João Guimarães

iSTARS Era Chair Holder

João C. Guimarães has a BSc in Computer Science and Systems Engineering (2007) and a PhD in Artificial Intelligence (2013) from University of Minho, Braga, Portugal. From 2009 to 2013, he was a visiting scholar at University of California, Berkeley, USA, where he developed machine learning models to understand and engineer the control of gene expression in bacteria. From 2014 to 2018, he conducted his postdoctoral research at the University of Basel, Switzerland, focusing on integrating multi-omics datasets and using systems biology approaches to study gene regulation in health and disease. After that, Joao pursued a career in industry leading data science teams at Roche and Farfetch (2019-2023). In 2023, Joao was selected as the ERA Chair Holder for the iSTARS (Informatics and Statistical Tools for the Advancement of Research Success) project, where he leads a multidisciplinary team working in the biomedical and healthcare fields, combining data science, machine learning, computational biology, genomics and systems biology.

Email: joao.guimaraes@medicina.ulisboa.pt

Research Area: Data Science | Computational and Systems Biology

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Publications

Correia, A.L., Guimaraes, J.C., Auf der Maur, P., De Silva, D., Trefny, M.P., Okamoto, R., Bruno, S., Schmidt, A., Mertz, K., Volkmann, K., Terracciano, L., Zippelius, A., Vetter, M., Kurzeder, C., Weber, W.P., Bentires-Alj, M.
Hepatic stellate cells suppress NK cell-sustained breast cancer dormancy
in Nature, 2021

Ghosh, S., Guimaraes, J. C., Lanzafame, M., Schmidt, A., Syed, A. P., Dimitriades, B., Börsch, A., Ghosh, S., Mittal, N., Montavon, T., Correia, A. L., Danner, J., Meister, G., Terracciano, L. M., Pfeffer, S., Piscuoglio, S., & Zavolan, M.
Prevention of dsRNA‐induced interferon signaling by AGO1x is linked to breast cancer cell proliferation
in The EMBO journal, 2020

Guimaraes, J. C., Mittal, N., Gnann, A., Jedlinski, D., Riba, A., Buczak, K., Schmidt, A., & Zavolan, M. .
A rare codon-based translational program of cell proliferation
in Genome Biology, 2020

Cambray, G., Guimaraes, J.C., & Arkin, A.
Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli
in Nature biotechnology, 2018

Essig, K., Kronbeck, N., Guimaraes, J. C., Lohs, C., Schlundt, A., Hoffmann, A., Behrens, G., Brenner, S., Kowalska, J., Lopez-Rodriguez, C., Jemielity, J., Holtmann, H., Reiche, K., Hackermüller, J., Sattler, M., Zavolan, M., & Heissmeyer, V.
Roquin targets mRNAs in a 3′-UTR-specific manner by different modes of regulation
in Nature communications, 2018

Essig, K., Hu, D., Guimaraes, J. C., Alterauge, D., Edelmann, S., Raj, T., Kranich, J., Behrens, G., Heiseke, A., Floess, S., Klein, J., Maiser, A., Marschall, S., Hrabĕ de Angelis, M., Leonhardt, H., Calkhoven, C. F., Noessner, E., Brocker, T., Huehn, J., Krug, A. B., Zavolan, M., Baumjohann, D., & Heissmeyer, V.
Roquin Suppresses the PI3K-mTOR Signaling Pathway to Inhibit T Helper Cell Differentiation and Conversion of Treg to Tfr Cells
in Immunity, 2017

Mittal, N., Guimaraes, J. C., Gross, T., Schmidt, A., Vina-Vilaseca, A., Nedialkova, D. D., Aeschimann, F., Leidel, S. A., Spang, A., & Zavolan, M.
The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan
in Nature communications, 2017

Guimaraes, J. C., & Zavolan, M.
Patterns of ribosomal protein expression specify normal and malignant human cells
in Genome biology, 2016

Guimaraes, J. C., Rocha, M., & Arkin, A. P.
Transcript level and sequence determinants of protein abundance and noise in Escherichia coli
in Nucleic acids research, 2014

Guimaraes, J. C., Rocha, M., Arkin, A. P., & Cambray, G.
D-Tailor: automated analysis and design of DNA sequences
in Bioinformatics, 2014