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Susana Vinga received a Mechanical Engineering degree (1999), a post-graduate degree in Probability and Statistics at Instituto Superior Técnico (IST-UTL), Biomedical specialization at Politecnico of Milan, and a PhD degree in Bioinformatics (2005) at ITQB-UNL (Portugal). From 2006-2013, she was a researcher in the Knowledge Discovery and Bioinformatics group at INESC-ID and invited assistant professor of Biostatistics and Informatics at the Faculty of Medical Sciences (FCM-UNL). Between 2013-2018 she was a Principal Investigator (Investigador FCT) at IDMEC, Instituto Superior Técnico, Universidade de Lisboa (Portugal), under this highly competitive program. Since 2018 she is an Associate Professor at Instituto Superior Técnico, Universidade de Lisboa, in a joint position between the Dept. of Computer Science and Engineering (DEI) and the Dept. of Bioengineering (DBE). She has been (co-)supervising 6 post-doc, 10 PhD (eight defended), and more than 60 MSc Theses, several internships, and grant holders. She has published in high-impact journals, achieving an ISI h-index=21 (Google h-index=28), with 100 publications. She has successfully coordinated as Principal Investigator three national FCT projects: DynaMo - Dynamic modeling, control and optimization of metabolic networks (2007-10), HIVCONTROL - Control based on dynamic modeling of HIV-1 infection for therapy design (2010-12), and PERSEIDS - Personalizing cancer therapy through integrated modeling and decision (2016-2019), and participated in several national and European projects (FP7, H2020) as a team member and work package leader in the areas of Biotechnology (project BacHBerry - BACterial Hosts for production of Bioactive phenolics from bERRY fruits to products, FP7) and Computational Biology (project SOUND - Statistical multi-Omics UNDerstanding of Patient Samples, H2020). Since January 2021, she is the PI of the European H2020 Twinning project OLISSIPO - Fostering Computational Biology Research and Innovation in Lisbon, which aims to strengthen INESC-ID/IST research profile in Computational Biology. Her main achievements are in the development of methods for Genomics, where she coined the area of alignment-free biological sequence analysis and comparison in a review, which was the 3rd most cited paper in Portugal in Computer Science. She has continuously published in this area by proposing new metrics and entropy measures for DNA and proteins and was the Editor of a special issue of Briefings in Bioinformatics (2014) on this theme. In Systems Biology, she is currently working on model identification of biological systems, developing parameter estimation methods for ordinary differential equations, both for biochemical and gene regulatory networks, and intra-host HIV infection. She is also designing control strategies for these systems, with application in the optimization of personalized pharmacological therapies in translational research. Other activities include creating and teaching several courses, serving as a reviewer for international journals, and participating in theses and conference program committees. She is an Associate Editor of BMC Bioinformatics, a top journal in Mathematical and Computational Biology, PLoS ONE, and Genes. She was granted in 2010 the Young Researcher Award of the UTL in the area of Informatics for the impact of her publications. In 2017 and also in 2022 she won the Prémio Científico da Universidade de Lisboa in the area of Computer Science. Since 2021, she is a member of the INESC-ID Board of Directors, Vice-President of DEI, and Senator of Univ. Lisboa.
Identification

Personal identification

Full name
Susana Vinga

Citation names

  • Vinga, Susana

Author identifiers

Ciência ID
9713-F74D-4805
ORCID iD
0000-0002-1954-5487
Google Scholar ID
tqCfgygAAAAJ
Researcher Id
B-8450-2008
Scopus Author Id
55893670600

Email addresses

  • susanavinga@tecnico.ulisboa.pt (Professional)

Telephones

Telephone
  • (+351) 218419504 (Professional)

Addresses

  • INESC-ID, Instituto Superior Técnico, Universidade de Lisboa. Av Rovisco Pais 1, 1049-001, Lisboa, Lisboa, Portugal (Professional)

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Exact Sciences - Mathematics - Statistics and Probability
  • Engineering and Technology - Electrotechnical Engineering, Electronics and Informatics - Automation and Control Systems
  • Engineering and Technology - Mechanical Engineering

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Italian Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Intermediate (B1) Advanced (C1) Intermediate (B1) Intermediate (B1)
German Beginner (A1)
Education
Degree Classification
2005
Concluded
Biological Sciences / Bioinformatics (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
"Biological sequence analysis by vector maps: alignment-free comparison of DNA and proteins" (THESIS/DISSERTATION)
Aprovada
2002
Concluded
Applied Mathematics - Probability and Statistics (Pós-Graduação)
Universidade de Lisboa Instituto Superior Técnico, Portugal
4
1999
Concluded
Mechanical Engineering - Automation and Robotics (Licenciatura)
Universidade de Lisboa Instituto Superior Técnico, Portugal
17
1993
Concluded
Ensino Secundário (Ensino secundário)
Esc. Sec. Herculano de Carvalho, Portugal
19
Affiliation

Science

Category
Host institution
Employer
2018/02 - Current Researcher (Research) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2013/09 - 2018/02 Principal Investigator (Research) Instituto de Engenharia Mecânica, Portugal
Instituto de Engenharia Mecânica, Portugal
(...)
2006/01 - 2013/09 Contracted Researcher (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

Teaching in Higher Education

Category
Host institution
Employer
2018/02 - Current Associate Professor (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal
Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - 2017 Invited Assistant Professor (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal
Universidade de Lisboa Instituto Superior Técnico, Portugal
2005/11 - 2013/08 Invited Assistant Professor (University Teacher) Universidade Nova de Lisboa Faculdade de Ciências Médicas, Portugal
Universidade Nova de Lisboa Faculdade de Ciências Médicas, Portugal
Projects

Grant

Designation Funders
2021/01/01 - 2023/12/31 OLISSIPO - Fostering Computational Biology Research and Innovation in Lisbon
Principal investigator
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
EU Framework Programme for Research and Innovation Spreading Excellence and Widening Participation
Ongoing
2019/01 - 2021/12 PREDICT - Terapia personalizada para doenças reumáticas por intermédio de aprendizagem automática
Provided by PTCRIS: PTDC/CCI-CIF/29877/2017
Fundação para a Ciência e a Tecnologia
2016/06 - 2019/12 PERSEIDS - Personalizing cancer therapy through integrated modeling and decision
Principal investigator
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2015/09 - 2018/08 SOUND - Statistical multi-Omics UNDerstanding of patient samples. Horizon 2020
2013/11 - 2016/10 BacHBerry - BACterial Hosts for production of Bioactive phenolics from bERRY fruits European Commission Seventh Framework Programme for Research and Technological Development
2013/07 - 2016/06 Large-Scale Data Management in Cloud Environments Fundação para a Ciência e a Tecnologia, I.P.
2013/04 - 2016/03 A Paradigm Shift in the Design of Analog and Mixed-Signal Nanoelectronic Circuits and Systems. Fundação para a Ciência e a Tecnologia, I.P.
2013/06 - 2015/10 Pharmacokinetic/Pharmacogenetic modulation of HIV infection therapy by bayesian and artificial intelligence methods Fundação para a Ciência e a Tecnologia, I.P.
2014/04 - 2015/03 CancerSys - Multiscale modeling for personalized therapy of bone metastasis
Principal investigator
Fundação para a Ciência e a Tecnologia, I.P.
2010/04 - 2013/10 EnviGP - Improving Genetic Programming for the Environment and Other Applications Fundação para a Ciência e a Tecnologia, I.P.
2010/04 - 2013/09 PneumoSyS - A systems biology approach to the role of pneumococcal carbon metabolism in colonization and invasive disease Fundação para a Ciência e a Tecnologia, I.P.
2011/01 - 2012/12 Projecto Estratégico - LA 21 - 2011-2012
123479UID
PEst-OE/EEI/LA0021/2011
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2010/01 - 2012/12 HIVCONTROL - Control based on dynamic modeling of HIV-1 infection for therapy design
Principal investigator
Fundação para a Ciência e a Tecnologia, I.P.
2009/03 - 2012/08 PNEUMOPATH - A comprehensive dissection of pneumococcal-host interactions European Commission Seventh Framework Programme for Research and Technological Development
2008/01 - 2010/12 GenEglobwq - Scanning for candidate genes underlying a pulp yield QTL in Eucalyptus globulus Fundação para a Ciência e a Tecnologia, I.P.
2008/01 - 2010/12 ARN - Algorithms for the identification of genetic Regulatory Networks Fundação para a Ciência e a Tecnologia, I.P.
2007/09 - 2010/12 DynaMo - Dynamical modeling, control and optimization of metabolic networks
Principal investigator
Fundação para a Ciência e a Tecnologia, I.P.

Contract

Designation Funders
2021/01/01 - 2025/12/31 Laboratório Associado em Energia, Transportes e Aeroespacial
LA/P/0079/2020
UID/EMS/50022/2019
Instituto de Engenharia Mecânica, Portugal

Universidade da Beira Interior, Portugal

Instituto de Ciência e Inovação em Engenharia Mecânica e Engenharia Industrial, Portugal

Associated Laboratory for Energy Transports and Aeronautics, Portugal

Associação para o Desenvolvimento da Aerodinâmica Industrial, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2021/01/01 - 2025/12/31 Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento em Lisboa
LA/P/0078/2020
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2021/03/01 - 2024/02/29 MONET - Redes multi-ómicas em gliomas
PTDC/CCI-BIO/4180/2020
Universidade do Minho, Portugal

Universidade Nova de Lisboa NOVAMath, Portugal

Instituto de Telecomunicações Lisboa, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Universidade Nova de Lisboa Associação para a Inovação e Desenvolvimento da FCT, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2020/04/01 - 2023/03/31 Salubridade de bivalves: sistema preditivo e de alerta precoce
DSAIPA/DS/0026/2019
Instituto Português do Mar e da Atmosfera, Portugal

Universidade Nova de Lisboa Laboratório para a Ciência da Computação e Informática, Portugal

Instituto de Telecomunicações Lisboa, Portugal

Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Universidade Nova de Lisboa Associação para a Inovação e Desenvolvimento da FCT, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2019/01/01 - 2022/06/30 Sistema Inteligente de Dados de Água
DSAIPA/DS/0089/2018
Instituto Politécnico de Setúbal, Portugal

Instituto Superior Técnico Centro de Estudos de Gestão, Portugal

Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal

Universidade de Lisboa Centro de Matemática Computacional e Estocástica, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Universidade de Lisboa Instituto de Investigação e Inovação em Engenharia Civil para a Sustentabilidade, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2019/01/01 - 2021/12/31 Terapia personalizada para doenças reumáticas por intermédio de aprendizagem automática
PTDC/CCI-CIF/29877/2017
Instituto de Telecomunicações Lisboa, Portugal

Universidade Nova de Lisboa, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2013/04/01 - 2016/12/31 Uma Mudança de Paradigma no Projecto de Circuitos e Sistemas Nanoelectrónicos Analógicos e de Modo Misto.
EXCL/EEI-ELC/0261/2012
Universidade Nova de Lisboa Centro de Tecnologias e Sistemas, Portugal

UNINOVA Instituto de Desenvolvimento de Novas Tecnologias, Portugal

Instituto de Telecomunicações Lisboa, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2013/07/01 - 2016/07/03 Tratamento de Dados em Larga-escala em Ambientes Nuvem
EXCL/EEI-ESS/0257/2012
Universidade de Lisboa Instituto Superior de Agronomia, Portugal

Centro de Estudos em Geografia e Ordenamento do Território, Portugal

Fundacao de Computacao Cientifica Nacional, Portugal

Instituto de Biologia Experimental e Tecnológica, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2014/04/01 - 2015/09/30 CancerSys - Modelação multiscala para a terapia personalizada de metástases ósseas
EXPL/EMS-SIS/1954/2013
Instituto de Engenharia Mecânica, Portugal

Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal

Instituto de Telecomunicações Lisboa, Portugal

Centro Hospitalar Universitário Lisboa Norte EPE, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2010/04/16 - 2013/10/15 EnviGP - Improving Genetic Programming for the Environment
PTDC/EIA-CCO/103363/2008
Universidade de Coimbra, Portugal

Universidade de Coimbra Centro de Informatica e Sistemas, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2007/05/01 - 2010/04/30 Genome-wide Analysis of Short RNAs as Modulators in Dehydration Stress Tolerance Using Yolerant and Genetic Model Systems
ERA-PG/0001/2006
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book
  1. Pinto, J.D.; Carvalho, A.M.; Vinga, S.. Outlier detection in cox proportional hazards models based on the concordance c-Index. 2015.
    10.1007/978-3-319-27926-8_22
  2. Cruz, L.P.; Vieira, S.M.; Vinga, S.. Fuzzy clustering for incomplete short time series data. 2015.
    10.1007/978-3-319-23485-4_36
  3. Costa, R.S.; Nguyen, S.; Hartmann, A.; Vinga, S.. Exploring the cellular objective in flux balance constraint-based models. 2014.
  4. Silva, S.; Ingalalli, V.; Vinga, S.; Carreiras, J.M.B.; Melo, J.B.; Castelli, M.; Vanneschi, L.; Gonçalves, I.; Caldas, J.. Prediction of forest aboveground biomass: An exercise on avoiding overfitting. 2013.
    10.1007/978-3-642-37192-9-41
Book chapter
  1. Ana Rita Baião; Carolina Peixoto; Marta B. Lopes; Pedro Reis Costa; Alexandra M. Carvalho; Susana Vinga. "Evaluating the Causal Role of Environmental Data in Shellfish Biotoxin Contamination on the Portuguese Coast". 2023.
    10.1007/978-3-031-49011-8_26
  2. Diogo Ribeiro; Filipe Ferraz; Marta B. Lopes; Susana Rodrigues; Pedro Reis Costa; Susana Vinga; Alexandra M. Carvalho. "Causal Graph Discovery for Explainable Insights on Marine Biotoxin Shellfish Contamination". 2023.
    10.1007/978-3-031-48232-8_44
  3. Beatriz N. Leitão; Paula Faustino; Susana Vinga. "Comparative Evaluation of Classification Indexes and Outlier Detection of Microcytic Anaemias in a Portuguese Sample". 2022.
    10.1007/978-3-031-16474-3_19
  4. André Ferreira; Sara C. Madeira; Marta Gromicho; Mamede de Carvalho; Susana Vinga; Alexandra M. Carvalho. "Predictive Medicine Using Interpretable Recurrent Neural Networks". 187-202. Springer International Publishing, 2021.
    10.1007/978-3-030-68763-2_14
  5. Lopes, M.B.; Vinga, Susana. "Learning Biomedical Networks: Toward Data-Informed Clinical Decision and Therapy". In Advances in Artificial Intelligence, Computation, and Data Science, 77-92. Springer International Publishing, 2021.
    10.1007/978-3-030-69951-2_3
  6. Pedro F. Ferreira; Alexandra M. Carvalho; Susana Vinga. "Variational Inference in Probabilistic Single-cell RNA-seq Models". 11-18. Springer International Publishing, 2020.
    10.1007/978-3-030-34585-3_2
  7. João Villa-Brito; Marta B. Lopes; Alexandra M. Carvalho; Susana Vinga. "Unravelling Breast and Prostate Common Gene Signatures by Bayesian Network Learning". 285-292. Springer International Publishing, 2020.
    10.1007/978-3-030-34585-3_25
  8. Eunice Carrasquinha; André Veríssimo; Marta B. Lopes; Susana Vinga. "Network-Based Variable Selection for Survival Outcomes in Oncological Data". 2020.
    10.1007/978-3-030-45385-5_49
  9. Manuel Anacleto; Susana Vinga; Alexandra M. Carvalho. "MSAX: Multivariate Symbolic Aggregate Approximation for Time Series Classification". 2020.
    10.1007/978-3-030-63061-4_9
  10. Cláudia Constantino; Alexandra M. Carvalho; Susana Vinga. "Sparse Consensus Classification for Discovering Novel Biomarkers in Rheumatoid Arthritis". 2020.
    10.1007/978-3-030-64583-0_13
  11. André Veríssimo; Marta B. Lopes; Eunice Carrasquinha; Susana Vinga. "Random Sample Consensus for the Robust Identification of Outliers in Cancer Data". 2020.
    10.1007/978-3-030-63061-4_11
  12. Peyroteo, Madalena M. A.; Belinha, Jorge; Vinga, Susana; Natal Jorge, R.; Dinis, Lúcia. "Mathematical Modelling of Spatio-temporal Cell Dynamics Observed During Bone Remodelling". In Lecture Notes in Computational Vision and Biomechanics, 129-158. Springer International Publishing, 2020.
    Published • 10.1007/978-3-030-37541-6_5
  13. Eunice Carrasquinha; André Veríssimo; Marta B. Lopes; Susana Vinga. "Variable Selection and Outlier Detection in Regularized Survival Models: Application to Melanoma Gene Expression Data". 431-440. Springer International Publishing, 2019.
    10.1007/978-3-030-13709-0_36
  14. Marta B. Lopes; André Veríssimo; Eunice Carrasquinha; Susana Vinga. "On the Role of Hub and Orphan Genes in the Diagnosis of Breast Invasive Carcinoma". 631-642. Springer International Publishing, 2019.
    10.1007/978-3-030-37599-7_52
Conference abstract
  1. Constantino, Cláudia; Oliveira, Francisco; Leocádio, Sónia; Silva, Mariana; Carla Oliveira; Castanheira, Joana; Silva, Angelo; et al. Corresponding author: Constantino, Cláudia. "Deep learning-based fully automatic segmentation of whole-body [18F]FDG PET/CT images from lymphoma patients: addition of CT data has poor impact on networks performance". Paper presented in 36th Annual Congress of the European Association of Nuclear Medicine, Vienna, 2023.
    Published
Conference paper
  1. Cláudia S. Constantino; Oliveira, Francisco; Sónia Leocádio; Mariana Silva; Carla Oliveira; Joana C. Castanheira; Ângelo Silva; et al. "A robust deep-learning model for fully automatic segmentation of lymphoma lesions on whole-body [18F]FDG PET/CT images". Paper presented in IEEE International Symposium on Biomedical Imaging, 2024.
    Accepted
  2. Joana Capacete; Folgado, João; Fernandes, Paulo R.; Vinga, Susana. "Bone remodeling under disease conditions and therapy: a biomechanochemical approach". Paper presented in 23rd Congress of the European Society of Biomechanics (ESB 2017), Sevilha, 2017.
    Published
  3. Peyroteo, M.; Belinha, J.; Vinga, S.; Dinis, L.; Natal Jorge, R.. "A model for bone remodeling: Cellular dynamics and mechanical loading". 2017.
    10.1109/ENBENG.2017.7889454
  4. Joana Capacete; Folgado, João; Fernandes, Paulo R.; Rui Coelho; Vinga, Susana; Natal Jorge, Renato; Belinha, Jorge. "A biomechanochemical bone remodeling model for disease and therapy dynamics". Paper presented in Mechanical Engineering Conference (CEM 2016), Porto, 2016.
    Published
  5. Monteiro, J.L.; Vinga, S.; Carvalho, A.M.. "Polynomial-time algorithm for learning optimal tree-augmented dynamic Bayesian networks". 2015.
  6. Pinto, J.D.; Carvalho, A.M.; Vinga, S.. "Outlier detection in survival analysis based on the concordance C-index". 2015.
  7. Portêlo, A.; Lemos, J.M.; Vinga, S.; Ribeiro, R.M.; Cruz, J.P.; Valadas, E.. "Parameter estimation and identifiability of a HIV-1 model". 2013.
    10.1109/MED.2013.6608798
  8. Hartmann, A.; Vinga, S.; Lemos, J.M.. "Hybrid identification of time-varying parameter with particle filtering and expectation maximization". 2013.
    10.1109/MED.2013.6608826
  9. Hartmann, A.; Vinga, S.; Lemos, J.M.. "Identification of HIV-1 dynamics: Estimating the noise model, constant and time-varying parameters of long-term clinical data". 2012.
  10. Costa, R.S.; Machado, D.; Neves, A.R.; Vinga, S.; Costa, Rafael S.; Machado, C. D.; Neves, Ana Rute; Vinga, Susana. "Multi-level dynamic modeling in biological systems: Application of hybrid Petri nets to network simulation". 2012.
    10.5220/0003785503170321
  11. Hartmann, A.; Vinga, S.; Lemos, J.M.. "Online Bayesian time-varying parameter estimation of HIV-1 time-series". 2012.
    10.3182/20120711-3-BE-2027.00277
  12. Hartmann, A.; Vinga, S.; Lemos, J.M.. "Unified modeling of several perturbation experiments in systems biology: A case study on the glucose uptake of lactococcus lactis". 2011.
  13. Pinheiro, J.V.; Lemos, J.M.; Vinga, S.. "Nonlinear MPC of HIV-1 infection with periodic inputs". 2011.
    10.1109/CDC.2011.6160806
Conference poster
  1. Vila-Santa, Ana; Lúcio, João; Sun, Wan; Correia, Joana; Marques, Nuno; Faria, Nuno; Vinga, Susana; et al. "Towards sustainable Yeast-based production of itaconic acid". Paper presented in 7th Conference on Physiology of Yeast and Filamentous Fungi (PYFF), 2019.
  2. Veríssimo, André; Carrasquinha, Eunice; Lopes, Marta B.; Sargot, Marie-France; Oliveira, Arlindo; Vinga, Susana. "Performance and stability analysis of sparse network-based survival models". Paper presented in Ascona Workshop 2019 - Statistical Challenges in Single-Cell Biology, 2019.
  3. Carrasquinha, Eunice; Lopes, M.B.; Veríssimo, André; Casimiro, S.; Beerenwinkel, N.; Vinga, Susana. "Ensemble outlier detection in cancer gene expression data". Paper presented in The 17th European Conference on Computational Biology (ECCB 2018), 2018.
  4. Carrasquinha, Eunice; Lopes, Marta B.; Veríssimo, André; Vinga, Susana. "Variable selection of high-dimensional longitudinal data and survival analysis of cancer gene expression data". Paper presented in 11th European Conference on Mathematical and Theoretical Biology, (ECMTB 2018), 2018.
  5. Lopes, Marta Belchior; Veríssimo, André; Casimiro, Sandra; Carrasquinha, Eunice; Vinga, Susana. "Network-based penalized logistic regression for the identification of common gene signatures in breast and prostate cancers.". Paper presented in Data Science, Statistics and Visualisation (DSSV 2018), 2018.
  6. Veríssimo, André; Carrasquinha, Eunice; Lopes, Marta B.; Oliveira, Arlindo; Sagot, Marie-France; Vinga, Susana. "Regularized survival analysis and feature clustering of TCGA breast cancer data.". Paper presented in From Single- to Multiomics: Applications and Challenges in Data Integration, 2017.
  7. Veríssimo, André; Carrasquinha, Eunice; Lopes, Marta B.; Sagot, Marie-France; Oliveira, Arlindo; Vinga, Susana. "Random Sample Consensus (RANSAC) for the robust identification of outliers in transcriptomic data.". Paper presented in European Conference on Computational Biology (ECCB 2017), 2017.
  8. Veríssimo, André; Carrasquinha, Eunice; Lopes, Marta B.; Sagot, Marie-France; Oliveira, Arlindo; Vinga, Susana. "Network-based sparse modeling of breast invasive carcinoma survival data.". Paper presented in Signal Processing with Adaptive Sparse Structured Representations (SPARS 2017), 2017.
    10.1158/0008-5472.sabcs12-p3-07-11
  9. Carrasquinha, Eunice; Veríssimo, André; Vinga, Susana. "Survival Analysis, robust or not robust?". Paper presented in Workshop of Joint Modeling and Beyond, 2016.
  10. Vila Santa, A; Moita, MR; Frazão, Carlos; Henriques, Sílvia F.; Sá-Correia, Isabel; Jarboe, LR; Vinga, Susana; Mira, NP. "Exploring a molecular systems biology approach to setup Saccharomyces cerevisiae as a cell factory for the production of itaconic acid". Paper presented in 32nd International Specialized Symposium in Yeasts, Perugia, 2015.
Journal article
  1. Silva, Mónica de Mendonça; Coletti, Roberta; Gonçalves, Céline S.; Martins, Eduarda P.; Costa, Bruno M.; Vinga, Susana; Lopes, Marta B.. "Updating TCGA glioma subtype classification through integration of molecular profiling data following 2016 and 2021 WHO guidelines". (2024):
    Submitted
  2. Costa, Luísa Marote; Colaço, João; Carvalho, Alexandra M.; Vinga, Susana; Teixeira, Andreia Sofia. "Using Markov chains and temporal alignment to identify clinical patterns in Dementia". Journal of Biomedical Informatics 140 (2023): 104328. http://dx.doi.org/10.1016/j.jbi.2023.104328.
    10.1016/j.jbi.2023.104328
  3. Peixoto, Carolina; Lopes, Marta B.; Martins, Marta; Casimiro, Sandra; Sobral, Daniel; Grosso, Ana Rita; Abreu, Catarina; et al. "Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization". BMC Bioinformatics 24 1 (2023): http://dx.doi.org/10.1186/s12859-022-05104-z.
    10.1186/s12859-022-05104-z
  4. André Patrício; Marta B. Lopes; Pedro Reis Costa; Costa, R; Rui Henriques; Susana Vinga. "Time-Lagged Correlation Analysis of Shellfish Toxicity Reveals Predictive Links to Adjacent Areas, Species, and Environmental Conditions". Toxins (2022): https://www.mdpi.com/2072-6651/14/10/679.
    10.3390/toxins14100679
  5. Carolina Peixoto; Marta Martins; Luís Costa; Susana Vinga. "Kidney Cancer Biomarker Selection Using Regularized Survival Models". Cells (2022): https://doi.org/10.3390/cells11152311.
    10.3390/cells11152311
  6. Antje Jensch; Marta B. Lopes; Susana Vinga; Nicole Radde. "ROSIE: RObust Sparse ensemble for outlIEr detection and gene selection in cancer omics data". Statistical Methods in Medical Research (2022): 096228022110724-096228022110724. https://doi.org/10.1177/09622802211072456.
    10.1177/09622802211072456
  7. Cláudia S. Constantino; Alexandra M. Carvalho; Susana Vinga. "Coupling sparse Cox models with clustering of longitudinal transcriptomics data for trauma prognosis". BioData Mining (2021): https://doi.org/10.1186/s13040-021-00257-8.
    10.1186/s13040-021-00257-8
  8. Joana Pinheiro Neto; Irina Alho; Luís Costa; Sandra Casimiro; Duarte Valério; Susana Vinga. "Dynamic modeling of bone remodeling, osteolytic metastasis and PK/PD therapy: introducing variable order derivatives as a simplification technique". Journal of Mathematical Biology 83 4 (2021): https://doi.org/10.1007/s00285-021-01666-3.
    10.1007/s00285-021-01666-3
  9. Susana Gomes; Susana Vinga; Rui Henriques. "Spatiotemporal Correlation Feature Spaces to Support Anomaly Detection in Water Distribution Networks". Water (2021): https://www.mdpi.com/2073-4441/13/18/2551.
    10.3390/w13182551
  10. Carolina Barata; Ana Maria Rodrigues; Helena Canhão; Susana Vinga; Alexandra M Carvalho. "Predicting Biologic Therapy Outcome of Patients With Spondyloarthritis: Joint Models for Longitudinal and Survival Analysis". JMIR Medical Informatics (2021): https://doi.org/10.2196/26823.
    10.2196/26823
  11. Rafaela C. Cruz; Pedro Reis Costa; Susana Vinga; Ludwig Krippahl; Marta B. Lopes. "A Review of Recent Machine Learning Advances for Forecasting Harmful Algal Blooms and Shellfish Contamination". Journal of Marine Science and Engineering (2021): https://doi.org/10.3390/jmse9030283.
    10.3390/jmse9030283
  12. Marta B. Lopes; Eduarda P. Martins; Susana Vinga; Bruno M. Costa. "The Role of Network Science in Glioblastoma". Cancers (2021): https://doi.org/10.3390/cancers13051045.
    10.3390/cancers13051045
  13. Jorge L. Serras; Susana Vinga; Alexandra M. Carvalho. "Outlier Detection for Multivariate Time Series Using Dynamic Bayesian Networks". Applied Sciences 11 4 (2021): 1955-1955. https://doi.org/10.3390/app11041955.
    10.3390/app11041955
  14. Marianne Borderes; Cyrielle Gasc; Emmanuel Prestat; Mariana Galvão Ferrarini; Susana Vinga; Lilia Boucinha; Marie-France Sagot. "A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog". NAR Genomics and Bioinformatics (2021): https://doi.org/10.1093/nargab/lqab009.
    10.1093/nargab/lqab009
  15. Ricardo Andrade; Mahdi Doostmohammadi; João L. Santos; Marie-France Sagot; Nuno P. Mira; Susana Vinga. "MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering". BMC Bioinformatics 21 1 (2020): https://doi.org/10.1186/s12859-020-3377-1.
    10.1186/s12859-020-3377-1
  16. Carolina Peixoto; Marta B. Lopes; Marta Martins; Luís Costa; Susana Vinga. "TCox: Correlation-Based Regularization Applied to Colorectal Cancer Survival Data". Biomedicines 8 11 (2020): 488-488. https://doi.org/10.3390/biomedicines8110488.
    10.3390/biomedicines8110488
  17. Raquel Miranda; Susana Vinga; Duarte Valério. "Studying Bone Remodelling and Tumour Growth for Therapy Predictive Control". Mathematics 8 5 (2020): 679-679. https://doi.org/10.3390/math8050679.
    10.3390/math8050679
  18. Hugo Loureiro; Eunice Carrasquinha; Irina Alho; Arlindo R. Ferreira; Luís Costa; Alexandra M. Carvalho; Susana Vinga. "Modelling cancer outcomes of bone metastatic patients: combining survival data with N-Telopeptide of type I collagen (NTX) dynamics through joint models". BMC Medical Informatics and Decision Making 19 1 (2019): https://doi.org/10.1186/s12911-018-0728-1.
    10.1186/s12911-018-0728-1
  19. Pieter Segaert; Marta B Lopes; Sandra Casimiro; Susana Vinga; Peter J Rousseeuw. "Robust identification of target genes and outliers in triple-negative breast cancer data". Statistical Methods in Medical Research 28 10-11 (2019): 3042-3056. https://doi.org/10.1177/0962280218794722.
    10.1177/0962280218794722
  20. Lopes, Marta B.; Casimiro, Sandra; Vinga, Susana. "Twiner: correlation-based regularization for identifying common cancer gene signatures". BMC Bioinformatics 20 1 (2019): http://dx.doi.org/10.1186/s12859-019-2937-8.
    10.1186/s12859-019-2937-8
  21. Rama, Kishan; Canhão, Helena; Carvalho, Alexandra M.; Vinga, Susana; Centro de Estudos de Doenças Crónicas (CEDOC); Escola Nacional de Saúde Pública (ENSP); NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM); et al. "AliClu - Temporal sequence alignment for clustering longitudinal clinical data". BMC Medical Informatics and Decision Making (2019): http://hdl.handle.net/10362/91150.
    https://doi.org/10.1186/s12911-019-1013-7
  22. Lopes, Marta B.; Veríssimo, André; Carrasquinha, Eunice; Casimiro, Sandra; Beerenwinkel, Niko; Vinga, Susana. "Ensemble outlier detection and gene selection in triple-negative breast cancer data". BMC Bioinformatics 19 1 (2018): http://dx.doi.org/10.1186/s12859-018-2149-7.
    10.1186/s12859-018-2149-7
  23. Carvalho, Sandra M.; Kloosterman, Tomas G.; Manzoor, Irfan; Caldas, José; Vinga, Susana; Martinussen, Jan; Saraiva, Lígia M.; et al. "Interplay between capsule expression and uracil metabolism in Streptococcus pneumoniae D39". (2018): http://www.scopus.com/inward/record.url?scp=85042932589&partnerID=8YFLogxK.
    https://doi.org/10.3389/fmicb.2018.00321
  24. Dudnik, Alexey; Almeida, A. Filipa; Andrade, Ricardo; Avila, Barbara; Bañados, Pilar; Barbay, Diane; Bassard, Jean-Etienne; et al. "BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits". (2018): http://hdl.handle.net/1822/54671.
    10.1007/s11101-017-9532-2
  25. Carrasquinha, Eunice; Veríssimo, André; Lopes, Marta B.; Vinga, Susana. "Identification of influential observationsin high-dimensional cancer survival data through the rank product test.". BioData Mining (2018):
    10.1186/s13040-018-0162-z
  26. András Hartmann; Ana Vila-Santa; Nicolai Kallscheuer; Michael Vogt; Alice Julien-Laferrière; Marie-France Sagot; Jan Marienhagen; Susana Vinga. "OptPipe - a pipeline for optimizing metabolic engineering targets". BMC Systems Biology (2017): https://doi.org/10.1186/s12918-017-0515-0.
    10.1186/s12918-017-0515-0
  27. Sobral,Luis; Ângelo,Ana C; Vinga,Susana; Azevedo,Clara. "Rotura do Tendão do Grande Peitoral: Revisão Sistemática dos Métodos de Reinserção". (2017): http://www.scielo.mec.pt/scielo.php?script=sci_arttext&pid=S1646-21222017000100002.
  28. Tomás, E.; Vinga, S.; Carvalho, A.M.. "Unsupervised learning of pharmacokinetic responses". Computational Statistics 32 2 (2017): 409-428. http://www.scopus.com/inward/record.url?eid=2-s2.0-85009797006&partnerID=MN8TOARS.
    10.1007/s00180-016-0707-x
  29. Lemos, J.M.; Caiado, D.V.; Coelho, R.; Vinga, S.. "Optimal and receding horizon control of tumor growth in myeloma bone disease". Biomedical Signal Processing and Control 24 (2016): 128-134. http://www.scopus.com/inward/record.url?eid=2-s2.0-84946566060&partnerID=MN8TOARS.
    10.1016/j.bspc.2015.10.004
  30. Costa, R.S.; Hartmann, A.; Vinga, S.. "Kinetic modeling of cell metabolism for microbial production". Journal of Biotechnology 219 (2016): 126-141. http://www.scopus.com/inward/record.url?eid=2-s2.0-84952802704&partnerID=MN8TOARS.
    10.1016/j.jbiotec.2015.12.023
  31. Coelho, R.M.; Lemos, J.M.; Alho, I.; Valério, D.; Ferreira, A.R.; Costa, L.; Vinga, S.. "Dynamic modeling of bone metastasis, microenvironment and therapy. Integrating parathyroid hormone (PTH) effect, anti-resorptive and anti-cancer therapy.". Journal of Theoretical Biology 391 (2016): 1-12. http://www.scopus.com/inward/record.url?eid=2-s2.0-84954151796&partnerID=MN8TOARS.
    10.1016/j.jtbi.2015.11.024
  32. Veríssimo, A.; Oliveira, A.L.; Sagot, M.-F.; Vinga, S.. "DegreeCox - a network-based regularization method for survival analysis". BMC Bioinformatics 17 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-85003601768&partnerID=MN8TOARS.
    10.1186/s12859-016-1310-4
  33. Hartmann, Andras; Neves, Ana Rute; Lemos, Joao M.; Vinga, Susana; Hartmann, A.; Neves, A.R.; Lemos, J.M.; Vinga, S.. "Identification and automatic segmentation of multiphasic cell growth using a linear hybrid model". Mathematical Biosciences 279 (2016): 83-89. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000381843800010&KeyUID=WOS:000381843800010.
    10.1016/j.mbs.2016.06.013
  34. Fernandes, Armando; Vinga, Susana. "Improving Protein Expression Prediction Using Extra Features and Ensemble Averaging". Plos One 11 3 (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000371724200085&KeyUID=WOS:000371724200085.
    10.1371/journal.pone.0150369
  35. Costa, Rafael S.; Vinga, Susana. "Control analysis of the impact of allosteric regulation mechanism in a Escherichia coli kinetic model: Application to serine production". Biochemical Engineering Journal 110 (2016): 59-70. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000374361500008&KeyUID=WOS:000374361500008.
    10.1016/j.bej.2016.01.013
  36. Julien-Laferriere, Alice; Bulteau, Laurent; Parrot, Delphine; Marchetti-Spaccamela, Alberto; Stougie, Leen; Vinga, Susana; Mary, Arnaud; Sagot, Marie-France. "A Combinatorial Algorithm for Microbial Consortia Synthetic Design". Scientific Reports 6 (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000378949200001&KeyUID=WOS:000378949200001.
    10.1038/srep29182
  37. Paixão, L.; Caldas, J.; Kloosterman, T.G.; Kuipers, O.P.; Vinga, S.; Neves, A.R.. "Transcriptional and metabolic effects of glucose on Streptococcus pneumoniae sugar metabolism". Frontiers in Microbiology 6 OCT (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84946829570&partnerID=MN8TOARS.
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  38. Hartmann, A.; Lemos, J.M.; Vinga, S.. "Modeling multiple experiments using regularized optimization: A case study on bacterial glucose utilization dynamics". Computers in Biology and Medicine 63 (2015): 301-309. http://www.scopus.com/inward/record.url?eid=2-s2.0-84934272888&partnerID=MN8TOARS.
    10.1016/j.compbiomed.2014.08.027
  39. Hartmann, A.; Lemos, J.M.; Costa, R.S.; Xavier, J.; Vinga, S.. "Identification of switched ARX models via convex optimization and expectation maximization". Journal of Process Control 28 (2015): 9-16. http://www.scopus.com/inward/record.url?eid=2-s2.0-84924427452&partnerID=MN8TOARS.
    10.1016/j.jprocont.2015.02.003
  40. Paixão, L.; Oliveira, J.; Veríssimo, A.; Vinga, S.; Lourenço, E.C.; Ventura, M.R.; Kjos, M.; et al. "Host glycan sugar-specific pathways in streptococcus pneumonia: Galactose as a key sugar in colonisation and infection". PLoS ONE 10 3 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84926329287&partnerID=MN8TOARS.
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  41. Paixão, L.; Oliveira, J.; Veríssimo, A.; Vinga, S.; Lourenço, E.C.; Ventura, M.R.. "Correction: Host glycan sugar-specific pathways in Streptococcus pneumonia: Galactose as a key sugar in colonisation and infection". PLoS ONE 10 4 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84929471870&partnerID=MN8TOARS.
    10.1371/journal.pone.0127483
  42. Costa, R.S.; Hartmann, A.; Gaspar, P.; Neves, A.R.; Vinga, S.. "An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production". Molecular BioSystems 10 3 (2014): 628-639. http://www.scopus.com/inward/record.url?eid=2-s2.0-84893489411&partnerID=MN8TOARS.
    10.1039/c3mb70265k
  43. Costa, R.S.; Veríssimo, A.; Vinga, S.. "KiMoSys: A web-based repository of experimental data for KInetic MOdels of biological SYStems". BMC Systems Biology 8 1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84908387275&partnerID=MN8TOARS.
    10.1186/s12918-014-0085-3
  44. Hartmann, A.; Lemos, J.M.; Costa, R.S.; Vinga, S.. "Identifying IIR filter coefficients using particle swarm optimization with application to reconstruction of missing cardiovascular signals". Engineering Applications of Artificial Intelligence 34 (2014): 193-198. http://www.scopus.com/inward/record.url?eid=2-s2.0-84904197005&partnerID=MN8TOARS.
    10.1016/j.engappai.2014.05.014
  45. Vinga, S.. "Information theory applications for biological sequence analysis". Briefings in Bioinformatics 15 3 (2014): 376-389. http://www.scopus.com/inward/record.url?eid=2-s2.0-84900804358&partnerID=MN8TOARS.
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  46. Vinga, S.. "Editorial: Alignment-free methods in computational biology". Briefings in Bioinformatics 15 3 (2014): 341-342. http://www.scopus.com/inward/record.url?eid=2-s2.0-84900806896&partnerID=MN8TOARS.
    10.1093/bib/bbu005
  47. Caldas, J.; Vinga, S.. "Global meta-analysis of transcriptomics studies". PLoS ONE 9 2 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84896283246&partnerID=MN8TOARS.
    10.1371/journal.pone.0089318
  48. Anunciação, O.; Vinga, S.; Oliveira, A.L.. "Using Information Interaction to Discover Epistatic Effects in Complex Diseases". PLoS ONE 8 10 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84886052456&partnerID=MN8TOARS.
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  49. Gaspar, P.; Carvalho, A.L.; Vinga, S.; Santos, H.; Neves, A.R.. "From physiology to systems metabolic engineering for the production of biochemicals by lactic acid bacteria". Biotechnology Advances 31 6 (2013): 764-788. http://www.scopus.com/inward/record.url?eid=2-s2.0-84882723516&partnerID=MN8TOARS.
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  50. Veríssimo, A.; Paixão, L.; Neves, A.R.; Vinga, S.. "BGFit: Management and automated fitting of biological growth curves". BMC Bioinformatics 14 1 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84884529451&partnerID=MN8TOARS.
    10.1186/1471-2105-14-283
  51. Azevedo,Clara; Vinga,Susana. "Reinserção artroscópica do supra-espinhoso: O que fazer com a longa porção do bicípite braquial? Estudo prospetivo de 42 doentes". (2012): http://www.scielo.mec.pt/scielo.php?script=sci_arttext&pid=S1646-21222012000100006.
  52. Almeida, Jonas S.; Grüneberg, Alexander; Maass,  Wolfgang; Vinga, Susana; NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM); Almeida, J.S.; Grüneberg, A.; Maass, W.; Vinga, S.. "Fractal MapReduce decomposition of sequence alignment". Algorithms for Molecular Biology 7 1 (2012): http://hdl.handle.net/10362/23600.
    https://doi.org/10.1186/1748-7188-7-12
  53. Rosa, Isadora; Fidalgo, Paulo; Soares, José; Vinga, Susana; Oliveira, Carla; Silva, João P.; Ferro, Susana M.; et al. "Adenoma incidence decreases under the effect of polypectomy". World Journal of Gastroenterology 18 11 (2012): 1243-1248. http://www.scopus.com/inward/record.url?scp=84858766237&partnerID=8YFLogxK.
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  54. Vinga, S.; Carvalho, A.M.; Francisco, A.P.; Russo, L.M.S.; Almeida, J.S.; Vinga, Susana; Carvalho,  Alexandra M; et al. "Pattern matching through Chaos Game Representation: Bridging numerical and discrete data structures for biological sequence analysis". Algorithms for Molecular Biology 7 1 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84860351022&partnerID=MN8TOARS.
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  55. Tenazinha, N.; Vinga, S.. "A survey on methods for modeling and analyzing integrated biological networks". IEEE/ACM Transactions on Computational Biology and Bioinformatics 8 4 (2011): 943-958. http://www.scopus.com/inward/record.url?eid=2-s2.0-79957637424&partnerID=MN8TOARS.
    10.1109/TCBB.2010.117
  56. CalÇada, D.; Vinga, S.; Freitas, A.T.; Oliveira, A.L.. "Quantitative modeling of the saccharomyces cerevisiae FLR1 regulatory network using an s-system formalism". Journal of Bioinformatics and Computational Biology 9 5 (2011): 613-630. http://www.scopus.com/inward/record.url?eid=2-s2.0-80053654755&partnerID=MN8TOARS.
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  57. Domingues, A.; Vinga, S.; Lemos, J.M.; Domingues, Alexandre; Vinga, Susana; Lemos, João M.; NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM). "Optimization strategies for metabolic networks". BMC Systems Biology 4 (2010): 3190-3195. http://www.scopus.com/inward/record.url?eid=2-s2.0-77955484209&partnerID=MN8TOARS.
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  58. Vinga, S.; Neves, A.R.; Santos, H.; Brandt, B.W.; Kooijman, S.A.L.M.. "Subcellular metabolic organization in the context of dynamic energy budget and biochemical systems theories". Philosophical Transactions of the Royal Society B: Biological Sciences 365 1557 (2010): 3429-3442. http://www.scopus.com/inward/record.url?eid=2-s2.0-78149277848&partnerID=MN8TOARS.
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  59. Vilela, Marco; Vinga, Susana; Maia, Marco A.Grivet Mattoso; Voit, Eberhard O.; Almeida, Jonas S.; NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM); Vilela, M.; et al. "Identification of neutral biochemical network models from time series data". BMC Systems Biology 3 (2009): http://www.scopus.com/inward/record.url?scp=67649663892&partnerID=8YFLogxK.
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  60. Almeida, J.S.; Vinga, S.; Almeida, J. S.; Vinga, Susana; NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM). "Biological sequences as pictures - A generic two dimensional solution for iterated maps". BMC Bioinformatics 10 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-65549110447&partnerID=MN8TOARS.
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  61. Fernandes, F.; Freitas, A.T.; Almeida, J.S.; Vinga, S.. "Entropic profiler - Detection of conservation in genomes using information theory". BMC Research Notes 2 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-77049089315&partnerID=MN8TOARS.
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  62. Casimiro, Ana; Vinga, Susana; Freitas,  Ana T; Oliveira, Arlindo L.; NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM); Casimiro, A.C.; Vinga, S.; Freitas, A.T.; Oliveira, A.L.. "An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance". BMC Bioinformatics 9 (2008): http://hdl.handle.net/10362/23352.
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  63. Oliveira, D.C.; Santos, M.; Milheiriço, C.; Carriço, J.A.; Vinga, S.; Oliveira, A.L.; de Lencastre, H.. "ccrB typing tool: An online resource for staphylococci ccrB sequence typing [1]". Journal of Antimicrobial Chemotherapy 61 4 (2008): 959-960. http://www.scopus.com/inward/record.url?eid=2-s2.0-41149162248&partnerID=MN8TOARS.
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  64. Vilela, M.; Chou, I.-C.; Vinga, S.; Vasconcelos, A.T.R.; Voit, E.O.; Almeida, J.S.. "Parameter optimization in S-system models". BMC Systems Biology 2 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-42649134526&partnerID=MN8TOARS.
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  65. Vilela, M.; Borges, C.C.H.; Vinga, S.; Vasconcelos, A.T.R.; Santos, H.; Voit, E.O.; Almeida, J.S.. "Automated smoother for the numerical decoupling of dynamics models". BMC Bioinformatics 8 (2007): http://www.scopus.com/inward/record.url?eid=2-s2.0-35448979185&partnerID=MN8TOARS.
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  66. Vinga, S.; Almeida, J.S.. "Local Renyi entropic profiles of DNA sequences". BMC Bioinformatics 8 (2007): http://www.scopus.com/inward/record.url?eid=2-s2.0-38949102609&partnerID=MN8TOARS.
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  67. Oliveira, D.C.; MilheiriÇo, C.; Vinga, S.; de Lencastre, H.. "Assessment of allelic variation in the ccrAB locus in methicillin-resistant Staphylococcus aureus clones". Journal of Antimicrobial Chemotherapy 58 1 (2006): 23-30. http://www.scopus.com/inward/record.url?eid=2-s2.0-33748082304&partnerID=MN8TOARS.
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  68. Almeida, J.S.; Vinga, S.; Almeida, Joana S.; Vinga, Susana; NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM). "Computing distribution of scale independent motifs in biological sequences". Algorithms for Molecular Biology 1 1 (2006): http://www.scopus.com/inward/record.url?eid=2-s2.0-34248384741&partnerID=MN8TOARS.
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  69. Gomes, A.R.; Vinga, S.; Zavolan, M.; De Lencastre, H.. "Analysis of the genetic variability of virulence-related loci in epidemic clones of methicillin-resistant Staphylococcus aureus". Antimicrobial Agents and Chemotherapy 49 1 (2005): 366-379. http://www.scopus.com/inward/record.url?eid=2-s2.0-11244316709&partnerID=MN8TOARS.
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  70. Vinga, S.; Gouveia-Oliveira, R.; Almeida, J.S.. "Comparative evaluation of word composition distances for the recognition of SCOP relationships". Bioinformatics 20 2 (2004): 206-215. http://www.scopus.com/inward/record.url?eid=2-s2.0-1042269469&partnerID=MN8TOARS.
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  71. Vinga, S.; Almeida, J.S.. "Rényi continuous entropy of DNA sequences". Journal of Theoretical Biology 231 3 (2004): 377-388. http://www.scopus.com/inward/record.url?eid=2-s2.0-6344221592&partnerID=MN8TOARS.
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  72. Vinga, S.; Almeida, J.. "Alignment-free sequence comparison - A review". Bioinformatics 19 4 (2003): 513-523. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037342499&partnerID=MN8TOARS.
    10.1093/bioinformatics/btg005
  73. Almeida, J.S.; Vinga, S.. "Universal sequence map (USM) of arbitrary discrete sequences". BMC Bioinformatics 3 (2002): http://www.scopus.com/inward/record.url?eid=2-s2.0-0002946570&partnerID=MN8TOARS.
    10.1186/1471-2105-3-6
Preprint
  1. Mónica L. Mendonça; Roberta Coletti; Céline S. Gonçalves; Eduarda P. Martins; Bruno M. Costa; Susana Vinga; Marta B. Lopes; et al. "Updating TCGA glioma classification through integration of molecular profiling data following the 2016 and 2021 WHO guidelines". 2023. https://doi.org/10.1101/2023.02.19.529134.
    10.1101/2023.02.19.529134

Other

Other output
  1. Predicting Biologic Therapy Outcome of Patients With Spondyloarthritis: Joint Models for Longitudinal and Survival Analysis (Preprint). 2020. Carolina Barata; Ana Maria Rodrigues; Helena Canhão; Susana Vinga; Alexandra M Carvalho. https://doi.org/10.2196/preprints.26823.
    10.2196/preprints.26823
  2. Latent variable modelling and variational inference for scRNA-seq differential expression analysis. 2019. Joana Godinho; Alexandra M. Carvalho; Susana Vinga. https://doi.org/10.1101/719856.
    10.1101/719856
  3. Scalable probabilistic matrix factorization for single-cell RNA-seq analysis. 2018. Pedro F. Ferreira; Alexandra M. Carvalho; Susana Vinga. https://doi.org/10.1101/496810.
    10.1101/496810
  4. Consensus outlier detection in survival analysis using the rank product test. 2018. Eunice Carrasquinha; André Veríssimo; Susana Vinga. https://doi.org/10.1101/421917.
    10.1101/421917
  5. glmSparseNet - network centrality metrics for elastic-net regularized models. Bioconductor R package version 0.99.31. 2018. Veríssimo, André; Vinga, Susana; Carrasquinha, Eunice; Lopes, Marta B.. https://bioconductor.org/packages/3.8/bioc/html/glmSparseNet.html.
  6. Sparse network-based regularization for the analysis of patientomics high-dimensional survival data. 2018. André Veríssimo; Eunice Carrasquinha; Marta B. Lopes; Arlindo L. Oliveira; Marie-France Sagot; Susana Vinga. https://doi.org/10.1101/403402.
    10.1101/403402
  7. MassBlast: A workflow to accelerate RNA-seq and DNA database analysis. 2017. André Veríssimo; Jean-Etienne Bassard; Alice Julien-Laferrière; Marie-France Sagot; Susana Vinga. https://doi.org/10.1101/131953.
    10.1101/131953
Activities

Supervision

Thesis Title
Role
Degree Subject (Type)
Institution / Organization
2018/04/01 - 2022/12/07 Computational Biology for Modeling Oncological Omics Data: the way towards personalized medicine.
Supervisor of Ana Carolina Amaral Peixoto
Doutoramento em Bioengenharia - MIT Portugal (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2021/07/06 Characterization of host-gut microbiota interactions and identification of key players based on a unified reference for standardized quantitative metagenomics and metabolic analysis framework
Co-supervisor
PhD Bioinformatics (PhD)
Université Claude Bernard Lyon 1, France
2014 - 2021/02/23 Adaptive Clinical Decision Support System for Personalized Medicine
Supervisor
Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2020/11/24 Models and algorithms for investigating and exploiting communities of microorganisms
Co-supervisor
PhD Bioinformatics (PhD)
Université Claude Bernard Lyon 1, France
2019 - 2019 Time series data imputation - Comparison of Dynamic Time Warping with Needleman-Wunsch algorithm
Supervisor
2019 - 2019 MSAX: Multivariate symbolic aggregate approximation for time series classification
Supervisor
2019 - 2019 Latent factors of Mult-Omics data and Clustering
Supervisor
2019 - 2019 Computational analysis of isoform level regulation in T helper cells
Co-supervisor
2019 - 2019 Prediction of Treatment Response in Patients with Multiple Myeloma undergoing Chemotherapy using MRI derived Imaging Biomarkers
Supervisor
2019 - 2019 The relationship between the speed of spread of HIV in the population and the virus evolutionary rate
Supervisor
2019 - 2019 Analysis of heterogeneous and high-dimensional data of rheumatic diseases patients through clustering methods.
Supervisor
2019 - 2019 Previsão de biotoxinas marinhas em moluscos bivalves baseada em aprendizagem automática
Supervisor
2019 - 2019 Identification of common gene signatures in microarray and RNA-sequencing data using network-based regularization
Supervisor
2019 - 2019 Latent variable modelling and variational inference for single-cell RNA-seq differential expression analysis
Supervisor
2018 - 2018 Temporal sequence alignment and agglomerative clustering for the analysis of medical longitudinal data
Supervisor
Engenharia Electrotécnica e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2018 Identification of Transcription Factors Binding Sites (TFBS) in Yeast using Information Theory
Supervisor
Engenharia Biológica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2018 Studying Bone Remodelling and Tumour Growth for Therapy Predictive Control
Supervisor
Engenharia Mecânica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2018 Unravelling breast and prostate common gene singnatures by Bayesian network learning
Supervisor
Engenharia Electrotécnica e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2018 Probabilistic Modelling of Single-cell Transcriptomics
Supervisor
Engenharia Electrotécnica e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2018 Outlier detection for multivariate time series.
Supervisor
2018 - 2018 Unveiling Interpretable Behavior In Two-Way High-Dimensional Clinical Data
Supervisor
2018 - 2018 Network-based Regularization for Survival Analysis.
Supervisor
2017 - 2017 Feature analysis to predict treatment outcome in rheumatoid arthritis
Supervisor
Engenharia Electrotécnica e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2017 - 2017 Dynamic Modeling of Bone Remodeling, Tumor Growth and Therapy:Simplifying and Diffusing with Variable Order Derivatives
Supervisor
Engenharia Mecânica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2017 - 2017 Cancer patients stratification using multivariate clustering analysis for therapy optimization
Supervisor
Engenharia Mecânica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2017 - 2017 Análise da Fiabilidade de um Captor Electroactivo Iónico (IPMC)
Supervisor
Engenharia Electrotécnica e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2017 - 2017 Non-linear mixed effect models for mechanical trials of biomaterials
Supervisor
Engenharia Mecânica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2017 - 2017 Modelling cancer progression through joint models for longitudinal and time-to-event data
Supervisor
Engenharia Electrotécnica e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - 2016 Tryptophan Metabolism Profiling for Psychiatric Diagnostic Support
Supervisor
Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - 2016 Biochemical and biomechanic integrated modeling of bone
Supervisor
Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - 2016 Localização Automática do Núcleo Subtalâmico para Estimulação Cerebral Profunda na Doença de Parkinson
Supervisor
Engenharia Mecânica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - 2016 Improvement of yeast-based production of itaconic acid guided by in silico metabolic modeling
Supervisor
Microbiologia (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2012 - 2016 Models and algorithms applied to metabolism: From revealing the responses to perturbations towards the design of microbial consortia
Co-supervisor
PhD BioInformatique (PhD)
Université Claude Bernard Lyon 1, France
2015 - 2015 Hybrid Modeling and Identification of Biomedical Time-series
Supervisor
Engenharia Electrotécnica e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2015 - 2015 Outlier detection in survival analysis
Supervisor
Engenharia Electrotécnica e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2015 - 2015 Fuzzy Clustering of Short Time Series with Missing Data for the Survival Prediction of Oncological Patients
Supervisor
Engenharia Mecânica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2015 - 2015 Modelagem da Metástase Óssea utilizando Derivadas Fracionárias
Supervisor
Engenharia Mecânica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2015 - 2015 Alternative splicing analysis for finding novel molecular signatures in renal carcinomas
Supervisor
Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2014 - 2014 Analyses of alternative splicing landscapes in clear cell renal cell carcinomas reveal putative novel prognosis factors
Supervisor
Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2010 - 2014 Application of data mining techniques to identify disease susceptibility from genotype data
Co-supervisor
PhD in Information Systems and Computer Engineering (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2006 - 2009 Automatic Reverse Engineering of Biochemical Systems from Time Series
Co-supervisor
PhD Thesis in Biology (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Jury of academic degree

Topic
Role
Candidate name (Type of degree)
Institution / Organization
2020 Metabolic Systems Biology for Stem Cell Bioprocesses
(Thesis) Arguer
João Alberto Pacheco Marques de Vasconcelos e Sá (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019 Mathematical modelling of the impacts of environment using metabolic networks and game theory.
(Thesis) Arguer
Taneli Pusa (PhD)
Université Claude Bernard Lyon 1, France
2019 How to make a single product per cell? Lessons from X chromosome inactivation and antigen receptor gene recombination
(Thesis) Arguer
Delphine Pessoa (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2018 Prospecção de genes aplicados à biodegradação de hidrocarbonetos e produção de surfactantes utilizando abordagens computacionais.
(Thesis) Arguer
Jorge dos Santos Oliveira (PhD)
2018 A mathematical model of the phosphoinositide pathway in human pulmonary epithelial cells
(Thesis) Main arguer
Daniel Vigário Olivença (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 Compression and analysis of genomic data
(Thesis) Main arguer
Diogo Rodrigo Marques Pratas (PhD)
Universidade de Aveiro, Portugal
2016 Towards the rational design of standard biological parts for Synthetic Biology: applications to microbial systems.
(Thesis) Main arguer
Rui Miguel Correia Portela (PhD)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2015 Functional enviromics: applications to bioprocess monitoring and control
(Thesis) Main arguer
Ines Azevedo Isidro (PhD)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2014 The Drosophila melanogaster network landscape: prediction and analysis of transcriptional regulatory and protein-protein interaction networks.
(Thesis) Arguer
Rogério Paulo Pelaio Candeias (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2014 Towards a risk assessment model for biocide use
(Thesis) Arguer
Joana Maria Rosado da Silva Coelho (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2012 Variability in Biological Systems: Modeling Consequences and Applications
(Thesis) Main arguer
Filipe de Sousa e Menezes Miguel Grácio (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2009 Global Tolerance of Biochemical Systems and its Design Implications
(Thesis) Arguer
Pedro Miguel Brás Macedo Coelho (PhD)
Universidade de Coimbra, Portugal
2008 Efficient Biclustering Algorithms for Time Series Gene Expression Data Analysis
Thesis Member
Sara Alexandra Cordeiro Madeira (PhD)

Journal scientific committee

Journal title (ISSN) Publisher
2021/12/16 - Current Frontiers in Bioinformatics
2019 - Current PLoS ONE (1932-6203) Public Library of Science
2019 - Current Genes (2073-4425) MDPI AG
2015 - Current BMC Bioinformatics (1471-2105) Springer (Biomed Central Ltd.)
Distinctions

Award

2022 Prémio Científico Universidade de Lisboa / Caixa Geral de Depósitos - Computer Science and Engineering
Caixa Geral de Depositos, Portugal

Universidade de Lisboa, Portugal
2017 Prémio Científico Universidade de Lisboa / Caixa Geral de Depósitos - Computer Science and Engineering
Universidade de Lisboa / Caixa Geral de Depósitos, Portugal
2010 Prémios Jovens Investigadores - Eng. Informática
UTL/Caixa Geral de Depósitos, Portugal
1989 Winner of the VII National Mathematical Olympiads

Other distinction

2012 Investigador FCT (Development Grant) - IF/00653/2012
Fundação para a Ciência e a Tecnologia, Portugal
2008 Travel Fellowship – ECCB’2008
2007 Travel Fellowship – ISBM/ECCB’2007
2006 Post-doctoral Grant Ref. SFRH/BPD/24254/2005
Fundação para a Ciência e a Tecnologia, Portugal
2001 PhD Grant Ref. SFRH/BD/3134/2000
Fundação para a Ciência e a Tecnologia, Portugal