Emanuel Gonçalves | Postdoctoral Fellow

Gonçalves, Emanuel

Emanuel is a computational biologist within the Cancer Genomics group. He is mostly focused on the analysis of high-throughput genomic and pharmacological screens to unravel vulnerabilities in cancer cells that can then be translated into potential novel therapies.

Publications

  • Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.

    Gonçalves E, Raguz Nakic Z, Zampieri M, Wagih O, Ochoa D et al.

    PLoS computational biology 2017;13;1;e1005297

  • Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition.

    Sciacovelli M, Gonçalves E, Johnson TI, Zecchini VR, da Costa AS et al.

    Nature 2016;537;7621;544-547

  • Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models.

    Gonçalves E, Bucher J, Ryll A, Niklas J, Mauch K et al.

    Molecular bioSystems 2013;9;7;1576-83

  • Benchmarking substrate-based kinase activity inference using phosphoproteomic data.

    Hernandez-Armenta C, Ochoa D, Gonçalves E, Saez-Rodriguez J and Beltrao P

    Bioinformatics (Oxford, England) 2017

  • System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.

    Terfve C, Sabidó E, Wu Y, Gonçalves E, Choi M et al.

    Journal of proteome research 2017;16;2;831-841

  • Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.

    Gonçalves E, Raguz Nakic Z, Zampieri M, Wagih O, Ochoa D et al.

    PLoS computational biology 2017;13;1;e1005297

  • Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition.

    Sciacovelli M, Gonçalves E, Johnson TI, Zecchini VR, da Costa AS et al.

    Nature 2016;537;7621;544-547

  • A Landscape of Pharmacogenomic Interactions in Cancer.

    Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP et al.

    Cell 2016;166;3;740-754

  • Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A.

    Rohwer N, Bindel F, Grimm C, Lin SJ, Wappler J et al.

    Oncotarget 2016;7;6;6693-710

  • A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.

    Ryll A, Bucher J, Bonin A, Bongard S, Gonçalves E et al.

    Bio Systems 2014;124;26-38

  • SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.

    Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP et al.

    BMC systems biology 2013;7;135

  • Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models.

    Gonçalves E, Bucher J, Ryll A, Niklas J, Mauch K et al.

    Molecular bioSystems 2013;9;7;1576-83

  • CySBGN: a Cytoscape plug-in to integrate SBGN maps.

    Gonçalves E, van Iersel M and Saez-Rodriguez J

    BMC bioinformatics 2013;14;17

  • Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

    Gonçalves E, Mirlach F and Saez-Rodriguez J

    F1000Research 2013;2;192

  • DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.

    Pacini C, Iorio F, Gonçalves E, Iskar M, Klabunde T et al.

    Bioinformatics (Oxford, England) 2013;29;1;132-4

  • CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms.

    Terfve C, Cokelaer T, Henriques D, MacNamara A, Goncalves E et al.

    BMC systems biology 2012;6;133

  • Optimization approaches for the in silico discovery of optimal targets for gene over/underexpression.

    Gonçalves E, Pereira R, Rocha I and Rocha M

    Journal of computational biology : a journal of computational molecular cell biology 2012;19;2;102-14

Gonçalves, Emanuel
Emanuel's Timeline
2017

Graduated from University of Cambridge and EMBL-EBI, PhD Systems Biology

2016

EMBO short­-term fellowship, EMBO / Visiting PhD at Sauer Lab ETH Zurich

2011

Graduated from University of Minho, BSc Computer Engineering

ERASMUS placement fellowship, University of Minho / EU ERASMUS ­ 2011

2010

Graduated from University of Minho, MSc Bioinformatics