Gil Poiares-Oliveira

☕️

Gil Poiares-Oliveira /ʒiɫ/

Researcher at INESC-ID

Hello!

I enjoy mixing together wet and computational approaches to gain a better understanding of complex biological systems, and discovering novel approaches for tackling disease.

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Interests

Medical Biotechnology
Systems Biology
Epigenetics and RNA Biology
Multiomics

Education

PhD Candidate, Bioengineering and Biosciences

Instituto Superior Técnico, University of Lisbon
MSc, Biotechnology

NOVA School of Science and Technology, NOVA University Lisbon
BSc, Biology (Molecular Biology and Genetics, Minor in Informatics)

Faculty of Sciences, University of Lisbon

Recent Publications

Gil Poiares-Oliveira, Jorge Dos Santos Oliveira, Luciana Peixoto, Daniel Faria (2025). Ready for BioData Management?. BioData.pt | ELIXIR Portugal.

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Gil Poiares-Oliveira (2024). BioData.Pt Data Stewardship Wizard. BioData.pt | ELIXIR Portugal.

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Gil Poiares-Oliveira (2024). DMPortal. BioData.pt | ELIXIR Portugal.

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João R. C. Ramos, José Pinto, Gil Poiares-Oliveira, Ludovic Peeters, Patrick Dumas, Rui Oliveira (2024). Deep Hybrid Modeling of a HEK293 Process: Combining Long Short-term Memory Networks with First Principles Equations. Biotechnology and Bioengineering.

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Cláudia Noronha-Estima (2023). Dissecting the Role of miR-34c-5p in Human CD4+ T Cells.

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Experience

PhD Candidate Researcher
INESC-ID September 2025 – Present
PhD candidate at the Information and Decision Suport Systems (IDSS) scientific area and the Life and Health Technologies Thematic Line (LHT-TL).
Invited Assistant Lecturer
Instituto Superior Técnico April 2025 – Present
Invited Assistant Lecturer at the Department of Computer Science and Engineering.
Bioinformatician
BioData.pt January 2023 – Present
Bioinformatician, trainer and systems administrator at BioData.pt.
Bioinformatics Technician
INESC-ID January 2023 – March 2025
Bioinformatics Technician hired by INESC-ID exclusively for the BioData.pt national research infrastructure. I perform technical bioinformatics work to support BioData.pt data management programmes.

Scientific Adviser: Prof. Ana Teresa Freitas, PhD
Research Collaborator
BioISI - Biosystems & Integrative Sciences Institute January 2021 – June 2022
The Biosystems and Integrative Sciences Research Institute - BioISI is a research institute in the fields of Molecular Biosciences and Systems Biology. It is associated with the Faculty of Sciences of the University of Lisbon.

Scientific adviser: Prof. Margarida Gama-Carvalho, PhD
Graduate Student Researcher
LAQV-REQUIMTE - Associated Laboratory for Green Chemistry October 2021 – March 2022
MSc student researcher at the Systems Biology and Engineering Group at LAQV/REQUIMTE, part of the SilicoMedia project in collaboration with GSK Biologicals.
Graduate Student Researcher
iMM - Instituto de Medicina Molecular João Lobo Antunes August 2020 – December 2020
Graduate Student Researcher that conducted biomedical research in the Sérgio de Almeida Lab at iMM on chromatin and epigenetics.

Education

PhD Candidate, Bioengineering and Biosciences
Instituto Superior Técnico, University of Lisbon September 2025 – Present
Doctoral candidate at the Department of Bioengineering (DBE)
MSc, Biotechnology
NOVA School of Science and Technology, NOVA University Lisbon September 2019 – June 2022
Final grade: 16/20
Dissertation approved with unanimity with a grade of 18/20

Relevant coursework:
- Biochemical Engineering I
- Biopharmaceuticals
- Synthetic and Systems Biology
- Applied Bioinformatics
- Regulation of Gene Expression
- Molecular Toxicology
Dissertation
BSc, Biology (Molecular Biology and Genetics, Minor in Informatics)
Faculty of Sciences, University of Lisbon September 2016 – June 2019
Relevant coursework by field:
- Molecular Biosciences: Cell Biology, Genetics, Fundamentals of Molecular Biology, Prokaryote Genetics, Eukaryote Genetics, Genetic Engineering, Energy Metabolism, Fundamentals of Bioinformatics
- General Life Sciences: Evolution, Animal Physiology, Plant Physiology, Ecology, Animal Biology I/II, Plant Biology
- Computer Science: Programming I/II, Introduction to Web Technologies, Databases, Computer Networks

Skills

Technical Skills

Molecular Biology

Microbiological culture, Animal cell culture (HEK293, U2OS), Molecular cloning, PCR, DNA/RNA extraction, Electrophoresis, qPCR (beginner), BSL-2 laboratory practices, Bioinformatics tools

Systems Biology

Hybrid modelling, flux analysis, genome-scale modelling, constraint-based modelling, dynamic modelling

Omics

NGS/RNA-Seq/Illumina data, RNA-Seq differential expression analysis pipeline development, Multiomics analysis and integration

Computing

Object-oriented programming, Artificial Intelligence, Deep Learning, Artificial Neural Networks, Networking, Web development, Relational databases, Git, Shell scripting, macOS/Linux, Backend development (Flask, Django, Gin), Drupal backend management, Linux server maintenance, OpenStack, SQL

Research Support Skills

Research support

Scientific conference organization, science communication

Pedagogy

Bloom’s Taxonomy, Principles of learning Enhancement of learner engagement and participation, Design of sessions/materials/courses, Assessment and feedback.

Projects

MALDIBANK

101188201

Type: Reearch project

Execution period: May 2025 - Apr 2029

Funder: European Comission

Budget: €9.7M

Role: Researcher

MALDIBANK is conceptualized as a global, cloud-based, open MALDI spectra databank for the identification of microorganisms, combining a vast spectrum database with advanced algorithmic tools.

GLIM-BioData – Gateway for Living Data Management

RI/00138/2024

Type: Data Management Centre Implementation Grant

Execution period: Sep 2024 - Dec 2025

Funder: Foundation for Science and Technology (PT)

Budget: €220k

Role: Researcher

The Gateway for Living Data Management centre (GLIM-BioData) will be the keystone initiative needed to cement BioData.pt as a primary provider of national expertise within the domain of management and valorisation of Portugal’s life and health scientific data.

ELIXIR-STEERS

101131096

Type: Research project

Execution period: Feb 2024 - Jan 2027

Funder: European Commission

Budget: €3.8M

Role: Researcher

The purpose of ELIXIR-STEERS is to build capacity for large-scale, cross-border data analysis and for this capacity to be embedded across member states.

ELIXIR Training Platform (2024-TECH-Training)

2024-TECH-TRAINING

Type: Commissioned Services

Execution period: Jan 2024 - Dec 2026

Funder: ELIXIR

Budget: €785k

Role: Researcher

The ELIXIR Training Platform aims to develop a training community that spans all ELIXIR member states (see the list of Training Coordinators). It aims to strengthen national training programmes, grow bioinformatics training capacity and competence across Europe, and empower researchers to use ELIXIR’s services and tools.

DATAREX - Data Management for Research in ELIXIR

2024-COMM-DATAREX

Type: Commissioned Services

Execution period: Jan 2024 - Dec 2026

Funder: ELIXIR

Budget: €300k

Role: Researcher

DATAREX will facilitate knowledge sharing, develop resources for RDM service providers, coordinate RDM training and content, and make recommendations for enhancing data brokering services.

BRIDGES

PT-BIODATA-2023-SEP-49

Type: Staff Exchange

Execution period: Jan 2024 - Sep 2024

Funder: ELIXIR

Budget: €15k

Role: Researcher

Staff exchange between ELIXIR and the Office of Data Science Strategy (ODSS) at the US National Institutes of Health (NIH) with the purpose of bridging the European and American bioinformatics communities. It focused on FAIR data practices, Trusted Research Environments, and Federated Learning.

Non-Academic Training

Ensuring More Accurate, Generalisable, and Interpretable Machine Learning Models for Bioinformatics

SIB Swiss Institute of Bioinformatics ∙ October 2024

This course focuses on best practices and advanced techniques in Machine Learning, aiming to provide you with the tools needed to develop more accurate, generalizable, and transparent models.

Ensuring More Accurate, Generalisable, and Interpretable Machine Learning Models for Bioinformatics

SIB Swiss Institute of Bioinformatics ∙ February 2024

In this crash course we will focus on CUDA as well as several CUDA-based API, including openMP GPU offloading and python APIs. Through concrete examples we will describe the principles at the core of a successful parallelization attempt.