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Marta Belchior Lopes is a researcher at Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa. She holds a PhD in Biotechnology, a Master's degree in Applied Mathematics and a 5-year degree in Biology. Her main research activities have been focused on the development of mathematical and computational tools with a data mining and machine learning substrate to extract meaningful information from high-dimensional data generated by high-throughput technologies. She has been working in the context of precision oncology, bioprocess monitoring, quality control and marine ecology applications. Marta develops her research at the Center for Mathemathics and Applications (NOVA Math) and at the Research and Development Unit for Industrial and Mechanical Engineering (UNIDEMI).
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Identification

Personal identification

Full name
Marta Belchior Lopes

Citation names

  • Lopes, Marta B.

Author identifiers

Ciência ID
FD16-A07F-7B12
ORCID iD
0000-0002-4135-1857
Google Scholar ID
https://scholar.google.pt/citations?user=hMw9OZ8AAAAJ&hl=pt-PT&oi=ao
Researcher Id
F-5378-2011
Scopus Author Id
55489480400

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Engineering and Technology - Industrial Biotechnology
  • Natural sciences - Biological Sciences - Marine Biology
Education
Degree Classification
2006/09/01 - 2011/02/07
Concluded
 Biotechnology (Doutoramento)
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Advances in near-infrared hyperspectral imaging for pharmaceutical anti-counterfeiting" (THESIS/DISSERTATION)
2003/09/01 - 2005/09/01
Concluded
 Applied Mathematics in Biological Sciences (Mestrado)
Universidade de Lisboa Instituto Superior de Agronomia, Portugal
"Strategies for avoiding overparametrization in statistical catch-at-age methods" (THESIS/DISSERTATION)
1997/09/01 - 2003/01/09
Concluded
 Marine Biology (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Feeeding ecology and morphological variation of Macroramphosus spp. and Capros aper in the Portuguese coast" (THESIS/DISSERTATION)
Affiliation

Science

Category
Host institution 		Employer
2019/12/16 - Current Auxiliary Researcher (Research) Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2019/01/01 - 2019/12/15 Contracted Researcher (Research) Instituto de Telecomunicações, Portugal
2018/10/01 - 2018/12/31 Postdoc (Research) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2016/10/01 - 2018/08/31 Postdoc (Research) Instituto de Engenharia Mecânica Centro de Sistemas Inteligentes, Portugal
2011/04/01 - 2016/09/30 Postdoc (Research) Instituto de Telecomunicações, Portugal
Projects

Contract

Designation Funders
2023/05/01 - Current PAS GRAS: De-risking metabolic, environmental and behavioral determinants of obesity in children, adolescents and young adults
101080329
Researcher
Horizon 2020
Ongoing
2023 - Current A Comprehensive Network Against Brain Cancer (Net4Brain)
CA22103
Researcher
European Cooperation in Science and Technology
Ongoing
2022/01/01 - Current OMICs approaches to reveal the anticancer properties of Virgin Olive Oil (VOOmics)
PTDC/BAA-AGR/4732/2021
Researcher
Fundação para a Ciência e a Tecnologia
Ongoing
2022 - Current Personalized medicine in chronic kidney disease: improved outcome based on Big Data (PerMediK)
Cost Action CA21165
Researcher
European Cooperation in Science and Technology
Ongoing
2021 - Current Pacto da Bioeconomia Azul - WP Bivalves
C644915664-00000026
Researcher
Ongoing
2019/12/27 - Current Statistical and machine learning techniques in human microbiome studies (ML4MICROBIOME)
Cost Action CA18131
Researcher
European Cooperation in Science and Technology
Concluded
2019/02/01 - Current Identifying biomarkers through translational research for prevention and stratification of colorectal cancer (TRANSCOLONCAN)
Cost Action CA17118
Researcher
European Cooperation in Science and Technology
Concluded
2021/03/01 - 2024/11/30 Multi-omic networks in gliomas (MONET)
PTDC/CCI-BIO/4180/2020
Principal investigator
Universidade Nova Centro de Matemática e Aplicações, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2020/04/01 - 2023/09/30 A machine leaning-based forecasting system for shellfish safety (MATISSE)
DSAIPA/DS/0026/2019
Principal investigator
Universidade Nova de Lisboa Laboratório para a Ciência da Computação e Informática, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2018/09/01 - 2021/12/31 Personalized therapy for rheumatic diseases via machine learning (PREDICT)
PTDC/CCI-CIF/29877/2017
Researcher
Instituto de Telecomunicações, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2016/10/01 - 2019/06/01 Personalizing cancer therapy through integrated modeling and decision (PERSEIDS)
PTDC/EMS­SIS/0642/2014
Researcher
Instituto de Engenharia Mecânica Centro de Sistemas Inteligentes, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2016/09/01 - 2018/08/31 Statistical Multi-Omics Understanding (SOUND)
Grant agreement no. 633974
Post-doc Fellow
Instituto de Engenharia Mecânica Centro de Sistemas Inteligentes, Portugal
 Horizon 2020
Concluded
2011/04/01 - 2012/03/31 Integrated methodologies for the development of bi and three-valent DNA-vaccines against Helycobacter pylori
PTDC/BIO/69242/06
Post-doc Fellow
Universidade Católica Portuguesa, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2006/03/01 - 2006/09/30 Geographycal heterogeneity of tuberculosis in Portugal
Directorate-General of Health
Research Fellow
Instituto Gulbenkian de Ciência, Portugal
Concluded
2006 - 2006 Expert Team to Support Human Biomonitoring in Europe (ESBIO)
No. 22580 FP6
Research Fellow
Universidade de Lisboa Instituto de Medicina Preventiva e Saúde Pública, Portugal
Concluded
2005/08/01 - 2005/12/31 NeoMAv - New methodologies for fisheries assessment
QCA-3/MARE-FEDER
Research Fellow
Instituto Português do Mar e da Atmosfera, Portugal
Concluded
2005/03/01 - 2005/07/31 NURSERIES - Importance of estuarine and coastal nursery areas for the maintenance of stocks of fish species with commercial interest in the Portuguese coast
FEDER 22-05-01-FDR-00037 - MARE, DGPA
Research Fellow
Centro de Ciências do Mar e do Ambiente, Portugal
Concluded
2002/09/01 - 2005/02/28 PELÁGICOS - Strengthening research capacity in the field of oceanography and fisheries biology applied to the management of pelagic marine resources
FCT-PLE/13/00
Scientific Initiation Fellow
Instituto Português do Mar e da Atmosfera, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2000/01/01 - 2001/06/30 FESTA II - Integrated functioning of the Tagus estuary and continental shelf, in response to anthropogenic pressure and global changes
POCTI/MGS/34457/99
Scientific Initiation Fellow
Centro de Ciências do Mar e do Ambiente, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book chapter
  1. Pessanha, Sofia; Silva, João; Lima, Rafael Rodrigues; Lopes, Marta B.. "Raman spectroscopic studies on mineralized tissues and skin appendages". In Applied Raman Spectroscopy, 157-168. Elsevier, 2025.
    10.1016/b978-0-443-21834-7.00010-4
  2. Brandão, João; Lopes, Marta B.; Carrasquinha, Eunice. "Refining Gene Selection and Outlier Detection in Glioblastoma Based on a Consensus Approach for Regularized Survival Models". In Bioinformatics and Biomedical Engineering, 17-32. Springer Nature Switzerland, 2024.
    10.1007/978-3-031-64629-4_2
  3. Ferraz, Filipe; Ribeiro, Diogo; Lopes, Marta B.; Pedro, Sónia; Vinga, Susana; Carvalho, Alexandra M.. "Comparative Analysis of Machine Learning Models for Time-Series Forecasting of Escherichia Coli Contamination in Portuguese Shellfish Production Areas". In Machine Learning, Optimization, and Data Science, 174-188. Springer Nature Switzerland, 2024.
    10.1007/978-3-031-53969-5_14
  4. Roberta Coletti; Marta B. Lopes. "Multi-omics Data Integration and Network Inference for Biomarker Discovery in Glioma". 2023.
    10.1007/978-3-031-49011-8_20
  5. Diogo Ribeiro; Filipe Ferraz; Marta B. Lopes; Susana Margarida 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
  6. 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
  7. Isabel Natário; Lopes, M.B.. "Processamento de informação - Bases de dados e Big data". In Novas Tecnologias em Saúde. Cascais, Portugal: Principia, 2022.
  8. 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
  9. Villa-Brito, J.; Lopes, M.B.; Carvalho, A.; Vinga, S.. "Unravelling breast and prostate common gene signatures by Bayesian network learning". In Computational Intelligence methods for Bioinformatics and Biostatistics. Springer Lecture Notes in Computer Science, 2020.
    10.1007/978-3-030-34585-3_25
  10. Veríssimo, A.; Lopes, M.B.; Carrasquinha, E.; Vinga, S.. "Random sample consensus for the robust identification of outliers in cancer data". In Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2019). Springer Lecture Notes in Bioinformatics. 2020.
    10.1007/978-3-030-63061-4_11
  11. Diegues, I.; Lopes, M.B.; Vinga, S.. "Identification of common gene signatures in microarray and RNA-sequencing data using network-based regularization". In Bioinformatics and Biomedical Engineering. Springer Lecture Notes in Computer Science, 2020.
    10.1007/978-3-030-45385-5_2
  12. Carrasquinha, E.; Veríssimo, A.; Lopes, M.B.; Vinga, S.. "Network-based variable selection for survival outcomes in oncological data". In Bioinformatics Research and Applications. Springer Lecture Notes in Computer Science, 2020.
    10.1007/978-3-030-45385-5_49
  13. Carrasquinha, E.; Veríssimo, A.; Lopes, M.B.; Vinga, S.. "Variable Selection and Outlier Detection in Regularized Survival Models: Application to Melanoma Gene Expression Data". In Machine Learning, Optimization, and Data Science, 431-440. Springer International Publishing, 2019.
    10.1007/978-3-030-13709-0_36
  14. Lopes, M.B.; Veríssimo, A.; Carrasquinha, E.; Vinga, S.. "On the role of hub and orphan genes in the diagnosis of breast invasive carcinoma". In Machine Learning, Optimization, and Data Science. Springer Lecture Notes in Computer Science, 2019.
    10.1007/978-3-030-37599-7_52
Conference paper
  1. Eliana Ibrahimi; Mina Norouzirad; Melisa Meto; Marta B. Lopes. "Regularized Generalized Linear Models to Disclose Host-Microbiome Associations in Colorectal Cancer". 2023.
    10.1145/3613347.3613362
  2. Sampaio, P.N.; Cunha, B.; Rosa, F.; Sales, K.; Lopes, M.B.; Calado, C.R.C.. "Molecular fingerprint of human gastric cell line infected by Helicobacter pylori". 2015.
    10.1109/ENBENG.2015.7088877
  3. Lopes, M.B.; Sales, K.C.; Lopes, V.V.; Calado, C.R.C.. "Real-time plasmid monitoring of batch and fed-batch Escherichia coli cultures by NIR spectroscopy". 2013.
    10.1109/ENBENG.2013.6518394
  4. Lopes, M.B.; Scholtz, T.; Silva, D.; Santos, I.; Silva, T.; Sampaio, P.; Couto, A.; Lopes, V.V.; Calado, C.R.C.. "Modelling, monitoring and control of plasmid bioproduction in Escherichia coli cultures". 2012.
    10.1109/ENBENG.2012.6331370
  5. Lopes, M.B.; Bioucas-Dias, J.M.; Figueiredo, M.A.T.; Wolff, J.-C.; Mistry, N.; Warrack, J.. "Comparison of near infrared and Raman hyperspectral unmixing performances for chemical identification of pharmaceutical tablets". 2011.
    10.1109/WHISPERS.2011.6080869
  6. Lopes, M.B.; Bioucas-Dias, J.M.; Figueiredo, M.A.T.; Wolff, J.-C.. "Spectral unmixing via minimum volume simplices: Application to near infrared spectra of counterfeit tablets". 2009.
    10.1109/WHISPERS.2009.5289081
Conference poster
  1. Coletti, Roberta; Carrilho, João; Martins, Eduarda P.; Gonçalves, Céline S.; Costa, Bruno M.; Lopes, Marta B.. "MINGLE: A new tool for advancing multi-omics netwrok integration and visualization". Paper presented in European Conference on Mathematical and Theoretical Biology (ECMTB), 2024.
  2. João Carrilho; Roberta Coletti; Lopes, Marta B.. "Unveiling gene signatures in glioma: A Comprehensive analysis using regularized logistic regression, dimensionality reduction, and outlier detection". Paper presented in XXVI Congresso da Sociedade Portuguesa de Estatística (SPE 2023), 2023.
  3. Roberta Coletti; Lopes, Marta B.. "Network inference and clustering: mathematical tools to discover glioma biomarkers from gene expression patient data". Paper presented in The 3rd Women in Mathematics Meeting in Portugal (WM23), 2023.
  4. João Carrilho; Roberta Coletti; Lopes, Marta B.. "Disclosing gene signatures in gliomas via classification and dimensionality reduction methods". Paper presented in The 5th Statistics on Health Decision Making: Personalized Medicine, 2023.
  5. Francisca Vieira; Regina Bispo; Lopes, Marta B.. "Integration of multi-omics data for classification of glioma types and identification of novel biomarkers". Paper presented in Bioinformatics Days XII Edition, 2023.
  6. João Carrilho; Lopes, M.B.. "Identification of transcriptomic markers of intertumoral heterogeneity in gliomas via sparse logistic regression with the elastic net penalty". Paper presented in 3rd Portuguese Meeting on Biomathematics, 2022.
  7. Roberta Coletti; Sofia Martins; Lopes, M.B.. "Disclosing sparse transcriptomics networks in gliomas using the graphical lasso". Paper presented in 3rd Portuguese Meeting on Biomathematics, 2022.
  8. Peixoto, C.; Lopes, M.B.; Martins, M.; Veríssimo, A.; Costa, L.; Vinga, S.. "Sparse models and network-based regularizers for the analysis of RNA-seq data from colorectal cancer". Paper presented in EMBO Workshop - Precision Health: Molecular Basis, Technology and Digital Health, 2019.
  9. Veríssimo, A.; Lopes, M.B.; Carrasquinha, E.; Vinga, S.. "Performance and stability analysis of sparse network-based survival models". Paper presented in Workshop on Statistical Challenges in Medical Data Science (Ascona Workshop 2019), 2019.
  10. 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.
  11. Carrasquinha, E.; Veríssimo, A.; Lopes, M.B.; Vinga, S.. "Survival analysis of high-dimensional cancer gene expression data". Paper presented in The European Conference on Mathematical and Theoretical Biology (ECMTB 2018), 2018.
  12. Veríssimo, A.; Carrasquinha, E.; Lopes, M.B.; Oliveira, A.L.; Sagot, M.-F.; Vinga, S.. "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.
  13. Veríssimo, A.; Lopes, M.B.; Carrasquinha, E.; Oliveira, A.L.; Sagot, M.-F.; Vinga, S.. "Random Sample Consensus (RANSAC) for the robust identification of outliers in transcriptomic data". Paper presented in Intelligent Systems for Molecular Biology / European Conference on Computational Biology (ISMB/ECCB 2017), 2017.
  14. Veríssimo, A.; Carrasquinha, E.; Lopes, M.B.; Sagot, M-F.; Oliveira, A.L.; Vinga, S.. "Network-based sparse modeling of breast invasive carcinoma survival data". Paper presented in Signal Processing with Adaptive Sparse Structured Representations (SPARS 2017), 2017.
  15. Veríssimo, A.; Carrasquinha, E.; Lopes, M.B.; Sagot, M.-F.; Oliveira, A.L.; Vinga, S.. "Network-based regularized optimization for cancer survival data analysis". Paper presented in Ascona Workshop 2017 - Statistical Challenges in Single-Cell Biology, 2017.
  16. Sampaio, P.N.; Sales, K.C.; Lopes, M.B.; Calado, C.R.C.. "In-situ prediction of a recombinant aspartic protease production in bioreactor with near infrared spectroscopy and partial least squares regression". Paper presented in The Portuguese Congress of Microbiology and Biotechnology (MicroBiotec 2013), 2013.
  17. Sales, K.C.; Rosa, F.O.; Lopes, M.B.; Sampaio, P.N.; Calado, C.R.C.. "Near-infrared (NIR) versus mid-infrared (MIR) spectroscopy to monitor the bioproduction of heterologous products". Paper presented in The Portuguese Congress of Microbiology and Biotechnology (MicroBiotec 2013), 2013.
  18. Cunha, B.R.; Sales, K.C.; Rosa, F.O.; Lopes, M.B.; Sampaio, P.N.; Calado, C.R.C.. "Evaluation of anti-bacterial agents using high-throughput FTIR spectroscopy". Paper presented in The Portuguese Congress of Microbiology and Biotechnology (MicroBiotec 2013), 2013.
  19. Lopes, M.B.; Sales, K.C.; Rosa, F.O.; Sampaio, P.N.; Calado, C.R.C.. "Tracking the effect of the culture design in the in-situ NIR monitoring of plasmid bioprocesses". Paper presented in The Portuguese Congress of Microbiology and Biotechnology (MicroBiotec 2013), 2013.
  20. Lopes, M.B.; Sales, K.C.; Lopes, V.V.; Calado, C.R.C.. "Real-time plasmid monitoring of batch and fed-batch Escherichia coli cultures by NIR spectroscopy". Paper presented in The Third IEEE-EMBS Portuguese Bioengineering Meeting (ENBENG 2013), 2013.
  21. Lopes, M.B.; Scholz, T.; Santos, T.; Felício-Silva, D.; Sampaio, P.N.; Couto, A.; Lopes, V.V.; Calado, C.R.C.. "Modelling, Monitoring and Control of Plasmid Bioproduction in Escherichia coli Cultures". Paper presented in The Second IEEE-EMBS Portuguese Bioengineering Meeting (ENBENG 2012), 2012.
  22. Lopes, M.B.; Bioucas-Dias, J.M.; Wolff, J.-C.; Figueiredo, M.A.T.. "Spectral unmixing via minimum volume simplices: application to near infrared spectra of counterfeit tablets". Paper presented in First IEEE Workshop on Hyperspectral Image and Signal Processing: Evolution in Remote Sensing (WHISPERS 2009), 2009.
  23. Lopes, M.B.; Wolff, J.-C.. "Sourcing counterfeit tablets using NIR-CI: a case study". Paper presented in The 11th Conference on Chemometrics in Analytical Chemistry (CAC2008), 2008.
  24. Lopes, M.B.; Ferreira, A.P.; Menezes, J.C.. "Near-infrared spectroscopy as an important tool for at-line monitoring and control of industrial Streptomyces fermentations: two case studies". Paper presented in The 13th International Conference on Near Infrared Spectroscopy (13th ICNIRS), 2007.
  25. Lopes, M.B.; Brás, L.P.; Ferreira, A.P.; Menezes, J.C.. "A bootstrap-based strategy for spectral interval selection in partial least squares regression". Paper presented in The 10th Scandinavian Symposium on Chemometrics (SSC10), 2007.
  26. Santos, H.; Lopes, M.B.; Afonso, G.; Bretes, L.; Guerreiro, H.; Silva, J.C.. "Colon and rectal cancer - Analysis of prognostic factors". Paper presented in XXVII Congresso Nacional de Gastrenterologia e Endoscopia Digestiva, 2007.
  27. Cabral, H.N.; Vasconcelos, R.; Vinagre, C. ; França, S.; Fonseca, V.; Maia, A.; Reis-Santos, P.. "Anthropogenic pressures in estuarine flatfish nurseries along the Portuguese coast". Paper presented in The 6th International Flatfish Symposium, 2005.
Journal article
  1. de Mendonça, Mónica Leiria; Coletti, Roberta; Gonçalves, Céline S.; Martins, Eduarda P.; Costa, Bruno M.; Vinga, Susana; Lopes, Marta B.. "Updating TCGA glioma classification through integration of molecular data following the latest WHO guidelines". Scientific Data 12 1 (2025):
    10.1038/s41597-025-05117-2
  2. Coletti, Roberta; Carrilho, João F.; Martins, Eduarda P.; Gonçalves, Céline S.; Costa, Bruno M.; Lopes, Marta B.. "A novel tool for multi-omics network integration and visualization: A study of glioma heterogeneity". Computers in Biology and Medicine 188 (2025): 109811.
    10.1016/j.compbiomed.2025.109811
  3. Lopes, Marta B.; Coletti, Roberta; Duranton, Flore; Glorieux, Griet; Jaimes Campos, Mayra Alejandra; Klein, Julie; Ley, Matthias; et al. "The Omics-Driven Machine Learning Path to Cost-Effective Precision Medicine in Chronic Kidney Disease". PROTEOMICS (2025):
    10.1002/pmic.202400108
  4. Kastendiek, Nina; Coletti, Roberta; Gross, Thilo; Lopes, Marta B.. "Exploring glioma heterogeneity through omics networks: from gene network discovery to causal insights and patient stratification". BioData Mining 17 1 (2024):
    10.1186/s13040-024-00411-y
  5. Musib, Laila; Coletti, Roberta; Lopes, Marta B.; Mouriño, Helena; Carrasquinha, Eunice. "Priority-Elastic net for binary disease outcome prediction based on multi-omics data". BioData Mining 17 1 (2024):
    10.1186/s13040-024-00401-0
  6. Porreca, Annamaria; Ibrahimi, Eliana; Maturo, Fabrizio; Marcos Zambrano, Laura Judith; Meto, Melisa; Lopes, Marta B.. "Robust prediction of colorectal cancer via gut microbiome 16S rRNA sequencing data". Journal of Medical Microbiology 73 10 (2024):
    10.1099/jmm.0.001903
  7. Coletti, Roberta; Leiria de Mendonça, Mónica; Vinga, Susana; Lopes, Marta B.. "Inferring Diagnostic and Prognostic Gene Expression Signatures Across WHO Glioma Classifications: A Network-Based Approach". Bioinformatics and Biology Insights 18 (2024):
    10.1177/11779322241271535
  8. Vieira, Francisca G; Bispo, Regina; Lopes, Marta B. "Integration of Multi-Omics Data for the Classification of Glioma Types and Identification of Novel Biomarkers". Bioinformatics and Biology Insights 18 (2024):
    10.1177/11779322241249563
  9. Laura Judith Marcos-Zambrano; Víctor Manuel López-Molina; Burcu Bakir-Gungor; Marcus Frohme; Kanita Karaduzovic-Hadziabdic; Thomas Klammsteiner; Eliana Ibrahimi; et al. "A toolbox of machine learning software to support microbiome analysis". Frontiers in Microbiology (2023):
    10.3389/fmicb.2023.1250806
  10. Eliana Ibrahimi; Marta B. Lopes; Xhilda Dhamo; Andrea Simeon; Rajesh Shigdel; Karel Hron; Blaž Stres; et al. "Overview of data preprocessing for machine learning applications in human microbiome research". Frontiers in Microbiology 14 (2023):
    10.3389/fmicb.2023.1250909
  11. Sofia Martins; Roberta Coletti; Marta B. Lopes. "Disclosing transcriptomics network-based signatures of glioma heterogeneity using sparse methods". BioData Mining 16 1 (2023):
    10.1186/s13040-023-00341-1
  12. Domenica D’Elia; Jaak Truu; Leo Lahti; Magali Berland; Georgios Papoutsoglou; Michelangelo Ceci; Aldert Zomer; et al. "Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action". Frontiers in Microbiology 14 (2023):
    10.3389/fmicb.2023.1257002
  13. Georgios Papoutsoglou; Sonia Tarazona; Marta B. Lopes; Thomas Klammsteiner; Eliana Ibrahimi; Julia Eckenberger; Pierfrancesco Novielli; et al. "Machine learning approaches in microbiome research: challenges and best practices". Frontiers in Microbiology 14 (2023):
    10.3389/fmicb.2023.1261889
  14. Carolina Peixoto; Marta B. Lopes; Marta Martins; Sandra Casimiro; Daniel Sobral; Ana Rita Grosso; Catarina Abreu; et al. "Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization". BMC Bioinformatics 24 1 (2023):
    10.1186/s12859-022-05104-z
  15. João F. Carrilho; Marta B. Lopes. "Classification and biomarker selection in lower-grade glioma using robust sparse logistic regression applied to RNA-seq data". REVISTA BRASILEIRA DE BIOMETRIA 40 4 (2022): 371-381.
    10.28951/bjb.v40i4.634
  16. Patrício, André; Lopes, M.B.; Costa, Pedro Reis; Costa, Rafael S.; Henriques, Rui; Vinga, Susana. "Time-Lagged Correlation Analysis of Shellfish Toxicity Reveals Predictive Links to Adjacent Areas, Species, and Environmental Conditions". Toxins 14 10 (2022): 679.
    10.3390/toxins14100679
  17. Cruz, Rafaela C.; Costa, Pedro R.; Krippahl, Ludwig; Lopes, M.B.. "Forecasting biotoxin contamination in mussels across production areas of the Portuguese coast with Artificial Neural Networks". Knowledge-Based Systems (2022): 109895.
    10.1016/j.knosys.2022.109895
  18. Jensch, Antje; Lopes, M.B.; Vinga, Susana; Radde, Nicole. "ROSIE: RObust Sparse ensemble for outlIEr detection and gene selection in cancer omics data". Statistical Methods in Medical Research 31 5 (2022): 947-958.
    10.1177/09622802211072456
  19. Cruz, Rafaela C.; Reis Costa, Pedro; Vinga, Susana; Krippahl, Ludwig; Lopes, M.B.. "A Review of Recent Machine Learning Advances for Forecasting Harmful Algal Blooms and Shellfish Contamination". Journal of Marine Science and Engineering 9 3 (2021): 283.
    10.3390/jmse9030283
  20. Lopes, M.B.; Martins, Eduarda P.; Vinga, Susana; Costa, Bruno M.. "The Role of Network Science in Glioblastoma". Cancers 13 5 (2021): 1045.
    10.3390/cancers13051045
  21. Moreno-Indias, Isabel; Lahti, Leo; Nedyalkova, Miroslava; Elbere, Ilze; Roshchupkin, Gennady; Adilovic, Muhamed; Aydemir, Onder; et al. "Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions". Frontiers in Microbiology 12 (2021):
    10.3389/fmicb.2021.635781
  22. Marcos-Zambrano, Laura Judith; Karaduzovic-Hadziabdic, Kanita; Loncar Turukalo, Tatjana; Przymus, Piotr; Trajkovik, Vladimir; Aasmets, Oliver; Berland, Magali; et al. "Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment". Frontiers in Microbiology 12 (2021):
    10.3389/fmicb.2021.634511
  23. Peixoto, Carolina; Lopes, M.B.; Martins, Marta; Costa, Luís; Vinga, Susana. "TCox: Correlation-Based Regularization Applied to Colorectal Cancer Survival Data". Biomedicines 8 11 (2020): 488.
    10.3390/biomedicines8110488
  24. Lopes, M.B.; Vinga, S.. "Tracking intratumoral heterogeneity in glioblastoma via regularized classification of single-cell RNA-Seq data". BMC Bioinformatics 21 59 (2020):
    10.1186/s12859-020-3390-4
  25. Lopes, M.B.; Casimiro, S.; Vinga, S.. "Twiner: correlation-based regularization for identifying common cancer gene signatures". BMC Bioinformatics 20 1 (2019): 356.
    10.1186/s12859-019-2937-8
  26. Segaert, P.; Lopes, M.B.; Vinga, S.; Rousseeuw, P.J.. "Robust identification of target genes and outliers in triple-negative breast cancer data.". Statistical methods in medical research (2018):
    10.1177/0962280218794722
  27. Lopes, M.B.; Veríssimo, A.; Carrasquinha, E.; Casimiro, S.; Beerenwinkel N; Vinga, S.. "Ensemble outlier detection and gene selection in triple-negative breast cancer data.". BMC bioinformatics (2018):
    10.1186/s12859-018-2149-7
  28. Lopes, M.B.; Amorim, A.; Calado, C.R.C.; Costa, P.R.. "Determination of Cell Abundances and Paralytic Shellfish Toxins in Cultures of the Dinoflagellate Gymnodinium catenatum by Fourier Transform Near Infrared Spectroscopy". Journal of Marine Science and Engineering 6 4 (2018): 147-147.
    10.3390/jmse6040147
  29. Lopes, M.B.; Calado, C.R.C.. "Assessing plasmid bioprocess reproducibility and C-source uptake stage through multivariate analysis of offline and online data". Journal of Chemical Technology and Biotechnology 93 10 (2018): 3056-3066.
    10.1002/jctb.5666
  30. Carrasquinha, E.; Veríssimo, A.; Lopes, M.B.; Vinga, S.. "Identification of influential observations in high-dimensional cancer survival data through the rank product test". BioData Mining (2018):
    10.1186/s13040-018-0162-z
  31. Sampaio, P.N.; Sales, K.C.; Rosa, F.O.; Lopes, M.B.; Calado, C.R.C.. "High-throughput FTIR-based bioprocess analysis of recombinant cyprosin production". Journal of Industrial Microbiology and Biotechnology 44 1 (2017): 49-61.
    10.1007/s10295-016-1865-0
  32. Sales, K.C.; Rosa, F.; Cunha, B.R.; Sampaio, P.N.; Lopes, M.B.; Calado, C.R.C.. "Metabolic profiling of recombinant Escherichia coli cultivations based on high-throughput FT-MIR spectroscopic analysis". Biotechnology Progress 33 2 (2017): 285-298.
    10.1002/btpr.2378
  33. Lopes, M.B.; Calado, C.R.C.; Figueiredo, M.A.T.; Bioucas-Dias, J.M.. "Does Nonlinear Modeling Play a Role in Plasmid Bioprocess Monitoring using Fourier Transform Infrared Spectra?". Applied Spectroscopy (2016):
    10.1177/0003702816670913
  34. Rosa, F.; Sales, K.C.; Carmelo, J.G.; Fernandes-Platzgummer, A.; da Silva, C.L.; Lopes, M.B.; Calado, C.R.C.. "Monitoring the ex-vivo expansion of human mesenchymal stem/stromal cells in xeno-free microcarrier-based reactor systems by MIR spectroscopy". Biotechnology Progress 32 2 (2016): 447-455.
    10.1002/btpr.2215
  35. Lopes, M.B.; Gonçalves, G.A.L.; Felício-Silva, D.; Prather, K.L.J.; Monteiro, G.A.; Prazeres, D.M.F.; Calado, C.R.C.. "In situ NIR spectroscopy monitoring of plasmid production processes: Effect of producing strain, medium composition and the cultivation strategy". Journal of Chemical Technology and Biotechnology 90 2 (2015): 255-261.
    10.1002/jctb.4431
  36. Rosa, F.; Sales, K.C.; Cunha, B.R.; Couto, A.; Lopes, M.B.; Calado, C.R.. "A comprehensive high-throughput FTIR spectroscopy-based method for evaluating the transfection event: estimating the transfection efficiency and extracting associated metabolic responses". Analytical and bioanalytical chemistry 407 26 (2015): 8097-8108.
    10.1007/s00216-015-8983-9
  37. Sales, K.C.; Rosa, F.; Sampaio, P.N.; Fonseca, L.P.; Lopes, M.B.; Calado, C.R.. "In situ near-infrared (NIR) versus high-throughput mid-infrared (MIR) spectroscopy to monitor biopharmaceutical production". Applied spectroscopy 69 6 (2015): 760-772.
    10.1366/14-07588
  38. Lopes, M.B.; Martins, G.; Calado, C.R.C.. "Kinetic modeling of plasmid bioproduction in Escherichia coli DH5a cultures over different carbon-source compositions". Journal of Biotechnology 186 (2014): 38-48.
    10.1016/j.jbiotec.2014.06.022
  39. Sampaio, P.N.; Sales, K.C.; Rosa, F.O.; Lopes, M.B.; Calado, C.R.. "In situ near infrared spectroscopy monitoring of cyprosin production by recombinant Saccharomyces cerevisiae strains". Journal of Biotechnology 188 (2014): 148-157.
    10.1016/j.jbiotec.2014.07.454
  40. Lopes, M.B.; Wolff, J.-C.; Bioucas-Dias, J.M.; Figueiredo, M.A.T.. "Study on the effect of pixel resolution and blending grade on near-infrared hyperspectral unmixing of tablets". Applied Spectroscopy 65 2 (2011): 193-200.
    10.1366/10-06079
  41. Lopes, M.B.; Wolff, J.-C.; Bioucas-Dias, J.M.; Figueiredo, M.A.T.. "Quantification of components in non-homogenous pharmaceutical tablets using near infrared reflectance imaging". Journal of Near Infrared Spectroscopy 18 5 (2010): 333-340.
    10.1255/jnirs.897
  42. Lopes, M.B.; Wolff, J.-C.; Bioucas-Dias, J.M.; Figueiredo, M.A.T.. "Reply to the comments on "near-infrared hyperspectral unmixing based on a minimum volume criterion for fast and accurate chemometric characterization of counterfeit tablets"". Analytical Chemistry 82 20 (2010): 8753-8754.
    10.1021/ac102443w
  43. Lopes, M.B.; Wolff, J.-C.; Bioucas-Dias, J.M.; Figueiredo, M.A.T.. "Near-infrared hyperspectral unmixing based on a minimum volume criterion for fast and accurate chemometric characterization of counterfeit tablets". Analytical Chemistry 82 4 (2010): 1462-1469.
    10.1021/ac902569e
  44. Lopes, M.B.; Wolff, J.-C.; Bioucas-Dias, J.M.; Figueiredo, M.A.T.. "Determination of the composition of counterfeit Heptodin™ tablets by near infrared chemical imaging and classical least squares estimation". Analytica Chimica Acta 641 1-2 (2009): 46-51.
    10.1016/j.aca.2009.03.034
  45. Lopes, M.B.; Wolff, J.-C.. "Investigation into classification/sourcing of suspect counterfeit Heptodin™ tablets by near infrared chemical imaging". Analytica Chimica Acta 633 1 (2009): 149-155.
    10.1016/j.aca.2008.11.036
  46. Brás, L.P.; Lopes, M.B.; Ferreira, A.P.; Menezes, J.C.. "A bootstrap-based strategy for spectral interval selection in PLS regression". Journal of Chemometrics 22 11-12 (2008): 695-700.
    10.1002/cem.1153
  47. Cabral, H.N.; Vasconcelos, R.; Vinagre, C. ; França, S.; Fonseca, V.; Maia, A.; Reis-Santos, P.; et al. "Relative importance of estuarine flatfish nurseries along the Portuguese coast". Journal of Sea Research 57 2-3 (2007): 209-217.
    10.1016/j.seares.2006.08.007
  48. Lopes, M.B.; Murta, A.G.; Cabral, H.N.. "Discrimination of snipefish Macroramphosus species and boarfish Capros aper morphotypes through multivariate analysis of body shape". Helgoland Marine Research 60 1 (2006): 18-24.
    10.1007/s10152-005-0010-7
  49. Lopes, M.B.; Murta, A.G.; Cabral, H.N.. "The ecological significance of the zooplanktivores, snipefish Macroramphosus spp. and boarfish Capros aper, in the food web of the south-east North Atlantic". Journal of Fish Biology 69 2 (2006): 363-378.
    10.1111/j.1095-8649.2006.01093.x
  50. Cabral, H.N.; Lopes, M.B.; Loeper, R.. "Trophic niche overlap between flatfishes in a nursery area on the Portuguese coast". Scientia Marina 66 3 (2002): 293-300.
    10.3989/scimar.2002.66n3293
Magazine article
  1. Lopes, M.B.; Wolff, J.-C.; Bioucas-Dias, José M.; Figueiredo, M.T.F.. "Investigating counterfeit medicines - the near infrared chemical imaging picture", NIR News, 2011
  2. Santos, H.; Sousa, D.; Caldeira, P.; Lopes, M.B.; Açucena, F.; Ramos, A.; Moniz, M.; Lopes, A.; Guerreiro, H.. "Survival and prognosis of patients with percutaneous endoscopic gastrotomy", Revista APNEP, 2008
Preprint
  1. Coletti, Roberta; Cerdeira, Jorge Orestes; Raydan, Marcos; Lopes, Marta Belchior. "Performance Assessment of an Unsupervised Variable Selection Approach for Biomarker Discovery and Glioblastoma Subtyping". 2025.
    10.1101/2025.03.11.642670
  2. Carrilho, João F.; Coletti, Roberta; Costa, Bruno M.; Lopes, Marta B.. "Multi-omics biomarker selection and outlier detection across WHO glioma classifications via robust sparse multinomial regression". 2024.
    10.1101/2024.08.26.24312601
  3. Coletti, Roberta; Carrilho, João; Martins, Eduarda P.; Gonçalves, Céline S.; Costa, Bruno M.; Lopes, Marta B.. "A Novel Tool for Multi-Omics Network Integration and Visualization: A Study of Glioma Heterogeneity". 2024.
    10.1101/2024.03.18.585500
  4. Kastendiek, Nina; Coletti, Roberta; Gross, Thilo; Lopes, Marta B.. "Exploring glioma heterogeneity through omics networks: from gene network discovery to causal insights and patient stratification". 2024.
    10.1101/2024.07.02.601715
  5. Medonça, Mónica L.; Coletti, Roberta; Gonçalves, Céline S.; Martins, Eduarda P.; Costa, Bruno M.; Vinga, Susana; Lopes, Marta B.. "Updating TCGA glioma classification through integration of molecular profiling data following the 2016 and 2021 WHO guidelines". 2023.
    10.1101/2023.02.19.529134
  6. Tavares, Sérgio; Costa, Pedro Reis; Krippahl, Ludwig; Lopes, Marta B.. "Satellite-based feature extraction and multivariate time-series prediction of biotoxin contamination in shellfish". 2023.
    10.48550/arXiv.2311.15000
  7. Coletti, Roberta; Mónica L. Mendonça; Susana Vinga; Lopes, Marta B.. "Inferring diagnostic and prognostic gene expression signatures across WHO glioma classifications: A network-based approach". 2023.
    10.48550/arXiv.2305.12207
  8. Francisca Vieira; Regina Bispo; Lopes, Marta B.. "Integration of multi-omics data for the classification of glioma types and identification of novel biomarkers". 2023.
    10.1101/2023.12.22.572983
  9. Veríssimo, André; Carrasquinha, Eunice; Lopes, Marta B.; Oliveira, Arlindo L.; Sagot, Marie-France; Vinga, Susana. "Sparse network-based regularization for the analysis of patientomics high-dimensional survival data". 2018.
    10.1101/403402
Thesis / Dissertation
  1. Lopes, Marta. "Advances in near-infrared hyperspectral imaging for pharmaceutical anti-counterfeiting". PhD, Universidade de Lisboa Instituto Superior Técnico, 2011.
  2. Lopes, Marta. "Strategies for avoiding overparametrization in statistical catch-at-age methods". Master, Universidade de Lisboa Instituto Superior de Agronomia, 2006.
  3. Lopes, Marta. "Feeding ecology and morphological variation of Macroramphosus spp. and Capros aper in the Portuguese coast". Degree, Universidade de Lisboa Faculdade de Ciências, 2003.

Other

Other output
  1. glmSparseNet - Network centrality metrics for elastic-net regularized models. Bioconductor R package. 2018. Veríssimo, André; Vinga, S.; Carrasquinha, E.; Lopes, M.B.. https://bioconductor.org/packages/3.8/bioc/html/glmSparseNet.html.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2025/03/25 Integrating multi-omics data and robust statistical learning for enhanced biomarker discovery, cancer diagnosis and treatment Spatial Omics and AI: Bridging Discovery and Translational Medicine
Fundação Champalimaud (Lisboa, Portugal)
2025/03/13 Integration and visualization of multi-omics data for precision medicine Al Horizons: Shaping the Future of Health, Technology, and Sustainability
University of Vic, Central University of Catalonia (Vic, Spain)
2025/01/21 Multi-omics biomarker discovery in oncology using statistical and machine learning methods NIMSB Seminars
(Portugal)
2024/10 Marcadores de prognostico e preditivos de cancro: A importância dos dados de ómica 2.º Congresso Português do Cancro do Pulmão (CPCP)
(Peniche, Portugal)
2024/10 Statistical and machine learning approaches for assisted decision-making in industry: applications in biopharmaceuticals and aquaculture NOVA Math Industry Day
(Caparica, Portugal)
2024/09 Advancing glioma research through multi-omics network discovery and analysis 1st Net4Brain Annual Meeting
(Ljubljana, Slovenia)
2024/07 Understanding omics links behind glioma heterogeneity: a network and clustering approach The 18th conference of the International Federation of Classification Societies (IFCS)
(San José, Costa Rica)
2024/07 Refining gene selection and outlier detection in glioblastoma based on a consensus approach for regularized survival models The 11th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO)
(Gran Canária, Spain)
2024/06 Unveiling glioma heterogeneity by gene-protein biomarker detection via network discovery and dimensionality reduction The 9th International Caparica Conference on Analytical Proteomics (ICAP)
(Caparica, Portugal)
2024/02/27 Biomarker discovery and precision oncology through sparsity-inducing methods Seminars of the Department of Mathematical Analysis and Applications of Mathematics, University of Science, Palacky University of Olomouc
(Olomouc, Czech Republic)
2024/02 Sparsity-inducing network inference and classification for the identification of gene expression signatures in gliomas The 15th Conference on Dynamical Systems Applied to Biology and Natural Sciences (DSABNS)
(Caparica, Portugal)
2023/12/21 Identifying brain tumor gene signatures through multi-omics network inference and classification IMS International Conference on Statistics and Data Science (ICSDS 2023)
Faculdade de Ciências, Universidade de Lisboa (Lisboa, Portugal)
2023/11 Causal graph discovery for explainable insights on marine biotoxin shellfish contamination The 24th International Conference on Intelligent Data Engineering and Automated Learning (IDEAL 2023)
Universidade de Évora (Évora, Portugal)
2023/10 Dimensionality reduction in survival models based on gene expression data: an application to brain cancer XXVI Congresso da Sociedade Portuguesa de Estatística (SPE 2023)
(Guimarães, Portugal)
2023/10 Classification and survival analysis of multi-omics data for the identification of novel diagnostic and prognostic biomarkers in glioma XXVI Congresso da Sociedade Portuguesa de Estatística (SPE 2023)
(Guimarães, Portugal)
2023/09 Evaluating the causal role of environmental data in shellfish biotoxin contamination on the Portuguese coast The 22nd Portuguese Conference on Artificial Intelligence (EPIA 2023)
(Faial, Portugal)
2023/09 Multi-omics data integration and network inference for biomarker discovery in glioma The 22nd Portuguese Conference on Artificial Intelligence (EPIA 2023)
(Faial, Portugal)
2023/09 Comparative analysis of machine learning models for time-series forecasting of Escherichia coli contamination in Portuguese shellfish production areas The 9th Annual Conference on machine Learning, Optimization and Data science (LOD 2023)
(Lake District, United Kingdom)
2023/09 Mathematical models in health sciences: Classification, festure selection and multi-omics networks COST Action PerMedik meeting
(Atenas, Greece)
2023/08 Feature extraction from satellite data for multivariate time-series forecasting of biotoxin contamination in shellfish The 25th International Conference on Computational Statistics (COMPSTAT 2023)
(London, United Kingdom)
2023/08 Network inference and robust clustering on high-dimensional data to investigate the molecular heterogeneity in glioma The 25th International Conference on Computational Statistics (COMPSTAT 2023)
(London, United Kingdom)
2023/07 Evaluating the impact of inclusion of molecular information in glioma classification on network-based biomarker discovery Data Science, Statistics & Visualisation (DSSV 2023)
(Antwerp, Belgium)
2023/06 On the role of temporal irregularities and spatial dependencies in the development of time-series models for predicting biotoxin contamination in shellfish 13th International Workshop on Modeling the Ocean (IWMO 2023)
(Hamburg, Germany)
2022/09/14 Predicting biotoxin shellfish contamination with artificial neural networks: towards a forecasting system for shellfish safety Littoral 2022
(Caparica, Portugal)
2022/07/22 Identification of driver genes in glioblastoma via regularized classification The 17th Conference of the International Federation of Classification Societies
Faculty of Economy, University of Porto (Porto, Portugal)
2022/05/24 Biomarker discovery in cancer transcriptomic data using network-based regularization ML4Microbiome Workshop
University of Tirana (Tirana, Albania)
2022/05/09 Forecasting mussel contamination by marine biotoxins using long short-term memory networks GlobalHAB Workshop
(Glasgow, United Kingdom)
2021/12/13 Building Molecular-Informed Decision Support Systems: Pharmaceutical, Biomedical, and Environmental Applications DBE/IST Seminars Autumn 2021
(Lisboa, Portugal)
2021/10/14 Forecasting biotoxin contamination in mussels via artificial neural network modelling 19th International Conference on Harmful Algae
(Mexico)
2021/07/27 Inteligência Artificial em Aplicações Biomédicas e Ambientais Conferência de Inteligência Artificial e Machine Learning
Universidade de Lúrio (Pemba, Mozambique)
2021/04/28 Biomarker discovery in cancer transcriptomic data using network-based regularization CEAUL/CMAT Seminar Series
(Lisboa, Portugal)
2020/03/04 Statistics and Machine Learning in Biomedical and Environmental Sciences Workshop Data Science and Big Data
(Caparica, Portugal)
2019/09/13 On the role of hub and orphan genes in the diagnosis of breast invasive carcinoma Machine Learning, Optimization, and Data Science (LOD 2019)
(Siena, Italy)
2019/09/04 Random sample consensus for the robust identification of outliers in cancer data Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2019)
(Bergamo, Italy)
2018/09/13 Variable selection and outlier detection in regularized survival models: application to melanoma gene expression data The Fourth International Conference on Machine Learning, Optimization, and Data Science (LOD 2018)
(Volterra, Italy)
2018/09/06 Unravelling breast and prostate common gene signatures by Bayesian network learning International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2018)
(Caparica, Portugal)
2018/07/09 Network-based penalized logistic regression for the identification of common gene signatures in breast and prostate cancers Data Science, Statistics & Visualisation (DSSV 2018)
(Vienna, Austria)
2018/07/09 Robust identification of target genes and outliers in triple-negative breast cancer data Data Science, Statistics & Visualisation (DSSV 2018)
(Vienna, Austria)
2017/07/16 Outlier detection in survival analysis: an application to ovarian cancer data The 61st World Statistics Congress (ISI 2017)
(Marrakech, Morocco)
2017/07/12 Consensus outlier detection in triple-negative breast cancer gene expression data Data Science, Statistics & Visualisation (DSSV 2017) - A Satellite Conference of the 61st World Statistics Congress
(Lisboa, Portugal)
2015/02/26 Molecular fingerprint of human gastric cell line infected by Helicobacter pylori The 4th IEEE-EMBS Portuguese Bioengineering Meeting (ENBENG2015)
(Porto, Portugal)
2013/12/06 Bypassing the need for reporter genes The Portuguese Congress of Microbiology and Biotechnology (MicroBiotec 2013)
(Aveiro, Portugal)
2012/09/23 On-line monitoring of plasmid production in an Escherichia coli bioprocess by near infrared spectroscopy The 9th European Symposium on Biochemical Engineering Science (ESBES 2012)
(Istanbul, Turkey)
2011/10/02 Near-infrared imaging and Raman mapping to understand the bigger picture of a counterfeit anti-viral medicine The 38th Federation of Analytical Chemistry and Spectroscopy Societies Conference (FACSS 2011)
(Reno, United States)
2011/06/06 Comparison of near infrared and Raman hyperspectral unmixing performances for chemical identification of pharmaceutical tablets The Third IEEE Workshop on Hyperspectral Image and Signal Processing: Evolution in Remote Sensing (WHISPERS 2011)
(Lisboa, Portugal)
2009/10/18 Comparison of LC/MS and ion mobility spectrometry combined with mass spectrometry for differentiation of counterfeit HeptodinTM The 36th Federation of Analytical Chemistry and Spectroscopy Societies Conference (FACSS2009)
(Louisville, Kentucky, United States)
2009/10/18 The near-infrared chemical imaging picture of counterfeit anti-viral drug HeptodinTM The 36th Federation of Analytical Chemistry and Spectroscopy Societies Conference (FACSS2009)
(Louisville, Kentucky, United States)
2008/11/21 ERCP - Prospective analysis of complications and risk factors XXIII Reunião Anual do Núcleo de Gastrenterologia dos Hospitais Distritais
(Portimão, Portugal)
2008/09/28 Determination of the composition of counterfeit drugs by near-infrared chemical imaging The 35th Federation of Analytical Chemistry and Spectroscopy Societies (FACSS2008)
(Reno, United States)
2008/04/14 Survival and prognosis of patients with percutaneous endoscopic gastrostomy X Annual Congress of the Portuguese Society of Enteric and Parenteric Nutrition
(Porto, Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2024 - Current Multi-disease biomarker discovery for drug repurposing
Supervisor
 Master in Computational Biology and Bioinformatics (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2024 - Current Identification of brain tumor molecular subtypes via regularized classification using correlation-based penalty
Supervisor
 Master in Mathematics and Applications (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2024 - Current Unraveling pancreatic cancer biology using multi-omics integration techniques
Co-supervisor
 Master in Biostatistics (Master)
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2023 - Current Unveiling multi-omics cancer biomarkers via Bioinformatics and Statistical Learning
Supervisor
 PhD Program in Mathematics (PhD)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2025/03/01 - 2025/06/01 The role of meta genomics and metabolomics in colorectal cancer staging
Supervisor
 ERASMUS + (Degree)
Univerzitet u Beogradu, Serbia
2024/05/25 - 2024/08/25 Unraveling the effects of smoking on human gut microbiome and associated Immune system Interactions
Supervisor
 ERASMUS + (Degree)
Universität Heidelberg, Germany
2023 - 2024 Deciphering glioma heterogeneity through multi-view clustering: towards improved disease molecular subtyping and personalised medicine
Supervisor
 Master in Mathematics and Applications (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2023 - 2024 Causal insights from multi-omics data: uncovering gene networks and potential therapeutic targets in glioma
Supervisor
 Master in Computational Biology and Bioinformatics (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2023 - 2024 A machine learning approach to the personalized prediction of SARS-COV-2 vaccination schedule
Supervisor
 Master in Analysis and Engineering of Big Data (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2023 - 2024 Dimensionality reduction in survival models based on gene expression data: An application to brain cancer
Co-supervisor
 Master in Biostatistics (Master)
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2023/09/11 - 2023/11/12 Exploring glioma heterogeneity through omics networks: from gene network discovery to causal insights and patient stratification
Supervisor
 ERASMUS + (Degree)
Carl von Ossietzky Universität Oldenburg, Germany
2022 - 2023 Evaluating the role of environmental variables on shellfish biotoxin contamination via supervised learning
Supervisor
 Integrated Master in Computer Science (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2022 - 2023 Unveiling novel glioma biomarkers through multi-omics integration and classification
Supervisor
 Master in Computational Biology and Bioinformatics (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2022 - 2023 Data mining and machine learning to develop a non-invasive differential sensing method for medical diagnostics
Co-supervisor
 Master in Biomedical Engineering (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2021 - 2023 Development of a deep learning-based tool to predict shellfish contamination by marine biotoxins
Supervisor
 Master in Analysis and Engineering of Big Data (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2021 - 2023 Unveiling the anticancer potential of hydroxytyrosol in LOVO cell spheroids
Co-supervisor
 Integrated Master in Biomedical Engineering (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2021 - 2023 Identification of genetic drivers of colorectal cancer via bioinformatics and machine learning
Supervisor
 Master in Analysis and Engineering of Big Data (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2021 - 2023 Biomarker selection and molecular subtyping in colon and rectal cancer via machine learning
Supervisor
 Integrated Master in Biomedical Engineering (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2020/09/01 - 2022/04 A Machine Learning approach to Sentinel-3 Imagery Feature Extraction In The Context Of Harmful Algal Blooms
Co-supervisor
 Integrated Master in Computer Science (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2020/01/01 - 2022/03 Telecom churn prediction: a big-data approach
Supervisor
 Master in Analysis and Engineering of Big Data (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2020/09/01 - 2022/01 Multivariate time-series forecasting of shellfish contamination by marine biotoxins
Supervisor
 Master in Analysis and Engineering of Big Data (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2020/09/01 - 2022/01 Identification of colorectal cancer genetic biomarkers via machine learning
Supervisor
 Master in Analysis and Engineering of Big Data (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2020 - 2022/01 Inferring breast cancer subtypes based on patients mutation profiles
Co-supervisor
 Integrated Master in Computer Science (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2021 - 2022 Disclosing multi-omics signatures of brain tumors
Supervisor
 Integrated Master in Biomedical Engineering (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2021 - 2022 Learning subspace representations in cancer mutation profiles via autoencoders for subtype identification
Co-supervisor
 Integrated Master in Computer Science (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2020/01/01 - 2021/11 Multivariate time-series forecasting of seafood safety
Co-supervisor
 Integrated Master's in Biomedical Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2019 Identification of common gene signatures in microarray and RNA-sequencing data using network-based regularization
Co-supervisor
 Ciências de Engenharia - Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2013 - 2014 Infrared Spectroscopy: A groundbreaking tool to monitor mammalian cells' processes. MSc Thesis in Biomedical Engineering
Co-supervisor
 Biomedical Engineering (Master)
Universidade Católica Portuguesa, Portugal
2013 - 2014 Metabolic monitoring of cell cultures based on high-throughput FT-IR spectroscopy analysis. MSc Thesis in Biomedical Engineering
Co-supervisor
 Biomedical Engineering (Master)
Universidade Católica Portuguesa, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2025/05/07 - 2025/05/08 Generative models for power, identifiability and goodness of fit testing, by Susan Holmes (2025/05/07 - 2025/05/08)
Other (President of the Organising Committee)
 Universidade Nova Centro de Matemática e Aplicações, Portugal
2025/03/26 - 2025/03/28 Short course on Neural Recommender Systems: Theory, Methods, and Applications, by Giulia Di Teodoro and Federico Siciliano (2025/03/26 - 2025/03/28)
Other (President of the Organising Committee)
 Universidade Nova Centro de Matemática e Aplicações, Portugal
2024/11/27 - 2024/11/28 Short course on Optimization Models for Unit Commitment in Electric Energy Systems, by Miguel Anjos (2024/11/27 - 2024/11/28)
Other (President of the Organising Committee)
 Universidade Nova Centro de Matemática e Aplicações, Portugal
2024/06/03 - 2024/06/21 NOVA Math Thematic Weeks - Exploring Pharmaceutical Frontiers in Drug Discover, Within-Host Dynamics, and Clinical Trials (2024/06/03 - 2024/06/21)
Workshop (Co-organisor)
 Universidade Nova Centro de Matemática e Aplicações, Portugal
2024/06/18 - 2024/06/19 Short course on Causal inference in drug discovery, by Tom Michoel (2024/06/18 - 2024/06/19)
Other (President of the Organising Committee)
 Universidade Nova Centro de Matemática e Aplicações, Portugal
2023/10/18 - 2023/10/20 Modern Statistics for Biology 2023 Training School (2023/10/18 - 2023/10/20)
Workshop (Member of the Organising Committee)
 Universiteti i Tiranës, Albania
2023/07/05 - 2023/07/13 NOVA Math Thematic Weeks - Mathematical Models in Health (2023/07/05 - 2023/07/13)
Workshop (Co-organisor)
 Universidade Nova Centro de Matemática e Aplicações, Portugal
2023/07/11 - 2023/07/12 Short course on Bioinformatics tools for multi-omics analysis, by Sonia Tarazona (2023/07/11 - 2023/07/12)
Other (President of the Organising Committee)
 Universidade Nova Centro de Matemática e Aplicações, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2022/01/17 - 2022/01/17 The 4th edition of the Winter School MathMasters 2022
Seminar
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2019/05/17 - 2019/05/18 The Wizardry of Artificial Intelligence: AI and Machine Learning in Cancer Imaging
Workshop
 Champalimaud Foundation
2019/05/14 - 2019/05/15 Copernicus Marine Service Training
Workshop
 Mercator Ocean International
2018/08/27 - 2018/08/29 New directions in single cell analysis
Workshop
 European Molecular Biology Laboratory (EMBL)
2017/04/03 - 2017/04/04 Advanced R programming
Workshop
 Dataprogrammers
2007/06/15 - 2007/06/16 Hyperspectral imaging
Workshop
 Technobothnia Research Centre
2006/04/10 - 2006/04/14 Advanced course on epidemiology of infectious diseases
Workshop
 Instituto Gulbenkian de Ciência

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2024 Assessing the impact of XIST and X chromosome dysregulation in systemic lupus erythematosus
(Thesis) Arguer
 Mafalda Soares (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2024 Charaterizing time ranges of costal upwelling via unsupervised clustering
(Thesis) Arguer
 João Vargues (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2023 Causal graph discovery for explainable insights on marine biotoxin shellfish contamination
(Thesis) Arguer
 Diogo Ribeiro (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023 Comparative analysis of machine learning models for time-series forecasting of Escherichia coli contamination in Portuguese shellfish production areas
(Thesis) Arguer
 Filipe Ferraz (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023 Modelos de aprendizagem automática para detetar o estado de parcelas florestais
(Thesis) Arguer
 Gonçalo Prates (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2023 Non-invasive urologic tumours monitoring: data mining and machine learning algorithms for urine gas and liquid analysis
(Thesis) Arguer
 Susana Fernandes (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2022/06/21 Assess the effect of angiogenesis inhibition in intra-tumor heterogeneity
(Thesis) Arguer
 David Pais (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2021 Survival analysis of transcriptomic oncological data for the identification of cancer biomarkers
(Thesis) Arguer
 Ana Beatriz Correia (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2020/07/08 Deciphering mechanisms underlying tumor heterogeneity using multi-omics approaches
(Thesis) Arguer
 Joonas Avik (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019/12/16 Latent factors of multi-omics data and clustering
(Thesis) Arguer
 Xia Anbang (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Conference scientific committee

Conference name Conference host
2024 - Current Inforum - Simpósio Nacional de Informática Lisbon, Portugal
2020 - Current International Conference on Machine Learning, Optimization, and Data Science Certosa di Pontignano, Siena, Tuscany, Italy
2023 - 2023 The 19th Annual Meeting of the Bioinformatics Italian Society Bari, Italy
Distinctions

Other distinction

2022 Call Stimulus for Institutional Scientific Employment (CEECINST/00042/2021)
Fundação para a Ciência e a Tecnologia, Portugal
2019 Call Stimulus for Institutional Scientific Employment (CEECINST/00102/2018)
Fundação para a Ciência e a Tecnologia, Portugal
2010 Post-Doctoral Grant (SFRH/BPD/73758/2010)
Fundação para a Ciência e a Tecnologia, Portugal
2006 PhD Grant (SFRH/BD/31084/2006)
Fundação para a Ciência e a Tecnologia, Portugal