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As the ERA Chair Holder for the iSTARS project and an Invited Full Professor at the University of Lisbon (FMUL), I lead a multidisciplinary research program at the intersection of Artificial Intelligence (AI) and medicine. My expertise lies in architecting machine learning solutions that leverage complex health data, including genomics, to improve clinical decision-making. My background spans diverse expertises, from developing predictive sequence-activity models for gene regulation during my doctoral work, to employing systems biology and multiomics approaches to study cancer and immunoregulation during my postdoctoral training. These efforts were highly productive, resulting in numerous high-impact publications. My unique trajectory also includes leading data science teams in industry at Roche and Farfetch. This experience in high-scale commercial data environments provided me with a distinct perspective on technical scalability and operational management. In 2023, I have returned to academia to establish a research group in health data science and genomics, uniquely positioned to bridge the gap between experimentalists, clinicians, and data scientists.
Identification

Personal identification

Full name
Joao C Guimaraes

Citation names

  • Guimaraes, Joao C

Author identifiers

Ciência ID
6D12-B75A-A378
ORCID iD
0000-0002-1664-472X
Google Scholar ID
8o1pjyIAAAAJ

Email addresses

  • joao.guimaraes@medicina.ulisboa.pt (Professional)

Telephones

Telephone
  • (+351) 21 798 510 (Professional)

Addresses

  • Avenida Professor Egas Moniz, 1649-028, Lisboa, Lisboa, Portugal (Professional)

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Exact Sciences - Computer and Information Sciences - Computer Sciences
  • Medical and Health Sciences - Clinical Medicine
  • Medical and Health Sciences - Basic Medicine

Languages

Language Speaking Reading Writing Listening Peer-review
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Portuguese (Mother tongue)
Education
Degree Classification
2009/03/01 - 2013/07/26
Concluded
Artificial Intelligence (Doutoramento)
Universidade do Minho, Portugal
"Design principles for controlling gene expression" (THESIS/DISSERTATION)
2002/09/01 - 2007/07/01
Concluded
Engenharia de Sistemas e Informática (Licenciatura)
Major in Inteligência Artificial
Universidade do Minho, Portugal
17/20
Affiliation

Science

Category
Host institution
Employer
2023/07/01 - Current Invited Coordinator Researcher (Research) Universidade de Lisboa Faculdade de Medicina, Portugal
2014/02/01 - 2018/11/30 Postdoc (Research) Universität Basel Department Biozentrum, Switzerland

Other Careers

Category
Host institution
Employer
2021/07/01 - 2023/06/30 Coordenador Técnico (Assistente Técnico) Farfetch UK Limited, United Kingdom
2018/12/01 - 2021/06/30 Coordenador Técnico (Assistente Técnico) F Hoffmann-La Roche AG, Switzerland
2008/01/01 - 2009/02/28 Assistente Técnico (Assistente Técnico) Novabase SGPS SA, Portugal
Projects

Grant

Designation Funders
2017/01 - 2017/12 Decoding ribosomal protein-mediated regulation in breast cancer
NOVUBJCG2017
Novartis (Switzerland)
2014/08 - 2017/07 Mediation of specificity in mRNA translation by heterogeneous ribosomes
51FSP0_157344
Schweizerischer Nationalfonds zur Förderung der wissenschaftlichen Forschung

Contract

Designation Funders
2024/09/10 - Current GLIM-BioData – Gateway for Living Data Management
RI/00138/2024
BioData.pt, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2021/01/01 - Current Informatics and Statistics for Advancement of Research Success
Principal investigator
European Commission
Ongoing
2025/04/01 - 2026/01/31 Development of a clinical decision-making support tool for predicting disease progression in oligometastatic breast cancer patients
2024.07424.IACDC
Principal investigator
Universidade de Lisboa Faculdade de Medicina, Portugal

Centro Hospitalar Universitário Lisboa Norte EPE, Portugal

Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2024/04/01 - 2024/09/30 iSTARS research platform for health data science
Principal investigator
Universidade de Lisboa Faculdade de Medicina, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2011/03/01 - 2014/07/31 ToMEGIM: Ferramentas Computacionais para Engenharia Metabólica usando Modelos Integrados de Escala Genómica
PTDC/EIA-EIA/115176/2009
Universidade do Minho, Portugal

Instituto de Biotecnologia e Bioengenharia, Portugal

Universidade do Minho Centro ALGORITMI, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Journal article
  1. Maria Cristina Faria-Teixeira; Inês M. N. Carvalho; Alexandra Dehesa-Santos; Francisco Salvado e Silva; Helena Afonso Agostinho; Francisco Do Vale; António Vaz-Carneiro; et al. "Geometric morphometrics based diagnostic model for Skeletal Class III patients". Communications Medicine (2026): https://doi.org/10.1038/s43856-026-01557-y.
    10.1038/s43856-026-01557-y
  2. Robert W. Baber; Miguel Â. Magalhães-Patrício; Maria V. Pires; Vasco Correia; Juan M. Lozano-Gil; João C. Guimarães; Chrysothemis C. Brown; Marc Dalod; Carlos M. Minutti. "Ontogenetic Diversification of Type 2 Conventional Dendritic Cells in the Bone Marrow: A Central Logic for Peripheral Immunity". Immunological Reviews 336 1 (2025): http://dx.doi.org/10.1111/imr.70077.
    10.1111/imr.70077
  3. Paula de Oliveira; Inês Sofia Vala; Pedro Faísca; Joao C Guimaraes; Filomena Pina; Esmeralda Poli; Isabel Diegues; et al. "Subtherapeutic Dose of Ionizing Radiation Reprograms the Pre-Metastatic Lung Niche, Accelerating Its Formation and Promoting Metastasis". International Journal of Molecular Sciences (2025): https://doi.org/10.3390/ijms26136145.
    10.3390/ijms26136145
  4. Ana Luísa Correia; Joao C. Guimaraes; Priska Auf der Maur; Duvini De Silva; Marcel P. Trefny; Ryoko Okamoto; Sandro Bruno; et al. "Hepatic stellate cells suppress NK cell-sustained breast cancer dormancy". Nature 594 7864 (2021): 566-571. https://doi.org/10.1038/s41586-021-03614-z.
    10.1038/s41586-021-03614-z
  5. Joao C. Guimaraes; Nitish Mittal; Alexandra Gnann; Dominik Jedlinski; Andrea Riba; Katarzyna Buczak; Alexander Schmidt; Mihaela Zavolan. "A rare codon-based translational program of cell proliferation". Genome Biology 21 1 (2020): https://doi.org/10.1186/s13059-020-1943-5.
    10.1186/s13059-020-1943-5
  6. Souvik Ghosh; Joao C Guimaraes; Manuela Lanzafame; Alexander Schmidt; Afzal Pasha Syed; Beatrice Dimitriades; Anastasiya Börsch; et al. "Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation". The EMBO Journal 39 18 (2020): https://doi.org/10.15252/embj.2019103922.
    10.15252/embj.2019103922
  7. Guillaume Cambray; Joao C Guimaraes; Adam Paul Arkin. "Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli". Nature Biotechnology 36 10 (2018): 1005-1015. https://doi.org/10.1038/nbt.4238.
    10.1038/nbt.4238
  8. Katharina Essig; Nina Kronbeck; Joao C. Guimaraes; Claudia Lohs; Andreas Schlundt; Anne Hoffmann; Gesine Behrens; et al. "Roquin targets mRNAs in a 3'-UTR-specific manner by different modes of regulation". Nature Communications (2018): https://doi.org/10.1038/s41467-018-06184-3.
    10.1038/s41467-018-06184-3
  9. Essig K; Hu D; Guimaraes JC; Alterauge D; Edelmann S; Raj T; Kranich J; et al. "Roquin Suppresses the PI3K-mTOR Signaling Pathway to Inhibit T Helper Cell Differentiation and Conversion of Treg to Tfr Cells.". Immunity (2017): http://europepmc.org/abstract/med/29246441.
    10.1016/j.immuni.2017.11.008
  10. Nitish Mittal; Joao C. Guimaraes; Thomas Gross; Alexander Schmidt; Arnau Vina-Vilaseca; Danny D. Nedialkova; Florian Aeschimann; et al. "The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan". Nature Communications (2017): https://doi.org/10.1038/s41467-017-00539-y.
    10.1038/s41467-017-00539-y
  11. Guimaraes JC; Zavolan M. "Patterns of ribosomal protein expression specify normal and malignant human cells.". (2016): http://europepmc.org/abstract/med/27884178.
  12. Guimaraes JC; Rocha M; Arkin AP. "Transcript level and sequence determinants of protein abundance and noise in Escherichia coli.". (2014): http://europepmc.org/abstract/med/24510099.
  13. Guimaraes JC; Rocha M; Arkin AP; Cambray G. "D-Tailor: automated analysis and design of DNA sequences.". (2014): http://europepmc.org/abstract/med/24398007.
  14. Cambray G; Guimaraes JC; Mutalik VK; Lam C; Mai QA; Thimmaiah T; Carothers JM; Arkin AP; Endy D. "Measurement and modeling of intrinsic transcription terminators.". (2013): http://europepmc.org/abstract/med/23511967.
    10.1093/nar/gkt163
  15. Mutalik VK; Guimaraes JC; Cambray G; Lam C; Christoffersen MJ; Mai QA; Tran AB; et al. "Precise and reliable gene expression via standard transcription and translation initiation elements.". (2013): http://europepmc.org/abstract/med/23474465.
    10.1038/nmeth.2404
  16. Mutalik VK; Guimaraes JC; Cambray G; Mai QA; Christoffersen MJ; Martin L; Yu A; et al. "Quantitative estimation of activity and quality for collections of functional genetic elements.". (2013): http://europepmc.org/abstract/med/23474467.
    10.1038/nmeth.2403
  17. Mutalik VK; Qi L; Guimaraes JC; Lucks JB; Arkin AP. "Rationally designed families of orthogonal RNA regulators of translation.". (2012): http://europepmc.org/abstract/med/22446835.
    10.1038/nchembio.919

Other

Other output
  1. From Biological Parts to Circuit Design. Synthetic Biology. 2013. Guimaraes, Joao C.; Liu, Chang C.; Arkin, Adam P.. http://dx.doi.org/10.1016/B978-0-12-394430-6.00004-2.
    10.1016/b978-0-12-394430-6.00004-2
Activities

Evaluation committee

Activity description
Role
Institution / Organization Funding entity
2026/01 - Current Evaluator for FCT in the call for Advanced Computing projects
Evaluator
Fundação para a Ciência e a Tecnologia
2021/01/01 - Current Evaluator for the MSCA Postdoctoral Fellowships
Evaluator
European Commission, Belgium European Commission

Journal scientific committee

Journal title (ISSN) Publisher
2023/01/01 - Current Frontiers
2020/01/01 - Current Bioinformatics (1367-4811) Oxford University Press
2020/01/01 - Current Nucleic Acids Research (1362-4962) Oxford University Press
2020/01/01 - Current Plos One (1932-6203) PLOS
Distinctions

Award

2013 PhD Award for research of practical utility
Associação Fraunhofer Portugal Research, Portugal
2011 Best poster award in “Biological computational design” at Synthetic Biology 5.0 conference, Stanford, CA, USA
National Science Foundation, United States

Other distinction

2009 PhD Fellowship
Fundação para a Ciência e a Tecnologia, Portugal