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Emanuel is an Assistant Professor at Instituto Superior Técnico (IST), University of Lisbon, and an Integrated Researcher at INESC-ID. His research interests fall under the areas of Cancer Systems Biology, Bioinformatics, and Machine Learning and focus on the development of computational models to provide data-driven hypotheses of biological phenomena for precision medicine. Previously, Emanuel was a Senior Data Scientist at precision medicine start-up Ophiomics, Lisbon, leading research and development of novel diagnostic and prognostic products for liver cancer patients using machine learning approaches. As a Postdoctoral Researcher at the Wellcome Sanger Institute, Cambridge, UK, he took part and lead international and multidisciplinary projects bridging machine learning with genomic and functional genomic assays, such as CRISPR-Cas9, and proteomics to characterize genetic vulnerabilities of cancer cells and put forward novel clinically actionable biomarkers for precision medicine. Emanuel graduated in Informatics Engineering (2010) from the University of Minho, where he also completed a Master's in Bioinformatics (2012), awarded with distinction, with thesis carried out at the European Bioinformatics Institute, Cambridge, UK. Emanuel obtained his PhD in Systems Biology from the University of Cambridge (2017) with work carried out at EMBL-EBI.
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Identification

Personal identification

Full name
Emanuel José Vieira Gonçalves

Citation names

  • Gonçalves, Emanuel

Author identifiers

Ciência ID
DC10-778A-73A8
ORCID iD
0000-0002-9967-5205
Google Scholar ID
gyEs3B0AAAAJ
Scopus Author Id
55389922800

Email addresses

  • emanuel.v.goncalves@tecnico.ulisboa.pt (Professional)

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Education
Degree Classification
2017/04
Concluded
 Systems Biology (Doctor of Philosophy)
Major in Biological Science at European Bioinformatics Institute
University of Cambridge, United Kingdom
"Modelling regulatory interactions between metabolism and signalling" (THESIS/DISSERTATION)
2012/09
Concluded
 Bioinformática (Mestrado)
Universidade do Minho, Portugal
"Integration of logic modelling and network visualization tools" (THESIS/DISSERTATION)
2010/09
Concluded
 Engenharia Informática (Licenciatura)
Universidade do Minho, Portugal
Affiliation

Science

Category
Host institution 		Employer
2021/09/01 - Current Principal Investigator (Research) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2020/10/01 - 2022/11/01 Visiting Researcher (Research) Wellcome Sanger Institute, United Kingdom
2017/05/01 - 2019/09/30 Postdoc (Research) Wellcome Sanger Institute, United Kingdom
Wellcome Sanger Institute, United Kingdom
2016/10/01 - 2017/04/01 Postdoc (Research) European Bioinformatics Institute, United Kingdom
European Bioinformatics Institute, United Kingdom
2012/01/10 - 2016/09/30 Contracted Researcher (Research) European Bioinformatics Institute, United Kingdom
European Bioinformatics Institute, United Kingdom
2015/09/01 - 2015/12/31 Visiting Researcher (Research) Eidgenössische Technische Hochschule Zürich Institut für Molekulare Systembiologie, Switzerland
Eidgenössische Technische Hochschule Zürich Institut für Molekulare Systembiologie, Switzerland
2012/01/01 - 2012/09/30 Visiting Researcher (Research) European Bioinformatics Institute, United Kingdom
European Bioinformatics Institute, United Kingdom
2011/10 - 2011/12 Researcher (Research) Universidade do Minho, Portugal
Universidade do Minho Centro de Engenharia Biológica, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2021/09/01 - Current Assistant Professor (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal
Universidade de Lisboa Instituto Superior Técnico, Portugal

Others

Category
Host institution 		Employer
2020/10/01 - 2021/08/31 Senior Data Scientist Ophiomics, Portugal
Ophiomics, Portugal
Projects

Grant

Designation Funders
2011/10/01 - 2021/12/31 ToMEGIM: Computational Tools for Metabolic Engineering using Genome-scale Integrated Models
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/115176/PT
Research Fellow
Universidade do Algarve Faculdade de Ciências e Tecnologia
2012/10/01 - 2016/09/30 BioPreDyn
ECFP7-KBBE-2011-5 Grant number 289434
PhD Student Fellow

Contract

Designation Funders
2024/10 - Current MALDIBANK: Multi-domain Open MALDI Spectra BANK for Identification of Microorganisms
HORIZON-INFRA-2024-TECH-01-01
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Ongoing
Outputs

Publications

Conference paper
  1. Gonçalves, E.; Rocha, I.; Rocha, M.. "Computational tools for strain optimization by tuning the optimal level of gene expression". 2012.
    10.1007/978-3-642-28839-5_29
  2. Evangelista, Pedro; Pinho, Jorge; Gonçalves, Emanuel; Maia, Paulo; Sobral, João Luis; Rocha, Miguel. "A Software Platform for Evolutionary Computation with Pluggable Parallelism and Quality Assurance". 2011.
    10.1007/978-3-642-23960-1_6
Journal article
  1. Pacini, Clare; Duncan, Emma; Gonçalves, Emanuel; Gilbert, James; Bhosle, Shriram; Horswell, Stuart; Karakoc, Emre; et al. "A comprehensive clinically informed map of dependencies in cancer cells and framework for target prioritization". Cancer Cell (2024): http://dx.doi.org/10.1016/j.ccell.2023.12.016.
    10.1016/j.ccell.2023.12.016
  2. Ohnmacht, Alexander Joschua; Rajamani, Anantharamanan; Avar, Göksu; Kutkaite, Ginte; Gonçalves, Emanuel; Saur, Dieter; Menden, Michael Patrick. "The pharmacoepigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity". Communications Biology 6 1 (2023): http://dx.doi.org/10.1038/s42003-023-05198-y.
    10.1038/s42003-023-05198-y
  3. Coelho, Matthew A.; Cooper, Sarah; Strauss, Magdalena E.; Karakoc, Emre; Bhosle, Shriram; Gonçalves, Emanuel; Picco, Gabriele; et al. "Base editing screens map mutations affecting interferon-¿ signaling in cancer". Cancer Cell 41 2 (2023): 288-303.e6. http://dx.doi.org/10.1016/j.ccell.2022.12.009.
    10.1016/j.ccell.2022.12.009
  4. Gonçalves, Emanuel; Poulos, Rebecca C.; Cai, Zhaoxiang; Barthorpe, Syd; Manda, Srikanth S.; Lucas, Natasha; Beck, Alexandra; et al. "Pan-cancer proteomic map of 949 human cell lines". Cancer Cell 40 8 (2022): 835-849.e8. http://dx.doi.org/10.1016/j.ccell.2022.06.010.
    10.1016/j.ccell.2022.06.010
  5. Gonçalves, Emanuel; Gonçalves-Reis, Maria; Pereira-Leal, José B.; Cardoso, Joana. "DNA methylation fingerprint of hepatocellular carcinoma from tissue and liquid biopsies". Scientific Reports 12 1 (2022): http://dx.doi.org/10.1038/s41598-022-15058-0.
    10.1038/s41598-022-15058-0
  6. Price, Stacey; Bhosle, Shriram; Gonçalves, Emanuel; Li, Xiaodun; McClurg, Dylan P.; Barthorpe, Syd; Beck, Alex; et al. "A suspension technique for efficient large-scale cancer organoid culturing and perturbation screens". Scientific Reports 12 1 (2022): http://dx.doi.org/10.1038/s41598-022-09508-y.
    10.1038/s41598-022-09508-y
  7. Nicola A. Thompson; Marco Ranzani; Louise van der Weyden; Vivek Iyer; Victoria Offord; Alastair Droop; Fiona Behan; et al. "Combinatorial CRISPR screen identifies fitness effects of gene paralogues". Nature Communications (2021): https://doi.org/10.1038/s41467-021-21478-9.
    10.1038/s41467-021-21478-9
  8. Clare Pacini; Joshua M. Dempster; Isabella Boyle; Emanuel Gonçalves; Hanna Najgebauer; Emre Karakoc; Dieudonne van der Meer; et al. "Integrated cross-study datasets of genetic dependencies in cancer". Nature Communications 12 1 (2021): https://doi.org/10.1038/s41467-021-21898-7.
    10.1038/s41467-021-21898-7
  9. Emanuel Gonçalves; Frezza, Christian. "Genome and metabolome: chance and necessity". Genome Biology 22 1 (2021): http://dx.doi.org/10.1186/s13059-021-02501-0.
    10.1186/s13059-021-02501-0
  10. Gonçalves, Emanuel; Thomas, Mark; Behan, Fiona M.; Picco, Gabriele; Pacini, Clare; Allen, Felicity; Vinceti, Alessandro; et al. "Minimal genome-wide human CRISPR-Cas9 library". Genome Biology 22 1 (2021): http://dx.doi.org/10.1186/s13059-021-02268-4.
    10.1186/s13059-021-02268-4
  11. Dwane, L.; Behan, F.M.; Gonçalves, E.; Lightfoot, H.; Yang, W.; Van Der Meer, D.; Shepherd, R.; et al. "Project Score database: A resource for investigating cancer cell dependencies and prioritizing therapeutic targets". Nucleic Acids Research 49 D1 (2021): D1365-D1372. http://www.scopus.com/inward/record.url?eid=2-s2.0-85099427747&partnerID=MN8TOARS.
    10.1093/nar/gkaa882
  12. Borzo Gharibi; Emanuel Gonçalves; Buhe Nashun; Alex Montoya; Katherine Mankalow; Stephanie Strohbuecker; Rahuman S M Sheriff; et al. "A FGF2-mediated incoherent feedforward loop induces Erk inhibition and promotes naïve pluripotency". bioRxiv (2020): http://dx.doi.org/10.1101/2020.11.11.378869.
  13. Annie Wai Yeeng Chai; Pei San Yee; Stacey Price; Shi Mun Yee; Hui Mei Lee; Vivian KH Tiong; Emanuel Gonçalves; et al. "Genome-wide CRISPR screens of oral squamous cell carcinoma reveal fitness genes in the Hippo pathway". eLife 9 (2020): https://doi.org/10.7554/eLife.57761.
    10.7554/eLife.57761
  14. Gonçalves, E.; Segura-Cabrera, A.; Pacini, C.; Picco, G.; Behan, F.M.; Jaaks, P.; Coker, E.A.; et al. "Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens". Molecular Systems Biology 16 7 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85087473746&partnerID=MN8TOARS.
    10.15252/msb.20199405
  15. Keating, S.M.; Waltemath, D.; König, M.; Zhang, F.; Dräger, A.; Chaouiya, C.; Bergmann, F.T.; et al. "SBML Level 3: an extensible format for the exchange and reuse of biological models". Molecular Systems Biology 16 8 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85089933733&partnerID=MN8TOARS.
    10.15252/msb.20199110
  16. Dempster, Joshua M.; Pacini, Clare; Pantel, Sasha; Behan, Fiona M.; Green, Thomas; Krill-Burger, John; Beaver, Charlotte M.; et al. "Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets". Nature Communications 10 1 (2019): http://dx.doi.org/10.1038/s41467-019-13805-y.
    10.1038/s41467-019-13805-y
  17. Abel Sousa; Emanuel Gonçalves; Bogdan Mirauta; David Ochoa; Oliver Stegle; Pedro Beltrao. "Multi-omics Characterization of Interaction-mediated Control of Human Protein Abundance levels". Molecular & Cellular Proteomics (2019): mcp.RA118.001280-mcp.RA118.001280. https://doi.org/10.1074/mcp.RA118.001280.
    10.1074/mcp.RA118.001280
  18. Picco, Gabriele; Chen, Elisabeth D.; Alonso, Luz Garcia; Behan, Fiona M.; Gonçalves, Emanuel; Bignell, Graham; Matchan, Angela; et al. "Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening". Nature Communications 10 1 (2019): http://dx.doi.org/10.1038/s41467-019-09940-1.
    10.1038/s41467-019-09940-1
  19. Behan, Fiona M.; Iorio, Francesco; Picco, Gabriele; Gonçalves, Emanuel; Beaver, Charlotte M.; Migliardi, Giorgia; Santos, Rita; et al. "Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens". Nature 568 7753 (2019): 511-516. http://dx.doi.org/10.1038/s41586-019-1103-9.
    10.1038/s41586-019-1103-9
  20. Gonçalves, Emanuel; Behan, Fiona M.; Louzada, Sandra; Arnol, Damien; Stronach, Euan A.; Yang, Fengtang; Yusa, Kosuke; et al. "Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects". Genome Biology 20 1 (2019): http://dx.doi.org/10.1186/s13059-019-1637-z.
    10.1186/s13059-019-1637-z
  21. Iorio, Francesco; Behan, Fiona M.; Gonçalves, Emanuel; Bhosle, Shriram G.; Chen, Elisabeth; Shepherd, Rebecca; Beaver, Charlotte; et al. "Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting". BMC Genomics 19 1 (2018): http://dx.doi.org/10.1186/s12864-018-4989-y.
    10.1186/s12864-018-4989-y
  22. Gonçalves, Emanuel; Sciacovelli, Marco; Costa, Ana S.H.; Tran, Maxine Gia Binh; Johnson, Timothy Isaac; Machado, Daniel; Frezza, Christian; Saez-Rodriguez, Julio. "Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells". Metabolic Engineering 45 (2018): 149-157. http://dx.doi.org/10.1016/j.ymben.2017.11.011.
    10.1016/j.ymben.2017.11.011
  23. Gönen, Mehmet; Weir, Barbara A.; Cowley, Glenn S.; Vazquez, Francisca; Guan, Yuanfang; Jaiswal, Alok; Karasuyama, Masayuki; et al. "A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines". Cell Systems 5 5 (2017): 485-497.e3. http://dx.doi.org/10.1016/j.cels.2017.09.004.
    10.1016/j.cels.2017.09.004
  24. Gonçalves, Emanuel; Fragoulis, Athanassios; Garcia-Alonso, Luz; Cramer, Thorsten; Saez-Rodriguez, Julio; Beltrao, Pedro. "Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer". Cell Systems 5 4 (2017): 386-398.e4. http://dx.doi.org/10.1016/j.cels.2017.08.013.
    10.1016/j.cels.2017.08.013
  25. Roumeliotis, Theodoros I.; Williams, Steven P.; Gonçalves, Emanuel; Alsinet, Clara; Del Castillo Velasco-Herrera, Martin; Aben, Nanne; Ghavidel, Fatemeh Zamanzad; et al. "Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells". Cell Reports 20 9 (2017): 2201-2214. http://dx.doi.org/10.1016/j.celrep.2017.08.010.
    10.1016/j.celrep.2017.08.010
  26. Hernandez-Armenta, Claudia; Ochoa, David; Gonçalves, Emanuel; Saez-Rodriguez, Julio; Beltrao, Pedro. "Benchmarking substrate-based kinase activity inference using phosphoproteomic data". Bioinformatics 33 12 (2017): 1845-1851. http://dx.doi.org/10.1093/bioinformatics/btx082.
    10.1093/bioinformatics/btx082
  27. Terfve, Camille; Sabidó, Eduard; Wu, Yibo; Gonçalves, Emanuel; Choi, Meena; Vaga, Stefania; Vitek, Olga; Saez-Rodriguez, Julio; Aebersold, Ruedi. "System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects". Journal of Proteome Research 16 2 (2017): 831-841. http://dx.doi.org/10.1021/acs.jproteome.6b00815.
    10.1021/acs.jproteome.6b00815
  28. Gonçalves, Emanuel; Raguz Nakic, Zrinka; Zampieri, Mattia; Wagih, Omar; Ochoa, David; Sauer, Uwe; Beltrao, Pedro; Saez-Rodriguez, Julio. "Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast". PLOS Computational Biology 13 1 (2017): e1005297. http://dx.doi.org/10.1371/journal.pcbi.1005297.
    10.1371/journal.pcbi.1005297
  29. Sciacovelli, Marco; Gonçalves, Emanuel; Johnson, Timothy Isaac; Zecchini, Vincent Roberto; da Costa, Ana Sofia Henriques; Gaude, Edoardo; Drubbel, Alizee Vercauteren; et al. "Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition". Nature 537 7621 (2016): 544-547. http://dx.doi.org/10.1038/nature19353.
    10.1038/nature19353
  30. Iorio, Francesco; Knijnenburg, Theo A.; Vis, Daniel J.; Bignell, Graham R.; Menden, Michael P.; Schubert, Michael; Aben, Nanne; et al. "A Landscape of Pharmacogenomic Interactions in Cancer". Cell 166 3 (2016): 740-754. http://dx.doi.org/10.1016/j.cell.2016.06.017.
    10.1016/j.cell.2016.06.017
  31. Rohwer, Nadine; Bindel, Fabian; Grimm, Christina; Lin, Suling J.; Wappler, Jessica; Klinger, Bertram; Blüthgen, Nils; et al. "Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A". Oncotarget 7 6 (2015): 6693-6710. http://dx.doi.org/10.18632/oncotarget.6793.
    10.18632/oncotarget.6793
  32. Ryll, A.; Bucher, J.; Bonin, A.; Bongard, S.; Gonçalves, E.; Saez-Rodriguez, J.; Niklas, J.; Klamt, S.. "A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models". Biosystems 124 (2014): 26-38. http://dx.doi.org/10.1016/j.biosystems.2014.07.002.
    10.1016/j.biosystems.2014.07.002
  33. Gonçalves, Emanuel; Mirlach, Franz; Saez-Rodriguez, Julio. "Cyrface: An interface from Cytoscape to R that provides a user interface to R packages". F1000Research 2 (2014): 192. http://dx.doi.org/10.12688/f1000research.2-192.v2.
    10.12688/f1000research.2-192.v2
  34. Chaouiya, Claudine; Bérenguier, Duncan; Keating, Sarah M; Naldi, Aurélien; van Iersel, Martijn P; Rodriguez, Nicolas; Dräger, Andreas; et al. "SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools". BMC Systems Biology 7 1 (2013): 135. http://dx.doi.org/10.1186/1752-0509-7-135.
    10.1186/1752-0509-7-135
  35. Gonçalves, Emanuel; Bucher, Joachim; Ryll, Anke; Niklas, Jens; Mauch, Klaus; Klamt, Steffen; Rocha, Miguel; Saez-Rodriguez, Julio. "Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models". Molecular BioSystems 9 7 (2013): 1576. http://dx.doi.org/10.1039/c3mb25489e.
    10.1039/c3mb25489e
  36. Gonçalves, Emanuel; Iersel, Martijn; Saez-Rodriguez, Julio. "CySBGN: A Cytoscape plug-in to integrate SBGN maps". BMC Bioinformatics 14 1 (2013): 17. http://dx.doi.org/10.1186/1471-2105-14-17.
    10.1186/1471-2105-14-17
  37. Pacini, Clare; Iorio, Francesco; Gonçalves, Emanuel; Iskar, Murat; Klabunde, Thomas; Bork, Peer; Saez-Rodriguez, Julio. "DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data". Bioinformatics 29 1 (2012): 132-134. http://dx.doi.org/10.1093/bioinformatics/bts656.
    10.1093/bioinformatics/bts656
  38. Gonçalves, Emanuel; Pereira, Rui; Rocha, Isabel; Rocha, Miguel. "Optimization Approaches for the In Silico Discovery of Optimal Targets for Gene Over/Underexpression". Journal of Computational Biology 19 2 (2012): 102-114. http://dx.doi.org/10.1089/cmb.2011.0265.
    10.1089/cmb.2011.0265
  39. Terfve, Camille; Cokelaer, Thomas; Henriques, David; MacNamara, Aidan; Goncalves, Emanuel; Morris, Melody K; Iersel, Martijn van; Lauffenburger, Douglas A; Saez-Rodriguez, Julio. "CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms". BMC Systems Biology 6 1 (2012): 133. http://dx.doi.org/10.1186/1752-0509-6-133.
    10.1186/1752-0509-6-133
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2024/07/30 Unsupervised Multi-omics Approaches for Cancer Drug Target and Biomarker Discovery HOPTEC webinar series
John Hopkins University and Instituto Superior Técnico
2024/07/08 Artificial Intelligence - Beyond genomics redeSAÚDE - Multiple Perspectives on Genomic Medicine in Oncology
Universidade de Lisboa (Lisboa, Portugal)
2024/05/17 Unsupervised learning of cancer multi-omics for drug target and biomarker discovery ELLIS Unit Lisbon Retreat 2024
ELLIS Unit Lisbon (Lisboa, Portugal)
2023/10/16 Self-supervised learning of cancer multi-omics for drug target and biomarker discovery {Un-}Conference: AI Methods for Health, Life, and Natural Science AI InScide Out
ELLIS: Un-Conference Meeting in Heidelberg
2023/05/19 Pan-cancer multi-omic map of cancer cell lines Friday Noon Seminar
i3S
2023/04/21 Artificial Intelligence - Applications to Cancer Genomics 2º Encontro Ibérico de Atualização de Sarcomas
IPO Lisboa
2022/11/11 Multiomics heterogeneity and integration in cancer INCDP2022 PhD program Computational Biology in Cancer Module
Champalimaud Foundation (Lisbon, Portugal)
2022/06/22 Metabolic models, Machine learning & Omics data S2M2 Summer School in Metabolic Modeling
Universidade do Minho (Braga, Portugal)
2022/06/15 A pan-cancer proteomic map of human cell lines i3S Cancer Program Retreat
i3S (Porto, Portugal)
2022/04/21 Protein driven machine learning and network approaches for precision medicine BioISI Research Seminar
Faculdade de Ciências da Universidade de Lisboa (FCUL) - BioISI (Lisbon, Portugal)
2022/02/10 Protein driven machine learning and network approaches for precision medicine OLISSIPO Twin Seminar
OLISSIPO
2022/02/06 Protein driven approaches for precision medicine Global QuBi monthly Science Meetings
AstraZeneca
2021/11/09 Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens AORTIC 2021 Conference
AORTIC
2020/03 Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens ELRIG UK Conference
Babraham Institute (Cambridge, United Kingdom)
2018/03 Structural rearrangements determine CRISPR/Cas9 efficacy in cancer Bioinformatics Open Days (BOD)
University of Minho (Braga, Portugal)
2016/11 Signalling regulation of metabolism in hereditary and leiomyomatosis renal cell cancer Proteomic Applications in Oncology
Cancer Research UK Cambridge Institute (Cambridge, United Kingdom)
2011/09/08 Strain Optimization Metaheuristics for Discovering the Optimal Level of Gene Expression Inforum, Coimbra
Universidade de Coimbra (Coimbra, Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2023/10 - Current Statistical Learning for Multi-Omics Integration in Precision Cancer Medicine
Co-supervisor
 PhD in Computer Science and Engineering (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/09 - Current Adversarial generative networks for proteomics imputation
Supervisor
 MSc Engineering Physics (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/09 - Current Deep learning techniques for cancer classification using multi omics data
Co-supervisor
 MSc Computer Science and Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/09 - Current Explaining multi-omics generative models for drug and biomarker discovery
Co-supervisor
 MSc Data Science Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/09 - Current Deep learning-based enhancement of CRISPR-Cas9 screens for the discovery of novel cancer targets
Co-supervisor
 MSc Biomedical Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/09 - Current Computational biology and machine learning approaches to dissect gene expression changes in the immune system during the formation of breast cancer metastases
Co-supervisor
 MSc Biomedical Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/01 - Current Role of CFTR in Epithelial Differentiation and EMT by Functional Genomics
Co-supervisor of Cláudia Alexandra da Silva Rodrigues
 PhD in Biochemistry (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal

Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2022/02 - 2033/06 Generative models to identify precision medicine approaches for cancer
Co-supervisor of Sofia Soares de Albergaria Apolinário
 MSc Data Science (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/01 - 2024/06 Synthetic data generation and imputation using deep learning
Supervisor
 MSc Aerospace Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/09 - 2023/11 Analysis of gene pleiotropy using machine learning methods
Co-supervisor of Raul Pacheco Sarkar
 MSc Biomedical Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/09 - 2023/11 Development of Python library to integrate metabolic and regulatory networks
Co-supervisor of Sebastião Zoio Martins Ferreira dos Santos
 MSc Computer Science and Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/09 - 2023/11 Clinical and molecular characterization of sarcomas using machine learning multiomics integration
Co-supervisor of Manuel Sérgio Sokolov Ravasqueira
 MSc Computer Science and Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/09 - 2023/11 Deep neural networks for multi omics integration
Co-supervisor of Nelson Alexandre Geada Trindade
 MSc Computer Science and Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/09 - 2023/11 Precision medicine and computational biology approaches to study protein networks and find novel therapeutic targets for cancer
Co-supervisor of Miguel Dinis Madeira Agostinho de Sousa
 MSc Biomedical Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/09 - 2023/01 PACMANS & DIPS: A bioinformatic project for PAncreatic Cancer MANagement with Surgery and DIgital Pathology Software
Co-supervisor of Mariana Correia Bento Mourão
 MSc Biomedical Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/01 - 2022/10 Sparse and Interpretable Models for Drug Mechanism-of-Action Discovery
Co-supervisor of Ana Rita do Nascimento Baião
 MSc Biomedical Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2024/09/05 - 2024/09/06 INForum 2024 (https://www.inforum.pt/) - Co-chair Bioinformatics Track (2024/09/05 - 2024/09/06)
Conference (Co-organisor)
2015/06/03 - 2015/06/03 Cambridge Science and Society meeting: Pandemic! The global threat of deadly diseases https://www.ebi.ac.uk/about/events/science-and-society-2015 (2015/06/03 - 2015/06/03)
Symposium (Member of the Organising Committee)
 European Bioinformatics Institute, United Kingdom
2014/06/04 - 2014/06/04 Cambridge Science and Society meeting: What is Life https://www.ebi.ac.uk/about/events/science-and-society-2014 (2014/06/04 - 2014/06/04)
Symposium (Member of the Organising Committee)
 European Bioinformatics Institute, United Kingdom
2013/11/21 - 2013/11/23 Competition in Biology: The race for survival from molecules to systems (2013/11/21 - 2013/11/23)
Conference (Member of the Organising Committee)
 EMBL Heidelberg Genome Biology, Germany
2013/03/14 - 2013/03/15 Bioinformatics Open Days First edition of Bioinformatics Open Days at University of Minho (2013/03/14 - 2013/03/15)
Conference (Member of the Organising Committee)
 Universidade do Minho, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2022/11/15 - 2022/11/18 Poster presentation: "Pan-cancer proteomic map of 949 human cell lines". Emanuel Gonçalves, Rebecca C Poulos, Zhaoxiang Cai, Syd Barthorpe, Srikanth S Manda, Natasha Lucas, Alexandra Beck, Daniel Bucio-Noble, Michael Dausmann, Caitlin Hall, Michael Hecker, Jennifer Koh, Sadia Mahboob, Iman Mali, James Morris, Laura Richardson, Akila J Seneviratne, Erin Sykes, Frances Thomas, Sara Valentini, Steven G Williams, Yangxiu Wu, Dylan Xavier, Karen L MacKenzie, Peter G Hains, Brett Tully, Phillip J Robinson, Qing Zhong, Mathew J Garnett, Roger R Reddel
Conference
 From functional genomics to systems biology
European Molecular Biology Organization, Germany
2020/09/22 - 2020/09/25 Poster presentation: Gonçalves, Emanuel, Mark Thomas, Fiona M Behan, Gabriele Picco, Clare Pacini, Felicity Allen, Mamta Sharma, David A. Jackson, Stacey Price, Charlotte M. Beaver, Oliver Dovey, David Parry-Smith, Francesco Iorio, Leopold Parts, Kosuke Yusa, Mathew J Garnett. “Minimal genome-wide human CRISPR-Cas9 library”.
Conference
 CRISPR and Beyond: Perturbations at Scale to Understand Genomes
2019/09/02 - 2019/09/04 Poster presentation: Gonçalves, Emanuel, Fiona M Behan, Sandra Louzada, Damien Arnol, Euan A. Stronach, Fengtang Yang, Kosuke Yusa, Oliver Stegle, Francesco Iorio, Mathew J Garnett. “Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects”.
Conference
 CRISPR and beyond: perturbations at scale to understand genomes, Cambridge UK
2018/12 - 2018/12 EMBO laboratory leadership course. Highly sought-after course focusing on the development of key skills, such as leadership, communication, scientific writing and research integrity among others, for a successful leader and researcher. Coordinated by Dr Samuel Krahl and Sašo Kocevar (22 training hours) EMBO laboratory leadership course
The European Molecular Biology Organization (EMBO), Germany
2018/11/10 - 2018/11/13 Poster presentation: Gonçalves, Emanuel, Fiona M Behan, Sandra Louzada, Damien Arnol, Euan A. Stronach, Fengtang Yang, Kosuke Yusa, Oliver Stegle, Francesco Iorio, Mathew J Garnett. “Structural rearrangements generate cell specific gene independent CRISPR-Cas9 loss-of-fitness effects”
Conference
 From Functional Genomics to Systems Biology, Heidelberg
2018/03/01 - 2018/03/02 Poster presentation: Gonçalves, Emanuel, Fiona M Behan, Francesco Iorio, Euan Stronach, Kosuke Yusa, Mathew Garnett. “CRISPR/Cas9 dropout screens inform cancer drug mode of action”.
Conference
 CRUK Cambridge Institute Annual International Symposium ‘Unanswered Questions in Precision Medicine’, Cambridge
2017/05/07 - 2017/05/11 Poster presentation: Gonçalves, Emanuel, Athanassios Fragoulis, Luz Garcia-Alonso, Thorsten Cramer, Julio Saez-Rodriguez, Pedro Beltrao. “Chromosomal rearrangements are commonly post-transcriptionally attenuated in cancer”.
Conference
 Data-Driven Biotechnology Conference, Copenhagen
2016/09/16 - 2016/09/20 Poster presentation: Gonçalves, Emanuel, Zrinka Raguz Nakic, Mattia Zampieri, Omar Wagih, David Ochoa, Uwe Sauer, Pedro Beltrão and Julio Saez-Rodriguez. “Systematic analysis of transcriptional and post-transcriptional regulation of metabolism in yeast”.
Conference
 International Conference on Systems Biology (ICSB 2016), Barcelona
2015/09/16 - 2015/09/18 Poster presentation: Gonçalves, Emanuel, David Ochoa, Pedro Beltrão and Julio Saez-Rodriguez. “Understanding metabolic regulation in Saccharomyces cerevisiae”.
Conference
 4th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2015), Heidelberg
2014/11/09 - 2014/11/14 Poster presentation: Gonçalves, Emanuel, Daniel Machado, Miguel Rocha and Julio Saez-Rodriguez. “Cell viability prediction from large-scale omics data using machine learning and mechanistic modelling approaches”.
Conference
 Seventh Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, San Diego
2014/05/20 - 2014/05/23 Poster presentation: Gonçalves, Emanuel, Sara Correia, Pedro Beltrão, Miguel Rocha and Julio Saez-Rodriguez. “Modelling Cell Lines Phenotype Integrating Metabolic and Regulatory Networks”.
Conference
 3rd Conference on Constraint-Based Reconstruction and Analysis, Virginia
2013/10/09 - 2013/10/10 Poster presentation: Gonçalves, Emanuel, Martijn van Iersel, and Julio Saez-Rodriguez. “Cytoscape plugins to visualize and model signalling networks and drug effects using R”.
Conference
 Cytoscape Workshop, Paris

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2023/09 Understanding Metastasis Organotropism Patterns Through Within-cell and Between-cells Molecular Interaction Networks
(Thesis) Main arguer
 João André Isidoro Miranda (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023/05 Predicting Allosteric Regulation at Genome Scale
(Thesis) Main arguer
 Elin Sandertun Røed (Master)
Norges teknisk-naturvitenskapelige universitet, Norway
2023/05 Assessing the performance of classifiers on sequence data: an application to cancer genomics
(Thesis) Main arguer
 Anto ´nio Jose ´ de Medeiros Mendonc ¸a Palma Ramos (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/04 Systems-level modelling of the cancer and immune metabolome to improve immunotherapeutic outcomes
(Thesis) Main arguer
 Sara Manso de Sousa Cardoso (PhD)
Universidade do Minho, Portugal
2023/01 Predicting metabolic fluxes from gene expression data using machine learning
(Thesis) Main arguer
 Marieke Cecilia van Eggelen (Master)
Norges teknisk-naturvitenskapelige universitet, Norway
2022/07 Integrative Pathway Analysis Approaches for Cancer Research And Drug Development
(Thesis) Main arguer
 José Vítor de Castro Vieira (PhD)
Universidade do Minho, Portugal
2021/12 A Metabolic-Regulatory Genome-Scale Integration for Saccharomyces cerevisiae: Predicting Targets for Increased Ethanol Production
(Thesis) Main arguer
 Carolina Correia Paiva Parada (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/07 Computational approaches for the integration of in vitro chemical and screening datasets
(Thesis) Main arguer
 Ana Beatriz Gonçalves da Cunha (Master)
Universidade do Minho, Portugal

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2023/09 - 2023/11 Computational Biology (Mestrado) Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/03 - 2023/04 Introduction to Algorithms and Data Structures LEIC (Licenciatura) Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/09 - 2022/11 Programação com Objectos Licenciatura em Engenharia Informática e de Computadores (Licenciatura) Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/05 - 2022/07 Inteligência Artificial Licenciatura em Engenharia Informática e de Computadores (Licenciatura) Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/09 - 2021/11 Programação com Objectos Licenciatura em Engenharia Informática e de Computadores (Licenciatura) Universidade de Lisboa Instituto Superior Técnico, Portugal
2019/08/03 - 2019/08/08 Systems Biology: From Large Datasets to Biological Insight Visualisation and modelling of signalling transduction networks using CytoCopteR Wellcome Genome Campus Advanced , United Kingdom
2018/06/03 - 2018/06/08 In Silico Systems Biology Wellcome Genome Campus Advanced Course, Cambridge, UK. Wellcome Genome Campus Advanced Course, United Kingdom
2017/07/09 - 2017/07/14 In Silico Systems Biology Wellcome Genome Campus Advanced Course Wellcome Genome Campus Advanced Course, United Kingdom
2016/09/21 - 2016/09/21 ISCB 2016 Workshop Hands-on course on logic modelling of signalling networks using CellNOptR. International Society for Computational Biology, United States
2016/08/03 - 2016/08/08 In Silico Systems Biology Wellcome Genome Campus Advanced Course, Cambridge, UK. Wellcome Genome Campus Advanced Course, United Kingdom
2015/06/07 - 2015/06/12 In Silico Systems Biology Visualisation and modelling of signalling transduction networks using CytoCopteR.

Interview (newspaper / magazine)

Activity description Newspaper / Forum
2020 Genome-wide CRISPR screens and drug screens come together to reveal cancer drug mechanism-of-action. Previewing Gonçalves, Emanuel, et al. 2020. Molecular Systems Biology preLights

Mentoring / Tutoring

Topic Student name
2017/09 - 2017/12 Screen design for drug combination screens Haynes Heaton
2016/05 - 2016/12 Java-based boolean logic modelling framework Mahdi Saber
2013/08 - 2014/02 Integrating logic modelling CellNOptR R package Cytoscape Franz Mirlach

Other jury / evaluation

Activity description Institution / Organization
2023/07 - Current PhD pre-thesis: Combining Network Biology and Artificial Intelligence to Improve Cancer Drugs Synergy Predictions Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
2022/11 - Current PhD pre-thesis: Integration of multi-modal genomics datasets with expert data: a patient centered approach to improve diagnosis and prognosis. Rogério Eduardo Ramos Ribeiro Universidade do Porto Faculdade de Ciências, Portugal
2022/04 - Current PhD pre-thesis: A computational framework towards the study of metabolic interactions of the gut microbiome and the human host in Type 2 Diabetes. Nadine Castelhano Santos Universidade do Minho, Portugal
Distinctions

Award

2024 Fulbright Scholarship for Faculty and Researchers
Fulbright Portugal, Portugal
2015 EMBO short-term fellowship
European Molecular Biology Organization, Germany
2013 Bolsa de Estudo Por Mérito - Master's in Bioinformatics
Universidade do Minho, Portugal
2012 ERASMUS placement fellowship
Universidade do Minho, Portugal