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André Salgado is a PhD student in Computer Science and Engineering at Instituto Superior Técnico (IST), conducting research at the Gulbenkian Institute for Molecular Medicine (GIMM) and INESC-ID. His doctoral work focuses on applying genomic language models (gLMs) to biomarker discovery, using colorectal cancer (CRC) as a case study. In his first PhD year, he developed a reproducible pipeline for shotgun metagenomic data processing, now used across GIMM initiatives—including the Microbiome in Health & Disease Translational Lab, the Advanced Breast Cancer Translational Lab, and the EU-funded ENDOTARGET project (Horizon Europe). He completed PhD coursework in research methodologies with top grades. His final project in the “Research Topics” course (18/20) evolved into a comparative study on taxonomic profilers for CRC biomarker discovery, now being finalized as a 15-page publication. This laid the foundation for his current focus on gLM-based alternatives to traditional pipelines. During this period, André also taught a 3-month Software Engineering course at IST, delivering weekly 3-hour practical classes to third-year undergraduates. He received a global teaching rating of 8.56/10, highlighting strong communication and mentorship skills. André is an active member of the BIOMICS Twinning Project (HORIZON-WIDERA-2023-ACCESS-02,grant number:101159926), a collaboration between GIMM, EMBL-EBI (UK), CRG (Spain), and ETH Zurich (Switzerland). Through BIOMICS, he receives advanced training in biomedical data science and benefits from an international community of computational researchers. In 2024, he received the DMM Conference Travel Grant from The Company of Biologists, a prestigious award supporting early-career researchers in disease-related research. With this support, he presented a poster at the Cold Spring Harbor Laboratory (CSHL) Microbiome Meeting in New York—one of the world’s leading microbiome conferences. His poster summarized first-year PhD research, including pipeline development and initial CRC microbiome analyses. Currently, André is completing a three-month research visit (March–June 2025) at the University of Cambridge, hosted by Dr. Alexandre Almeida in the Microbiome Function and Diversity group. This collaboration was instrumental for benchmarking traditional ML Pipelines for CRC prediction, and his continued guidance remains valuable for the remainder of the PhD. Previously, André earned a Master’s in Computer Science and Engineering at IST and joined the Health and Medical Data Analytics (HMDA) program. As part of this program, he attended a summer school in France and a semester abroad at UPM (Spain), taking courses in Big Data, Machine Learning, Complex Data in Health, and Data Visualization. His thesis on circular DNA alignment earned a perfect score (20/20), was presented at ISBRA 2023, and published in the proceedings. He also placed 4th internationally in the EIT Health Innovation Challenge with a digital health solution—Portugal’s top result. His academic path began with a Bachelor’s in Computer Science and Engineering at the University of Beira Interior, where he earned a 19/20 in his final project course, conducting research on software reliability. Early experiences include a summer internship at GLINTT, contributing to a healthcare-focused project, and a highly impactful internship at SAP Portugal, where he developed an internal tool that has since been adopted across SAP.
Identificação

Identificação pessoal

Nome completo
André Filipe Cisneiros Ferreira Salgado

Nomes de citação

  • SALGADO, ANDRÉ

Identificadores de autor

Ciência ID
591E-1935-291A
ORCID iD
0000-0002-2940-0767

Endereços de correio eletrónico

  • andre.salgado@tecnico.ulisboa.pt (Profissional)
  • andre.salgado@gimm.pt (Profissional)

Websites

Domínios de atuação

  • Ciências Exatas - Ciências da Computação e da Informação
  • Ciências Exatas - Ciências da Computação e da Informação - Bioinformática

Idiomas

Idioma Conversação Leitura Escrita Compreensão Peer-review
Inglês Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1)
Português (Idioma materno)
Formação
Grau Classificação
2024/02/16 - 2028/02/12
Em curso
Engenharia Informática e de Computadores (Doutoramento)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/09/30 - 2023/11/30
Concluído
Engenharia Informática e de Computadores (Mestrado)
Especialização em Bioinformática e Biologia Computacional
Universidade de Lisboa Instituto Superior Técnico, Portugal
"CSA-MEM: Enhancing Circular DNA Multiple Alignment through Text Indexing Algorithms" (TESE/DISSERTAÇÃO)
17
2018/09/12 - 2021/07/13
Concluído
Engenharia Informática (Licenciatura)
Universidade da Beira Interior, Portugal
13
Percurso profissional

Docência no Ensino Superior

Categoria Profissional
Instituição de acolhimento
Empregador
2024/02/09 - 2024/08/09 Assistente Convidado (Docente Universitário) Universidade de Lisboa Instituto Superior Técnico, Portugal

Outros

Categoria Profissional
Instituição de acolhimento
Empregador
2024/02/12 - Atual PhD Student Gulbenkian Institute for Molecular Medicine, Portugal
2024/02/12 - Atual PhD Student Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2023/04/10 - 2024/02/09 Master Student Fellow Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2021/09/01 - 2022/09/01 UX and Cloud Development Trainee SAP Portugal, Portugal
2019/07/01 - 2019/07/15 Summer Intern Glintt, Portugal
Projetos

Bolsa

Designação Financiadores
2022/04/10 - 2024/02/09 Precise and Efficient Learning using Attention Mechanisms
PTDC/CCI-INF/4703/2021
Bolseiro de Mestrado
Fundação para a Ciência e a Tecnologia

Outro

Designação Financiadores
2025/01/01 - Atual BIOMICS - Fostering Excellent Research, Training and Innovation in Biomedical Data Science
PhD student member
Gulbenkian Institute for Molecular Medicine, Portugal
European Commission
Em curso
Produções

Publicações

Artigo em conferência
  1. André Salgado; Francisco Fernandes; Ana Teresa Freitas. "CSA-MEM: Enhancing Circular DNA Multiple Alignment Through Text Indexing Algorithms". Trabalho apresentado em 19th International Symposium on Bioinformatics Research and Applications (ISBRA), Wroclaw, 2023.
    Publicado • 10.1007/978-981-99-7074-2_41
Poster em conferência
  1. André Salgado. "Enhancing colorectal cancer detection—Integrating Portuguese microbiome and clinical data for early diagnosis.". Trabalho apresentado em Microbiome 2024 - COLD SPRING HARBOR LABORATORY, 2024.
Atividades

Participação em evento

Descrição da atividade
Tipo de evento
Nome do evento
Instituição / Organização
2024/10/29 - 2024/11/02 Poster presentation - Enhancing colorectal cancer detection—Integrating Portuguese microbiome and clinical data for early diagnosis.
Conferência
Microbiome 2024 - COLD SPRING HARBOR LABORATORY
Cold Spring Harbor Laboratory, Estados Unidos
2023/10/26 - 2023/10/27 2nd Microbiome PT Summit
2023/10/09 - 2023/10/12 Project presentation at the 19th International Symposium on Bioinformatics Research and Applications (ISBRA)
Conferência
19th International Symposium on Bioinformatics Research and Applications (ISBRA)
Siec Badawcza Lukasiewicz - PORT Polski Osrodek Rozwoju Technologii, Polónia
2022/09/01 - 2022/09/16 Summer school on Learning from Health Data, organised within the framework of the EIT Heatlh Master's Degree in Health and Medical Data Analytics (HMDA). Completed 42 hours of lectures on data analytics and applications, coaching on innovation & entrepreneurship, group and personal work.
Université Grenoble Alpes, França

European Scientific Institute, França

Curso / Disciplina lecionado

Disciplina Curso (Tipo) Instituição / Organização
2024/02 - 2024/04 Engenharia de Software Engenharia Informática e de Computadores (Licenciatura) Universidade de Lisboa Instituto Superior Técnico, Portugal

Expedição científica

Descrição da atividade Instituição / Organização
2025/03/16 - 2025/06/13 Three-month research visit (March–June 2025) at the University of Cambridge, hosted by Dr. Alexandre Almeida in the Microbiome Function and Diversity group. University of Cambridge Department of Veterinary Medicine, Reino Unido
Distinções

Prémio

2024 Prémio de Mérito Académico Jerónimo Martins em Engenharia Informática e de Computadores
Universidade de Lisboa Instituto Superior Técnico, Portugal
2024 Prémio Impacto UÉvora 2023
Universidade de Évora, Portugal
2024 DMM Conference Travel Grant
The Company of Biologists Ltd, Reino Unido
2023 Barcelona Finals - 4th prize i-Days 2023
EIT Health, Alemanha
2023 Évora I-DAYS 2023 - Winning Team
Universidade de Évora, Portugal

EIT Health, Alemanha