---|---|---|
2024/10 - Current | MALDIBANK: Multi-domain Open MALDI Spectra BANK for Identification of Microorganisms
HORIZON-INFRA-2024-TECH-01-01
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
|
Ongoing
|
Outputs
Publications
Conference paper |
|
Journal article |
|
Activities
Oral presentation
Presentation title | Event name Host (Event location) |
|
---|---|---|
2024/07/30 | Unsupervised Multi-omics Approaches for Cancer Drug Target and Biomarker Discovery | HOPTEC webinar series
John Hopkins University and Instituto Superior Técnico
|
2024/07/08 | Artificial Intelligence - Beyond genomics | redeSAÚDE - Multiple Perspectives on Genomic Medicine in Oncology
Universidade de Lisboa (Lisboa, Portugal)
|
2024/05/17 | Unsupervised learning of cancer multi-omics for drug target and biomarker discovery | ELLIS Unit Lisbon Retreat 2024
ELLIS Unit Lisbon (Lisboa, Portugal)
|
2023/10/16 | Self-supervised learning of cancer multi-omics for drug target and biomarker discovery | {Un-}Conference: AI Methods for Health, Life, and Natural Science AI InScide Out
ELLIS: Un-Conference Meeting in Heidelberg
|
2023/05/19 | Pan-cancer multi-omic map of cancer cell lines | Friday Noon Seminar
i3S
|
2023/04/21 | Artificial Intelligence - Applications to Cancer Genomics | 2º Encontro Ibérico de Atualização de Sarcomas
IPO Lisboa
|
2022/11/11 | Multiomics heterogeneity and integration in cancer | INCDP2022 PhD program Computational Biology in Cancer Module
Champalimaud Foundation (Lisbon, Portugal)
|
2022/06/22 | Metabolic models, Machine learning & Omics data | S2M2 Summer School in Metabolic Modeling
Universidade do Minho (Braga, Portugal)
|
2022/06/15 | A pan-cancer proteomic map of human cell lines | i3S Cancer Program Retreat
i3S (Porto, Portugal)
|
2022/04/21 | Protein driven machine learning and network approaches for precision medicine | BioISI Research Seminar
Faculdade de Ciências da Universidade de Lisboa (FCUL) - BioISI (Lisbon, Portugal)
|
2022/02/10 | Protein driven machine learning and network approaches for precision medicine | OLISSIPO Twin Seminar
OLISSIPO
|
2022/02/06 | Protein driven approaches for precision medicine | Global QuBi monthly Science Meetings
AstraZeneca
|
2021/11/09 | Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens | AORTIC 2021 Conference
AORTIC
|
2020/03 | Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens | ELRIG UK Conference
Babraham Institute (Cambridge, United Kingdom)
|
2018/03 | Structural rearrangements determine CRISPR/Cas9 efficacy in cancer | Bioinformatics Open Days (BOD)
University of Minho (Braga, Portugal)
|
2016/11 | Signalling regulation of metabolism in hereditary and leiomyomatosis renal cell cancer | Proteomic Applications in Oncology
Cancer Research UK Cambridge Institute (Cambridge, United Kingdom)
|
2011/09/08 | Strain Optimization Metaheuristics for Discovering the Optimal Level of Gene Expression | Inforum, Coimbra
Universidade de Coimbra (Coimbra, Portugal)
|
Supervision
Thesis Title Role |
Degree Subject (Type) Institution / Organization |
|
---|---|---|
2023/10 - Current | Statistical Learning for Multi-Omics Integration in Precision Cancer Medicine
Co-supervisor
|
PhD in Computer Science and Engineering (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
2023/09 - Current | Adversarial generative networks for proteomics imputation
Supervisor
|
MSc Engineering Physics (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
2023/09 - Current | Deep learning techniques for cancer classification using multi omics data
Co-supervisor
|
MSc Computer Science and Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
2023/09 - Current | Explaining multi-omics generative models for drug and biomarker discovery
Co-supervisor
|
MSc Data Science Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
2023/09 - Current | Deep learning-based enhancement of CRISPR-Cas9 screens for the discovery of novel cancer targets
Co-supervisor
|
MSc Biomedical Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
2023/09 - Current | Computational biology and machine learning approaches to dissect gene expression changes in the immune system during the formation
of breast cancer metastases
Co-supervisor
|
MSc Biomedical Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
2022/01 - Current | Role of CFTR in Epithelial Differentiation and EMT by Functional Genomics
Co-supervisor of Cláudia Alexandra da Silva Rodrigues
|
PhD in Biochemistry (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal |
2022/02 - 2033/06 | Generative models to identify precision medicine approaches for cancer
Co-supervisor of Sofia Soares de Albergaria Apolinário
|
MSc Data Science (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
2023/01 - 2024/06 | Synthetic data generation and imputation using deep learning
Supervisor
|
MSc Aerospace Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
2022/09 - 2023/11 | Analysis of gene pleiotropy using machine learning methods
Co-supervisor of Raul Pacheco Sarkar
|
MSc Biomedical Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
2022/09 - 2023/11 | Development of Python library to integrate metabolic and regulatory networks
Co-supervisor of Sebastião Zoio Martins Ferreira dos Santos
|
MSc Computer Science and Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
2022/09 - 2023/11 | Clinical and molecular characterization of sarcomas using machine learning multiomics integration
Co-supervisor of Manuel Sérgio Sokolov Ravasqueira
|
MSc Computer Science and Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
2022/09 - 2023/11 | Deep neural networks for multi omics integration
Co-supervisor of Nelson Alexandre Geada Trindade
|
MSc Computer Science and Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
2022/09 - 2023/11 | Precision medicine and computational biology approaches to study protein networks and find novel therapeutic targets for cancer
Co-supervisor of Miguel Dinis Madeira Agostinho de Sousa
|
MSc Biomedical Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
2022/09 - 2023/01 | PACMANS & DIPS: A bioinformatic project for PAncreatic Cancer MANagement with Surgery and DIgital Pathology Software
Co-supervisor of Mariana Correia Bento Mourão
|
MSc Biomedical Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
2022/01 - 2022/10 | Sparse and Interpretable Models for Drug Mechanism-of-Action Discovery
Co-supervisor of Ana Rita do Nascimento Baião
|
MSc Biomedical Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
Event organisation
Event name Type of event (Role) |
Institution / Organization | |
---|---|---|
2024/09/05 - 2024/09/06 | INForum 2024 (https://www.inforum.pt/) - Co-chair Bioinformatics Track (2024/09/05 - 2024/09/06)
Conference (Co-organisor)
|
|
2015/06/03 - 2015/06/03 | Cambridge Science and Society meeting: Pandemic! The global threat of deadly diseases
https://www.ebi.ac.uk/about/events/science-and-society-2015 (2015/06/03 - 2015/06/03)
Symposium (Member of the Organising Committee)
|
European Bioinformatics Institute, United Kingdom |
2014/06/04 - 2014/06/04 | Cambridge Science and Society meeting: What is Life
https://www.ebi.ac.uk/about/events/science-and-society-2014 (2014/06/04 - 2014/06/04)
Symposium (Member of the Organising Committee)
|
European Bioinformatics Institute, United Kingdom |
2013/11/21 - 2013/11/23 | Competition in Biology: The race for survival from molecules to systems (2013/11/21 - 2013/11/23)
Conference (Member of the Organising Committee)
|
EMBL Heidelberg Genome Biology, Germany |
2013/03/14 - 2013/03/15 | Bioinformatics Open Days
First edition of Bioinformatics Open Days at University of Minho (2013/03/14 - 2013/03/15)
Conference (Member of the Organising Committee)
|
Universidade do Minho, Portugal |
Event participation
Activity description Type of event |
Event name Institution / Organization |
|
---|---|---|
2022/11/15 - 2022/11/18 | Poster presentation: "Pan-cancer proteomic map of 949 human cell lines". Emanuel Gonçalves, Rebecca C Poulos, Zhaoxiang Cai,
Syd Barthorpe, Srikanth S Manda, Natasha Lucas, Alexandra Beck, Daniel Bucio-Noble, Michael Dausmann, Caitlin Hall, Michael
Hecker, Jennifer Koh, Sadia Mahboob, Iman Mali, James Morris, Laura Richardson, Akila J Seneviratne, Erin Sykes, Frances Thomas,
Sara Valentini, Steven G Williams, Yangxiu Wu, Dylan Xavier, Karen L MacKenzie, Peter G Hains, Brett Tully, Phillip J Robinson,
Qing Zhong, Mathew J Garnett, Roger R Reddel
Conference
|
From functional genomics to systems biology
European Molecular Biology Organization, Germany
|
2020/09/22 - 2020/09/25 | Poster presentation: Gonçalves, Emanuel, Mark Thomas, Fiona M Behan, Gabriele Picco, Clare Pacini, Felicity Allen, Mamta Sharma,
David A. Jackson, Stacey Price, Charlotte M. Beaver, Oliver Dovey, David Parry-Smith, Francesco Iorio, Leopold Parts, Kosuke
Yusa, Mathew J Garnett. “Minimal genome-wide human CRISPR-Cas9 library”.
Conference
|
CRISPR and Beyond: Perturbations at Scale to Understand Genomes |
2019/09/02 - 2019/09/04 | Poster presentation: Gonçalves, Emanuel, Fiona M Behan, Sandra Louzada, Damien Arnol, Euan A. Stronach, Fengtang Yang, Kosuke
Yusa, Oliver Stegle, Francesco Iorio, Mathew J Garnett. “Structural rearrangements generate cell-specific, gene-independent
CRISPR-Cas9 loss of fitness effects”.
Conference
|
CRISPR and beyond: perturbations at scale to understand genomes, Cambridge UK |
2018/12 - 2018/12 | EMBO laboratory leadership course. Highly sought-after course focusing on the development of key skills, such as leadership, communication, scientific writing and research integrity among others, for a successful leader and researcher. Coordinated by Dr Samuel Krahl and Sašo Kocevar (22 training hours) | EMBO laboratory leadership course
The European Molecular Biology Organization (EMBO), Germany
|
2018/11/10 - 2018/11/13 | Poster presentation: Gonçalves, Emanuel, Fiona M Behan, Sandra Louzada, Damien Arnol, Euan A. Stronach, Fengtang Yang, Kosuke
Yusa, Oliver Stegle, Francesco Iorio, Mathew J Garnett. “Structural rearrangements generate cell specific gene independent
CRISPR-Cas9 loss-of-fitness effects”
Conference
|
From Functional Genomics to Systems Biology, Heidelberg |
2018/03/01 - 2018/03/02 | Poster presentation: Gonçalves, Emanuel, Fiona M Behan, Francesco Iorio, Euan Stronach, Kosuke Yusa, Mathew Garnett. “CRISPR/Cas9
dropout screens inform cancer drug mode of action”.
Conference
|
CRUK Cambridge Institute Annual International Symposium ‘Unanswered Questions in Precision Medicine’, Cambridge |
2017/05/07 - 2017/05/11 | Poster presentation: Gonçalves, Emanuel, Athanassios Fragoulis, Luz Garcia-Alonso, Thorsten Cramer, Julio Saez-Rodriguez,
Pedro Beltrao. “Chromosomal rearrangements are commonly post-transcriptionally attenuated in cancer”.
Conference
|
Data-Driven Biotechnology Conference, Copenhagen |
2016/09/16 - 2016/09/20 | Poster presentation: Gonçalves, Emanuel, Zrinka Raguz Nakic, Mattia Zampieri, Omar Wagih, David Ochoa, Uwe Sauer, Pedro Beltrão
and Julio Saez-Rodriguez. “Systematic analysis of transcriptional and post-transcriptional regulation of metabolism in yeast”.
Conference
|
International Conference on Systems Biology (ICSB 2016), Barcelona |
2015/09/16 - 2015/09/18 | Poster presentation: Gonçalves, Emanuel, David Ochoa, Pedro Beltrão and Julio Saez-Rodriguez. “Understanding metabolic regulation
in Saccharomyces cerevisiae”.
Conference
|
4th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2015), Heidelberg |
2014/11/09 - 2014/11/14 | Poster presentation: Gonçalves, Emanuel, Daniel Machado, Miguel Rocha and Julio Saez-Rodriguez. “Cell viability prediction
from large-scale omics data using machine learning and mechanistic modelling approaches”.
Conference
|
Seventh Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, San Diego |
2014/05/20 - 2014/05/23 | Poster presentation: Gonçalves, Emanuel, Sara Correia, Pedro Beltrão, Miguel Rocha and Julio Saez-Rodriguez. “Modelling Cell
Lines Phenotype Integrating Metabolic and Regulatory Networks”.
Conference
|
3rd Conference on Constraint-Based Reconstruction and Analysis, Virginia |
2013/10/09 - 2013/10/10 | Poster presentation: Gonçalves, Emanuel, Martijn van Iersel, and Julio Saez-Rodriguez. “Cytoscape plugins to visualize and
model signalling networks and drug effects using R”.
Conference
|
Cytoscape Workshop, Paris |
Jury of academic degree
Topic Role |
Candidate name (Type of degree) Institution / Organization |
|
---|---|---|
2023/09 | Understanding Metastasis Organotropism Patterns Through Within-cell and Between-cells Molecular Interaction Networks
(Thesis) Main arguer
|
João André Isidoro Miranda (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
|
2023/05 | Predicting Allosteric Regulation at Genome Scale
(Thesis) Main arguer
|
Elin Sandertun Røed (Master)
Norges teknisk-naturvitenskapelige universitet, Norway
|
2023/05 | Assessing the performance of classifiers on sequence data: an application to cancer genomics
(Thesis) Main arguer
|
Anto ´nio Jose ´ de Medeiros Mendonc ¸a Palma Ramos (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
2023/04 | Systems-level modelling of the cancer and immune metabolome to improve immunotherapeutic outcomes
(Thesis) Main arguer
|
Sara Manso de Sousa Cardoso (PhD)
Universidade do Minho, Portugal
|
2023/01 | Predicting metabolic fluxes from gene expression data using machine learning
(Thesis) Main arguer
|
Marieke Cecilia van Eggelen (Master)
Norges teknisk-naturvitenskapelige universitet, Norway
|
2022/07 | Integrative Pathway Analysis Approaches for Cancer Research And Drug Development
(Thesis) Main arguer
|
José Vítor de Castro Vieira (PhD)
Universidade do Minho, Portugal
|
2021/12 | A Metabolic-Regulatory Genome-Scale Integration for Saccharomyces cerevisiae: Predicting Targets for Increased Ethanol Production
(Thesis) Main arguer
|
Carolina Correia Paiva Parada (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
|
2021/07 | Computational approaches for the integration of in vitro chemical and screening datasets
(Thesis) Main arguer
|
Ana Beatriz Gonçalves da Cunha (Master)
Universidade do Minho, Portugal
|
Course / Discipline taught
Academic session | Degree Subject (Type) | Institution / Organization | |
---|---|---|---|
2023/09 - 2023/11 | Computational Biology | (Mestrado) | Universidade de Lisboa Instituto Superior Técnico, Portugal |
2023/03 - 2023/04 | Introduction to Algorithms and Data Structures | LEIC (Licenciatura) | Universidade de Lisboa Instituto Superior Técnico, Portugal |
2022/09 - 2022/11 | Programação com Objectos | Licenciatura em Engenharia Informática e de Computadores (Licenciatura) | Universidade de Lisboa Instituto Superior Técnico, Portugal |
2022/05 - 2022/07 | Inteligência Artificial | Licenciatura em Engenharia Informática e de Computadores (Licenciatura) | Universidade de Lisboa Instituto Superior Técnico, Portugal |
2021/09 - 2021/11 | Programação com Objectos | Licenciatura em Engenharia Informática e de Computadores (Licenciatura) | Universidade de Lisboa Instituto Superior Técnico, Portugal |
2019/08/03 - 2019/08/08 | Systems Biology: From Large Datasets to Biological Insight Visualisation and modelling of signalling transduction networks using CytoCopteR | Wellcome Genome Campus Advanced , United Kingdom | |
2018/06/03 - 2018/06/08 | In Silico Systems Biology Wellcome Genome Campus Advanced Course, Cambridge, UK. | Wellcome Genome Campus Advanced Course, United Kingdom | |
2017/07/09 - 2017/07/14 | In Silico Systems Biology Wellcome Genome Campus Advanced Course | Wellcome Genome Campus Advanced Course, United Kingdom | |
2016/09/21 - 2016/09/21 | ISCB 2016 Workshop Hands-on course on logic modelling of signalling networks using CellNOptR. | International Society for Computational Biology, United States | |
2016/08/03 - 2016/08/08 | In Silico Systems Biology Wellcome Genome Campus Advanced Course, Cambridge, UK. | Wellcome Genome Campus Advanced Course, United Kingdom | |
2015/06/07 - 2015/06/12 | In Silico Systems Biology Visualisation and modelling of signalling transduction networks using CytoCopteR. |
Interview (newspaper / magazine)
Activity description | Newspaper / Forum | |
---|---|---|
2020 | Genome-wide CRISPR screens and drug screens come together to reveal cancer drug mechanism-of-action. Previewing Gonçalves, Emanuel, et al. 2020. Molecular Systems Biology | preLights |
Mentoring / Tutoring
Topic | Student name | |
---|---|---|
2017/09 - 2017/12 | Screen design for drug combination screens | Haynes Heaton |
2016/05 - 2016/12 | Java-based boolean logic modelling framework | Mahdi Saber |
2013/08 - 2014/02 | Integrating logic modelling CellNOptR R package Cytoscape | Franz Mirlach |
Other jury / evaluation
Activity description | Institution / Organization | |
---|---|---|
2023/07 - Current | PhD pre-thesis: Combining Network Biology and Artificial Intelligence to Improve Cancer Drugs Synergy Predictions | Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal |
2022/11 - Current | PhD pre-thesis: Integration of multi-modal genomics datasets with expert data: a patient centered approach to improve diagnosis and prognosis. Rogério Eduardo Ramos Ribeiro | Universidade do Porto Faculdade de Ciências, Portugal |
2022/04 - Current | PhD pre-thesis: A computational framework towards the study of metabolic interactions of the gut microbiome and the human host in Type 2 Diabetes. Nadine Castelhano Santos | Universidade do Minho, Portugal |
Distinctions
Award
2024 | Fulbright Scholarship for Faculty and Researchers
Fulbright Portugal, Portugal
|
2015 | EMBO short-term fellowship
European Molecular Biology Organization, Germany
|
2013 | Bolsa de Estudo Por Mérito - Master's in Bioinformatics
Universidade do Minho, Portugal
|
2012 | ERASMUS placement fellowship
Universidade do Minho, Portugal
|