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    Susana Vinga
    Associate Professor

    Instituto Superior Técnico
    Dept. Computer Science and Engineering / Dept. Bioengineering

    INESC-ID
    R. Alves Redol 9, 1000-029 Lisboa, Portugal
    Tel. (+351) 213 100 384
    Email: susanavinga@tecnico.ulisboa.pt

    		logo Tecnico logo INESC-ID

     

    Research interests

    Systems and Computational Biology, in particular dynamic modeling, control and optimization of biological networks, and the analysis of high-dimensional clinical data. Focus in model identification of biological systems, and also machine learning and biostatistics for personalized medicine. More information here.

    My short curriculum vitae. My Researcher ID profile, Google Citations, ORCID, and SCOPUS.

    I received the award Prémios Jovens Investigadores UTL/Deloitte e UTL/Caixa Geral de Depósitos 2010. In 2017 I was awarded the Prémio Científico da Universidade de Lisboa/Caixa Geral de Depósitos in the area of Computer Science and Engineering.

    KDBIO/INESC-ID and IST organized RECOMB'2010 - Fourteenth International Conference on Research in Computational Molecular Biololgy, that was held in Lisbon in August 2010.

     

    Present and Past Positions

  • 2018-Present: Associate Professor, Dept of Computer Science and Engineering and Dept of Bioengineering @ Instituto Superior Técnico, Universidade de Lisboa. Teaching:
    • Bioinformatics/Computational Biology, 2020/2021 - 1º Semestre - MBiotec, MECD, MEIC-A, MEIC-T, MEBiom, MEEC.
    • Functional Genomics and Bioinformatics, 2020/2021 - 2º Semestre - MEBiol, MEEC.
    • Microbial Cell Factories, 2020/2021 - 2º Semestre - MBiotec, MicroBio, MEBiol.
    • Introdução aos Algoritmos e Estruturas de Dados (IAED), 2017/2018 - 2ºSemestre - LEIC-A.
    • Projecto de MEIC, 2020/2021 - 2º Semestre - MEIC-A, MEIC-T
    • Projecto em Biotecnologia, 2020/2021 - 2º Semestre - MBiotec

  • 2018-Present: Senior Researcher @ INESC-ID, IDSS lab.

  • 2013-2018: Principal Investigador (Investigador FCT - Development Grant - IF/00653/2012) at CSI) @ Instituto de Engenharia Mecânica (IDMEC)
    • IF2012 Research Project "Integrative Computational Physiology"

  • 2013-2016: Invited Assistant Professor in Área Científica de Controlo, Automação e Informática Industrial ACCAII) @ Instituto Superior Técnico (IST). Teaching:
    • Microbial Cell Factories, 2013/2014 - 2ºSemestre - MicroBio.
    • Controlo de Sistemas, (2ºSemestre 2013/2014 - 2ºSemestre - LEAN, MEMec.
    • Sinais e Sistemas Mecatrónicos (SSM2), 2013/2014 - 1ºSemestre, LEAN, MEMec.

  • 2006-13: Post-doctoral Researcher in the Knowledge Discovery and Bioinformatics group (KDBIO) @ Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID).

  • 2005-13: Invited Assistant Professor of Biostatistics and Informatics at NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa (NMS/UNL).

     

    Current and past projects

    Principal Investigator

    • OLISSIPO - Fostering Computational Biology Research and Innovation in Lisbon (nr. 951970, Vinga S, PI). Funding EU (Horizon 2020 call WIDESPREAD-05-2020 – Twinning). 1 Jan 2021 – 31 Dec 2023.
    • PERSEIDS – Personalizing cancer therapy through integrated modeling and decision (PTDC/EMS-SIS/0642/2014, Vinga S, PI). Funding (FCT). 17 Jun 2016 – 16 Dec 2019.
    • CANCERSYS – Multiscale modeling for personalized therapy of bone metastasis (EXPL/EMS-SIS/1954/2013, Vinga S, PI). Funding (FCT). 1 Apr 2014 – 30 Sep 2015.
    • BONESYS – Bone biochemical and biomechanic integrated modeling: addressing remodeling, disease and therapy dynamics. (Vinga S, IDMEC, PI). Funding (LAETA). 1 Jul 2015 – 31 Dec 2017.
    • HIVCONTROL - Control based on dynamic modeling of HIV-1 infection for therapy design (PTDC/EEA-CRO/100128/2008, Vinga S, PI). Funding (FCT). 1 Jan 2010 – 31 Dec 2012.
    • DYNAMO – Dynamic modeling, control and optimization of metabolic networks (PTDC/EEA-ACR/69530/2006, Vinga S, PI). Funding (FCT). Sep 2007 – 31-Dec 2010.

    Workpackage/Task Leader

    International Projects

    • SOUND – Statistical multi-Omics UNDerstanding of Patient Samples. Financed by: H2020-PHC-2014-two-stage, PHC-32-2014 (RIA). Prime contractor: EMBL (Wolfgang Huber, PI). Contract No. 633974. 1 Sep 2015 – 31 Aug 2018.
    • BACHBERRY – BACterial Hosts for production of Bioactive phenolics from bERRY fruits. Financed by: FP7. KBBE.2013.3.1-01: Plant High Value Products – from discovery to final Product. Prime contractor: Danmarks Tekniske Universitet DTU (Jochen Förster, PI). FP7- 613793. 1 Nov 2013 – 31 Oct 2016.

    National Projects

    • MONET - Multi-omic networks in gliomas (PTDC/CCI-BIO/4180/2020, Lopes MB, PI). Funding (FCT). 1 Mar 2021 – 28 Feb 2024.
    • MATISSE - A machine learning-based forecasting system for shellfish safety (DSAIPA/DS/0026/2019, Lopes MB, PI). Funding (FCT). 1 Apr 2020 – 31 May 2023.
    • PREDICT – Personalized therapy for RhEumatic DIseases via machine learning (PTDC/CCI-CIF/29877/2017, Carvalho AM, PI). Funding (FCT). 1 Jan 2019 – 31 Dec 2021.
    • INTELEGEN – Pharmacokinetic/Pharmacogenetic modulation of HIV infection therapy by bayesian and artificial intelligence methods (PTDC/DTP-FTO/1747/2012, Morais J, PI). Funding (FCT). 1 Jun 2013 – 31 Oct 2015.
    • PNEUMOSYS – A systems biology approach to the role of pneumococcal carbon metabolism in colonization and invasive disease (PTDC/SAU-MII/100964/2008, Neves AR, PI). Funding (FCT). 1 Jan 2010 – 31 Dec 2012.

    Participation as member

    • WISDOM – Water Intelligence System Data (DSAIPA/DS/0089/2018, Carriço N, PI). Funding (FCT). 1 Jan 2019 – 31 Dec 2021.
    • TTRAFFIC – Toxicity and Transport for Fungal production of Industrial Compounds. ERA-IB-2-6/0003/2014. (N Mira, PI, IST-ID). Funding (FCT). 1 Apr 2016 – 31 Mar 2019.
    • NEMESIS – Nonlinear Mixed Effects (NLME) Models applied to the Mechanical Testing of Biomaterials. Funded by LAETA. (Martins P, INEGI, PI).
    • DISRUPTIVE – Paradigm Shift in the Design of Analog and Mixed-Signal Nanoelectronic Circuits and Systems (EXCL/EEI-ELC/0261/2012, Goes J, PI). Funding (FCT). 1 Apr 2013 – 31 Mar 2016.
    • DATASTORM – Large-Scale Data Management in Cloud Environments. (EXCL/EEI-ESS/0257/2012, Silva M, PI). Funding (FCT). 1 Jul 2013 – 30 Jun 2016.
    • ENVIGP - Improving Genetic Programming for the Environment and Other Applications (PTDC/EIA-CCO/103363/2008, Silva S, PI). Funding (FCT). 16 Apr 2010 – 15 Apr 2013.
    • PNEUMOPATH – A comprehensive dissection of pneumococcal-host interactions. Prime contractor: University of Leicester (Peter Andrew, PI). Financed by EUFP7 (Contract 222983). From Mar-2010 to Feb-2012.
    • ARN – Algorithms for the identification of genetic Regulatory Networks (PTDC/EIA/67722/2006, Freitas AT, PI). Funding (FCT). 1 Jan 2008 – 31 Dec 2010.
    • GENEGLOBWQ – Scanning for candidate genes underlying a pulp yield QTL in Eucalyptus globules (PTDC/AGR-GPL/66564/2006, Paiva J, PI). Funding (FCT). 1 Jan 2008 – 31 Dec 2010
    • STRESSSRNA – Genome-wide Analysis of Short RNAs as Modulators in Dehydration Stress Tolerance Using Yolerant and Genetic Model Systems. Prime contractor: U. Bonn (D. Bartels, PI). Financed by EU (ERA-PG/0001/2006). From 01-06-2007 to 30-05-2010.
    • MAGIC – Unveiling Metabolic and Genetic Networks in Living Cells. Prime contractor: INESC-ID (A.T.Freitas, PI). Financed by INESC-ID (IE02ID01004). From 01-03-2006 to 31-12-2007.

     

    Education

  • Mar. 2001- Feb. 2005 - PhD student in Biology/Bioinformatics - grant SFRH / BD / 3134 / 2000 from Portuguese Science Foundation (FCT) - under the supervision of Jonas S Almeida in the Biomathematics Group @ ITQB/UNL (Instituto de Tecnologia Química e Biológica/Universidade Nova de Lisboa). PhD Thesis title: Biological sequence analysis by vector maps: alignment-free comparison of DNA and proteins - defense on the 25 Feb. 2005.
  • 2000-2002 - Graduate Courses in Probability and Statistics (Mathematics Department, Instituto Superior Técnico - Lisboa)
  • 1999 - Mechanical Engineering ( Instituto Superior Técnico - Lisboa )
  • 1998/99 - ERASMUS Program Politecnico di Milano - Italy: Biomedical Engineering
  • 1990/2000 - Music/Piano Course - Instituto Gregoriano de Lisboa

     

    Presentations and publications

    Papers

    Check here.

    Book chapters

    • Biological sequence analysis by vector-valued functions: revisiting alignment-free methodologies for DNA and protein classification
      in Advanced Computational Methods for Biocomputing and Bioimaging, T.D. Pham, H. Yan, and D.I. Crane, Editors.
      Nova Science Publishers, New York. 2007 [PREPRINT]

    National Journal Articles

    • Análise e comparação de sequências biológicas através de funções vectoriais
      Boletim da Sociedade Portuguesa de Estatística, pp. 24-39, Oct. 2007.

    Invited talks

    • Pattern matching through Iterative Function Systems: bridging numerical and graph structures for biosequence analysis. Workshop in Structure Discovery in Biology: Motifs, Networks & Phylogenies. Schloss Dagstuhl - Leibniz Center for Informatics, Germany. Jul 15-20, 2012.
    • Numerical and graph algorithms for genomics - application to infectious diseases. Workshop in Discrete algorithms in the biosciences. University of Göttingen, Germany. Oct 18-19, 2011.
    • Iterated maps: past achievements and cloudy future. Workshop in Alignment-free sequence comparison. Palazzo Cavalli-Franchetti - Venice, Italy. June 21-24, 2011.
    • 8 Jan 2010. Reverse engineering of biochemical networks - understanding systems biology of cells. Universidade da Madeira, Funchal, Portugal.
    • 18-19 Mar 2010. New applications of alignment-free methods for biological sequence analysis and comparison. 13th Portugaliae Genetica - Genome Anatomy. IPATIMUP, Porto, Portugal.
    • 30 Oct - 1 Nov 2009 8th Short Course of the Portuguese Biophysical Society: Systems Biology . Reverse Engineering of Biochemical Networks. Santarém, Portugal.
    • 3-5 Oct 2008 - II Iberian Mathematical Meeting . Dynamical analysis and design of biochemical kinetic networks. Badajoz, Spain.
    • 11-14 Jun 2007 - CBI07: International Workshop on Collaborative Bioinformatics 2007 (RIBIO/EMBnet) Dynamic modeling and control of metabolic networks. Malaga, Spain.
    • 9 Oct 2006 - IV Encontro de Eng.ª Biomédica IST/FML Biological sequence analysis by vector-valued functions: alignment-free methodologies for DNA and protein classification. Lisboa, Portugal. [Abstract]
    • 30 Nov-3 Dec 2005 - MicroBiotec'2005 Information theory and stochastic modeling of biological sequences. Póvoa de Varzim, Portugal. [Abstract]

     

    Last Update: 5 Apr 2021