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Gil Poiares Oliveira is a Molecular and Computational Biologist, holding a BSc in Biology with a Minor in Informatics from the Faculty of Sciences of the University of Lisbon, and a MSc in Biotechnology from the NOVA School of Science and Technology of NOVA University Lisbon. His main scientific interests lie in understanding complex biological systems and applying that knowledge towards the development of novel biotechnological approaches to tackle human disease. He has had biomedical research experience in both laboratorial and computational settings, for academia, industry, and research infrastructures. His formal scientific career started in 2020 with fundamental biomedical research in the field of epigenetics at the João Lobo Antunes Institute for Molecular Medicine (FMUL-ULisboa), studying the effects of 3D DNA structures in the rescuing of splicing junctions in genes associated with spinal muscular atrophy. Between 2021 and 2022, he conducted applied research under the supervision of Prof. Rui Oliveira, at the Department of Chemistry of the NOVA School of Science and Technology, in collaboration with GSK Biologicals. He developed a digital twin of the HEK293 cell line metabolism, using hybrid genome-scale modelling approaches towards high-yield vaccine production, a venture that earned him a research fellowship at the University, in addition to his Master's dissertation. Between 2022 and 2023, he deepened his knowledge and experience in genomics, focusing on RNA-seq pipelines, and advanced NGS/ONT sequencing systems, through a research partnership with BioISI (Ciências ULisboa) under the scientific advisement of Prof. Margarida Gama-Carvalho (DQB, Ciências ULisboa). From 2023 to 2025, he worked at BioData.pt—the national biological data research infrastructure and national node of ELIXIR—where he was appointed Deputy Node Coordinator and Deputy Training Coordinator, and was engaged in a number of European projects and ELIXIR activities as a bioinformatics and research data management (RDM) expert. Namely, he was a work-package co-leader in the ELIXIR Train-the-Trainer implementation study devoted to fostering trainers at the European level, a member of the EU INFRATECH project MALDIBANK, which seeks to revolutionise the future of microbial identification using MALDI-TOF technology and artificial intelligence (AI). At the national level, he is one of the authors and trainers of BioData.pt’s “Ready for BioData.pt Management?” capacity building programme on RDM for the life and health sciences, having co-organised training courses throughout the country. He is still a member of the editorial board of the RDMkit, a web portal for RDM best practices to enable FAIR data by design. Currently, he is a researcher at INESC-ID within the Information and Decision Support Systems scientific area and is part of the Life and Health Technologies thematic line, using single and multiomics approaches to leverage biological knowledge out of large datasets. In 2025 and 2026, he also served as a Teaching Assistant with the Department of Computer Science and Engineering of the Instituto Superior Técnico. He's the co-author of three research articles in ISI-indexed publications, one of which in a Q1 journal, in addition to one paper in preprint and one upcoming book chapter on omics data management.
Identification

Personal identification

Full name
MÁRIO GIL POIARES RODRIGUES DE OLIVEIRA

Citation names

  • Gil P. Oliveira
  • Mário Gil Poiares Rodrigues de Oliveira
  • Poiares-Oliveira, Gil

Author identifiers

Ciência ID
D019-5596-42E2
ORCID iD
0000-0003-4638-2879
AuthenticusID
R-00K-EQM
Google Scholar ID
IvGHLzkAAAAJ
Researcher Id
AAE-9440-2021
Scopus Author Id
57932405100

Email addresses

  • gil.oliveira@tecnico.ulisboa.pt (Professional)
  • gil.poiares@inesc-id.pt (Professional)

Telephones

Telephone
  • (+351) 213100300 Ext.: 2512 (Professional)

Addresses

  • INESC-ID, Rua Alves Redol, 9, 1000-029, Lisboa, Lisboa, Portugal (Professional)

Websites

Knowledge fields

  • Natural sciences - Biological Sciences - Molecular Biology
  • Natural sciences - Biological Sciences - Genetics and Heredity
  • Engineering and Technology - Industrial Biotechnology
  • Medical and Health Sciences - Medical Biotechnology
  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Medical and Health Sciences - Medical Biotechnology - Gene-based Diagnostics and Therapeutic Interventions
  • Medical and Health Sciences - Basic Medicine - Human Genetics
  • Medical and Health Sciences - Medical Biotechnology - Technologies Involving the Manipulation of Cells, Tissues, Organs or the Whole Organism

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Spanish; Castilian Intermediate (B1) Intermediate (B1) Intermediate (B1) Intermediate (B1) Intermediate (B1)
French Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2025/10/02 - 2029/10/02
Ongoing
Bioengineering and Biosciences (Doutoramento)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019/09 - 2022/06/28
Concluded
Biotechnology (Mestrado)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
"Development of a novel hybrid genome-scale modelling method and showcase with HEK293 cell cultures" (THESIS/DISSERTATION)
16
2016/09 - 2019/06/21
Concluded
Biology (Licenciatura)
Major in Biologia Molecular e Genética com Minor em Informática
Universidade de Lisboa Faculdade de Ciências, Portugal
14
Affiliation

Science

Category
Host institution
Employer
2025/09/02 - Current Researcher (Research) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2025/03/18 - 2025/10/14 Contracted Researcher (Research) BioData.pt, Portugal
2023/06/05 - 2025/03/17 Contracted Researcher (Research) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
BioData.pt, Portugal
2022/09/07 - 2023/03/31 Research Trainee (Research) Universidade de Lisboa Faculdade de Ciências, Portugal
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2021/01 - 2022/07/31 Researcher (Research) Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
2020/08/25 - 2020/12 Research Trainee (Research) Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal
Universidade de Lisboa Faculdade de Medicina, Portugal

Teaching in Higher Education

Category
Host institution
Employer
2025/02/18 - Current Invited Assistant (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal
2025/04/28 - 2025/06/27 Invited Assistant (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal

Positions / Appointments

Category
Host institution
Employer
2023 - 2025/10/14 ELIXIR Portugal Deputy Node Coordinator BioData.pt, Portugal
BioData.pt, Portugal
(...)
2023 - 2025/10/14 ELIXIR Portugal Deputy Training Coordinator BioData.pt, Portugal
BioData.pt, Portugal
(...)

Others

Category
Host institution
Employer
2017 - 2018/01 Project Management Department Member - Life Sciences Júnior Empresa Ciências, Portugal
Projects

Grant

Designation Funders
2021/10/01 - 2022/03/31 SILICOMEDIA - In silico culture or feed media design based on prior metabolic knowledge: Application to the Production phase of a mammalian cell line
LAQV/BI/006/2021
Research Fellow
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal

Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal

Universidade Nova de Lisboa Departamento de Química, Portugal
GlaxoSmithKline Biologicals SA
Concluded

Contract

Designation Funders
2025/11/10 - 2026/05/10 Coffee Flower
2022.01547.PTDC
Researcher
Universidade de Lisboa Instituto Superior de Agronomia, Portugal

FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal

Universidade Federal de Viçosa, Brazil

Universidade Federal de Lavras, Brazil

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Universidade Federal do Espírito Santo, Brazil

Universidade Nova de Lisboa Associação para a Inovação e Desenvolvimento da FCT, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2025/05/01 - 2025/10/15 MALDIBANK - Multi-domain Open MALDI Spectra Archive for Identification of Microorganisms
Researcher
BioData.pt, Portugal
European Commission
Ongoing
2024/09/10 - 2025/10/15 GLIM-BioData – Gateway for Living Data Management
RI/00138/2024
Researcher
BioData.pt, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2024/02/01 - 2025/10/15 ELIXIR-STEERS
Researcher
BioData.pt, Portugal
European Commission
Ongoing
2024/01/01 - 2025/10/15 ELIXIR Training Platform (24-TECH-Training)
Researcher
BioData.pt, Portugal
ELIXIR
Ongoing
2024/01/01 - 2025/10/15 DATAREX - Data Management for Research in ELIXIR
Researcher
BioData.pt, Portugal
ELIXIR
Ongoing
2023/12 - 2025/10/15 ELIXIR Train-The-Trainer CoS
2024-PEOPLE-TtT
Researcher
BioData.pt, Portugal
ELIXIR
Ongoing
2024/01 - 2024/07 Building bridges to foster the ambition to reach the frontiers of science with global significance and impact: collaboration between the Office of Data Science Strategy (ODSS) at the US National Institutes of Health (NIH) and ELIXIR
Researcher
BioData.pt, Portugal
ELIXIR
Concluded
Outputs

Publications

Book chapter
  1. Pina-Martins, Francisco; Poiares-Oliveira, Gil; OLIVEIRA, JORGE; Pesquita, Cátia. "FAIR Omics Data Management: Overview, Challenges, and Best Practices". In Omics Approaches in Biomedicine and Biotechnology, edited by Gama-Carvalho, Margarida; Figueiredo, Andreia; Francisco R. Pinto. Springer Cham, 2026.
    In press
Conference poster
  1. Gil Poiares-Oliveira; Jorge S. Oliveira; Luciana Peixoto; Daniel Faria. "Ready for BioData Management? Capacity building for Portuguese researchers in research data management". 2025.
    10.5281/zenodo.15981232
  2. OLIVEIRA, JORGE; Cisneiros, Miguel; Santos, Miguel; Silva, Jorge M.; Poiares-Oliveira, Gil; Faria, Daniel; SILVA, MÁRIO J; Freitas, Ana T.. "Advancing FEGA Portugal". Paper presented in ELIXIR All Hands Meeting 2025, 2025.
    10.7490/f1000research.1120225.1
  3. Poiares-Oliveira, Gil; Jorge S. Oliveira; Peixoto, Luciana; Faria, Daniel. Corresponding author: Faria, Daniel. "Ready for BioData Management? Capacitating Portuguese researchers in research data management.". 2025.
    10.7490/F1000RESEARCH.1120205.1
  4. Gil Poiares-Oliveira. "BioData.pt Data Stewardship Wizard". 2024.
    10.5281/zenodo.14288138
  5. Gil Poiares-Oliveira. "DMPortal". 2024.
    10.5281/zenodo.14288023
  6. Gil Poiares-Oliveira; Jorge dos Santos Oliveira; Peixoto, L.; Daniel Faria. "Ready for BioData Management?". Paper presented in BioData.pt | ELIXIR Portugal All Hands 2024, 2024.
    10.5281/zenodo.15102388
  7. Estima, Cláudia; Marques, Madalena; Gil Poiares-Oliveira; Ana Espada de Sousa; Gama-Carvalho, Margarida. Corresponding author: Estima, Cláudia. "Dissecting the role of miR-34c-5p in Human CD4+ T cells". Paper presented in XLVIII Annual Meeting of the Portuguese Society for Immunology, 2023.
  8. Estima, Cláudia; Marques, Madalena; Gil Poiares-Oliveira; B. Farias, Guilherme; Ana E Sousa; Gama-Carvalho, Margarida. Corresponding author: Estima, Cláudia. "The impact of miR-34c-5p on the transcriptome of Human CD4+ T cells". Paper presented in RNA in Disease - IX ptRNA Meeting, 2023.
Journal article
  1. Alper, Pinar; D'Anna, Flora; Droesbeke, Bert; Andrabi, Munazah; Andrade Buono, Rafael; Bianchini, Federico; Bösl, Korbinian; et al. Corresponding author: Coppens, Frederik. "RDMkit: A research data management toolkit for life sciences". Patterns 6 9 (2025): 101345. https://doi.org/10.1016/j.patter.2025.101345.
    Open access • Published • 10.1016/j.patter.2025.101345
  2. Ramos, João R. C.; Pinto, José; Gil Poiares-Oliveira; Peeters, Ludovic; Dumas, Patrick; Oliveira, Rui. Corresponding author: Oliveira, Rui. "Deep hybrid modeling of a HEK293 process: Combining long short-term memory networks with first principles equations". Biotechnology and Bioengineering (2024): http://dx.doi.org/10.1002/bit.28668.
    Open access • Published • 10.1002/bit.28668
  3. Ramos, João R. C.; Gil P. Oliveira; Dumas, Patrick; Oliveira, Rui. "Genome-scale modeling of Chinese hamster ovary cells by hybrid semi-parametric flux balance analysis". Bioprocess and Biosystems Engineering 45 (2022): 1889-1904. http://dx.doi.org/10.1007/s00449-022-02795-9.
    Open access • Published • 10.1007/s00449-022-02795-9
Online resource
  1. ELIXIR. Research Data Management Kit. A deliverable from the EU-funded ELIXIR-CONVERGE project (grant agreement 871075).. 2021. https://rdmkit.elixir-europe.org.
Preprint
  1. Estima, Cláudia; Luta, Raquel; Faria Araújo, Tomás; Ferreira-Fernandes, Carolina; Poiares-Oliveira, Gil; Paulo-Pedro, Margarida; Marques, Madalena; Sousa, Ana E; Gama-Carvalho, Margarida. Corresponding author: Gama-Carvalho, Margarida. "miR-34c-5p is a novel regulator of T cell differentiation that targets FOXP3". 2025. https://doi.org/10.1101/2025.07.25.665590.
    10.1101/2025.07.25.665590
Thesis / Dissertation
  1. "Development of a HEK293 Cell-line Digital Twin Based on Hybrid Semi-Parametric Modeling at the Genome-Scale". Master, Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, 2022. https://hdl.handle.net/10362/142477.
Website
  1. Poiares-Oliveira, Gil. BioData.pt. 2024. https://biodata.pt.

Other

Dataset
  1. Ramos, João R. C.; Poiares-Oliveira, Gil; Dumas, Patrick; Oliveira, Rui. CHO hybrid semi-parametric flux balance analysis (HybridFBA) implementation code in MATLAB. ResearhGate. 2022.
    10.13140/RG.2.2.32550.64326
Other output
  1. Training Data Stewards for Life Sciences - Introduction to Data lifecycle. 2025. Inês Chaves; Poiares-Oliveira, Gil.
    10.5281/zenodo.17232807
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2025/05/06 GLIM-BioData: Portal para a Gestão de Dados da Vida e Saúde Jornadas FCCN
Fundação para a Computação Científica Nacional (Coimbra, Portugal)
2022/09/13 Development of a HEK293 Cell-line Digital Twin Based on Hybrid Semi-Parametric Modeling at the Genome-Scale GSK Vaccines Staff Meeting
GlaxoSmithKline Biologicals SA (Rixensart, Belgium)
2022/02 Development of a HEK293 Cell-line Digital Twin Based on Hybrid Semi-Parametric Modeling at the Genome-Scale Jornadas de Investigação do DQ e DCV
Departamentos de Química e Ciências da Vida da NOVA School of Science and Technology (Caparica, Portugal)

Event organisation

Event name
Type of event (Role)
Institution / Organization
2024/10/02 - 2024/10/04 BioData.pt | ELIXIR-PT All Hands 2024 (2024/10/02 - 2034/10/02)
Meeting (Co-organisor)
BioData.pt, Portugal
2023/09/01 - 2023/12/27 2nd Microbiome PT Summit Organising Committee Member (2023/10/26 - 2023/10/27)
Symposium (Member of the Organising Committee)
BioData.pt, Portugal
2023/11/13 - 2023/11/14 BioData.pt | ELIXIR-PT All Hands 2023 (2023/11/13 - 2023/11/14)
Meeting (Co-organisor)
BioData.pt, Portugal

Association member

Society Organization name Role
2017 - 2019/06 AEFCL - Associação dos Estudantes da Faculdade de Ciências de Lisboa Membro da Direção

Committee member

Activity description
Role
Institution / Organization
2024/03 - Current Editorial Board Member - RDMkit
Member
ELIXIR, United Kingdom
2019 - 2020 Membro Suplente - Comissão Pedagógica da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa
Other
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2016 - 2019/09 Pedagogical Council of the Biology BSc
Member
Universidade de Lisboa Faculdade de Ciências, Portugal
2016/09 - 2019/06 Comissão de Curso da Licenciatura em Biologia da Faculdade de Ciências da Universidade de Lisboa
Member
Universidade de Lisboa Faculdade de Ciências, Portugal
2018 - 2019 Member of the School Council of the Faculty of Sciences of the University of Lisbon
Member
Universidade de Lisboa Faculdade de Ciências, Portugal
2018 - 2019 Comissão ad-hoc de Boas Práticas Pedagógicas - Faculdade de Ciências da Universidade de Lisboa
Member
Universidade de Lisboa Faculdade de Ciências, Portugal
2018 - 2018 Member of the Pedagogical Council of the Faculty of Sciences of the University of Lisbon
Member
Universidade de Lisboa Faculdade de Ciências, Portugal

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2026/02/18 - Current Biomedical Decision and Information Technology Engenharia Biomédica (Mestrado) Universidade de Lisboa Instituto Superior Técnico, Portugal
2025/12/03 - 2025/12/03 ELIXIR-GOBLET Train-the-Trainer Università degli Studi della Campania Luigi Vanvitelli, Italy

ELIXIR, United Kingdom
2025/10/09 - 2025/10/10 Ready for BioData Management? Intensive Course at the University of Coimbra (Outros) BioData.pt, Portugal
2025/07/03 - 2025/07/04 Ready for BioData Management? Intensive Course at CIIMAR (Outros) BioData.pt, Portugal
2025/04/28 - 2025/06/27 Bases de Dados (Databases) Ciências de Engenharia - Engenharia Informática e de Computadores (Licenciatura) Universidade de Lisboa Instituto Superior Técnico, Portugal
2025/03/08 - 2025/03/08 All of the genes, none of the code (Workshop at XX ENEEB) (Outros)
2024/09/30 - 2024/10/01 Health Research Data Management Programa Doutoral do Centro Académico de Medicina de Lisboa (ramo de Medicina; ramo de Ciências Biomédicas; ramo de Ciências e Tecnologias da Saúde) (Doutoramento) BioData.pt, Portugal

Universidade de Lisboa Faculdade de Medicina, Portugal
2024/03/16 - 2024/03/16 Computational Tools and Resources for the Life Sciences (Workshop at ITQB NOVA) (Outros) Universidade do Minho Escola de Engenharia, Portugal
2024/02/24 - 2024/02/24 Computational Tools and Resources for Biomedicine (Workshop at XIX ENEEB) (Outros) Universidade de Lisboa Faculdade de Ciências, Portugal
2024/01/29 - 2024/01/30 Ready for BioData Management? Intensive Course at CCMAR BioData.pt, Portugal

Centro de Ciências do Mar, Portugal
Distinctions

Other distinction

2024 Full Member of the Ordem dos Biólogos
Ordem dos Biólogos, Portugal
2019 Graduate Member of the Ordem dos Biólogos
Ordem dos Biólogos, Portugal