Emanuel Gonçalves

INESC-ID, IST - Universidade de Lisboa

Biography

Emanuel Gonçalves is an Assistant Professor at the Instituto Superior Técnico - Universidade de Lisboa and an Integrated Researcher at INESC-ID. His work lies at the interface of computer science, biology, and medicine, and is dedicated to training multidisciplinary engineers capable of bridging these vital fields.

Our research group is developing machine learning models that integrate large-scale multi-modal cancer datasets (multi-omics, CRISPR functional screens, electronic health records) to predict tumour biomarkers. This work focuses on identifying and prioritizing therapeutic targets to combat drug resistance and accelerate the translation of discoveries into clinical applications.

Emanuel Gonçalves earned a PhD from the University of Cambridge (2017), with research carried out at the European Bioinformatics Institute (EMBL-EBI). Earlier training includes an Informatics Engineering degree and a Master’s in Bioinformatics from the University of Minho.

Relevant Publications

Synthetic augmentation of cancer cell line multi-omic datasets using unsupervised deep learning

Cai Z., Apolinário S., Baião A.R., Pacini C., Sousa M.D., Vinga S., Reddel R.R., Robinson P.J., Garnett M.J., Zhong Q., Gonçalves E., Nature Communications (2024).

https://doi.org/10.1038/s41467-024-54771-4
Synthetic lethality in cancer drug discovery: challenges and opportunities

Gonçalves E., Ryan C.J., Adams D.J., Nature Reviews Drug Discovery (2025).

https://doi.org/10.1038/s41573-025-01273-7
A technical review of multi-omics data integration methods: from classical statistical to deep generative approaches

Baião A.R., Cai Z., Poulos R.C., Robinson P.J., Reddel R.R., Zhong Q., Vinga S., Gonçalves E., Briefings in Bioinformatics (2025).

https://doi.org/10.1093/bib/bbaf355
A comprehensive clinically informed map of dependencies in cancer cells and framework for target prioritization

Pacini C., Duncan E., Gonçalves E., Gilbert J., Bhosle S., Horswell S., Karakoc E., Lightfoot H., Curry E., Muyas F., Bouaboula M., Pedamallu C.S., Cortes-Ciriano I., Behan F.M., Zalmas L.-P., Barthorpe A., Francies H., Rowley S., Pollard J., Beltrao P., Parts L., Iorio F., Garnett M.J., Cancer Cell (2024).

https://doi.org/10.1016/j.ccell.2023.12.016
Minimal genome-wide human CRISPR-Cas9 library

Gonçalves E., Thomas M., Behan F.M., Picco G., Pacini C., Allen F., Vinceti A., Sharma M., Jackson D.A., Price S., Beaver C.M., Dovey O., Parry-Smith D., Iorio F., Parts L., Yusa K., Garnett M.J., Genome Biology (2021).

https://doi.org/10.1186/s13059-021-02268-4
Pan-cancer proteomic map of 949 human cell lines

Gonçalves E., Poulos R.C., Cai Z., Barthorpe S., Manda S.S., Lucas N., Beck A., Bucio-Noble D., Dausmann M., Hall C., Hecker M., Koh J., Lightfoot H., Mahboob S., Mali I., Morris J., Richardson L., Seneviratne A.J., Shepherd R., Sykes E., Thomas F., Valentini S., Williams S.G., Wu Y., Xavier D., MacKenzie K.L., Hains P.G., Tully B., Robinson P.J., Zhong Q., Garnett M.J., Reddel R.R., Cancer Cell (2022).

https://doi.org/10.1016/j.ccell.2022.06.010
Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens

Behan F.M., Iorio F., Picco G., Gonçalves E., Beaver C.M., Migliardi G., Santos R., Rao Y., Sassi F., Pinnelli M., Ansari R., Harper S., Jackson D.A., McRae R., Pooley R., Wilkinson P., van der Meer D., Dow D., Buser-Doepner C., Bertotti A., Trusolino L., Stronach E.A., Saez-Rodriguez J., Yusa K., Garnett M.J., Nature (2019).

https://doi.org/10.1038/s41586-019-1103-9
Base editing screens map mutations affecting interferon-γ signaling in cancer

Coelho M.A., Cooper S., Strauss M.E., Karakoc E., Bhosle S., Gonçalves E., Picco G., Burgold T., Cattaneo C.M., Veninga V., Consonni S., Dinçer C., Vieira S.F., Gibson F., Barthorpe S., Hardy C., Rein J., Thomas M., Marioni J., Voest E.E., Bassett A., Garnett M.J., Cancer Cell (2023).

https://doi.org/10.1016/j.ccell.2022.12.009
Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens

Gonçalves E., Segura-Cabrera A., Pacini C., Picco G., Behan F.M., Jaaks P., Coker E.A., van der Meer D., Barthorpe A., Lightfoot H., Mironenko T., Beck A., Richardson L., Yang W., Lleshi E., Hall J., Tolley C., Hall C., Mali I., Thomas F., Morris J., Leach A.R., Lynch J.T., Sidders B., Crafter C., Iorio F., Fawell S., Garnett M.J., Molecular Systems Biology (2020).

https://doi.org/10.15252/msb.20199405
Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition

Sciacovelli M., Gonçalves E., Johnson T.I., Zecchini V.R., da Costa A.S.H., Gaude E., Drubbel A.V., Theobald S.J., Abbo S.R., Tran M.G.B., Rajeeve V., Cardaci S., Foster S., Yun H., Cutillas P., Warren A., Gnanapragasam V., Gottlieb E., Franze K., Huntly B., Maher E.R., Maxwell P.H., Saez-Rodriguez J., Frezza C., Nature (2016).

https://doi.org/10.1038/nature19353