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I am a researcher at NOVA School of Science and Technology, Universidade NOVA de Lisboa. I hold a PhD in Biotechnology, a Master’s degree in Applied Mathematics and a 5-year degree in Marine Biology. My main research activities have been focused on the development of mathematical and computational tools based on data mining and machine learning to extract meaningful information from high-dimensional data generated by high-throughput technologies. I've been developing my work in the context of precision medicine, bioprocess monitoring, quality control, and marine ecology applications.

RESEARCH AREAS

Molecule

MACHINE LEARNING

Test Tubes

MARINE SCIENCE

BIOINFORMATICS

Gears

BIOENGINEERING

Fishing Boat
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WORK EXPERIENCE

RESEARCHER

Faculdade de Ciências e Tecnologia

Universidade Nova de Lisboa

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RESEARCHER

Instituto de Telecomunicações

October 2016 - August 2018

April 2011 - September 2016

POST-DOCTORAL FELLOW

Instituto de Telecomunicações

POST-DOCTORAL FELLOW

Instituto de Engenharia Mecânica (IDMEC), Instituto Superior Técnico

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December 2019 -

January 2019 - December 2019

September 2018 - December 2018

POST-DOCTORAL FELLOW

Instituto de Engenharia de Sistemas e Computadores - Investigação e  Desenvolvimento (INESC-ID)

EDUCATION

February 2011

BIOTECHNOLOGY

INSTITUTO SUPERIOR TÉCNICO, UNIVERSIDADE DE LISBOA

PhD Dissertation: Advances in near-infrared hyperspectral imaging for pharmaceutical anti-counterfeiting

June 2006

APPLIED MATHEMATICS

INSTITUTO SUPERIOR DE AGRONOMIA, UNIVERSIDADE DE LISBOA

MSc Dissertation: Strategies for avoiding overparametrization in statistical catch-at-age methods

July 2007 - August 2007

INTERNSHIP, ELECTRICAL ENGINEERING

DEPARTMENT, UNIVERSITY OF WASHINGTON, USA

Project: Statistical estimation in big data sets

September 2003

MARINE BIOLOGY

FACULDADE DE CIÊNCIAS, UNIVERSIDADE DE LISBOA

5-year degree Dissertation: Feeding ecology and morphological variation of Macroramphosus spp. and Capros aper in the Portuguese coast

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PROJECTS

 

March 2023 -

Management Committee Member

Cost Action CA21165 - Personalized medicine in chronic kidney disease: improved outcome based on Big Data (PerMediK)
Funding: European Cooperation in Science and Technology

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January 2022 -

Researcher

OMICs approaches to reveal the anticancer properties of Virgin Olive Oil (VOOmics)
Funding: Portuguese Foundation for Science and Technology (PTDC/BAA-AGR/4732/2021)

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March 2021 -

Principal Investigator

Multi-omic networks in gliomas (MONET)
Funding: Portuguese Foundation for Science and Technology (PTDC/CCI-BIO/4180/2020)

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April 2020 -

Principal Investigator

A machine leaning-based forecasting system for shellfish safety (MATISSE)
Funding: Portuguese Foundation for Science and Technology (DSAIPA/DS/0026/2019)

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January 2020 -

Researcher

Artificial intelligence on the management of the degree of readiness in urban firefighting (AI-4-MUFF)
Funding: Portuguese Foundation for Science and Technology (DSAIPA/DS/0088/2019)

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January 2020 -

Management Committee Member

Cost Action CA18131 - Statistical and machine learning techniques in human microbiome studies (ML4MICROBIOME)
Funding: European Cooperation in Science and Technology 

 

February 2019 -

Researcher

Cost Action CA17718 - Identifying biomarkers through translational research for prevention and stratification of colorectal cancer (TANSCOLONCAN)
Funding: European Cooperation in Science and Technology 


January 2019 - 

Researcher

Personalized therapy for rheumatic diseases via machine learning (PREDICT)
Funding: Portuguese Foundation for Science and Technology (PTDC/CCI-CIF/29877/2017)

October 2016 - December 2019

Researcher

Personalizing cancer therapy through integrated modeling decision (PERSEIDS)
Funding: Portuguese Foundation for Science and Technology (PTDC/EMSSIS/0642/2014)

 

September 2016 - August 2018

Post-doctoral grant

Statistical multi-omics understanding of patient samples (SOUND)
Funding: European Union (H2020 No. 633974)


April 2011 - March 2012

Post-doctoral grant

Integrated methodologies for the development of bi- and three-valent DNA-vaccine against Helycobacter pylori

Funding: Portuguese Foundation for Science and Technology (PTDC/BIO/69242/2006)


April - September 2006

Research grant

Geographycal heterogeneity of the incidence of Tuberculosis in Portugal
Funding: Directorate General of Health, Portugal


March - August 2005

​Research grant

Importance of nurseries areas for the maintenance of important marine commercial fish (NURSERIES)

Funding: Direcção Geral de Pescas e Aquicultura (FEDER 22-05-01-FDR-00037-Programa MARE)


September 2003 - February 2005

​Research grant

New methods for assessing fisheries resources (NeoMAv)
Funding: Former Portuguese Institute for Fisheries and Sea Research (IPIMAR) (QCA-3/MARE-FEDER)


September 2002 - February 2005

​Research grant

PELÁGICOS

Funding: Portuguese Foundation for Science and Technology (FCT-PLE/13/00)


October 1999 - June 2001

Undegraduate 

Integrated functioning of the Tagus estuary and continental shelf, in response to anthropogenic pressure and global changes (FESTA II)

Funding: Portuguese Foundation for Science and Technology (POCTI/MGS/34457/99)

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Home: Text
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PUBLICATIONS

BOOK CHAPTERS

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  1. Lopes, M.B.; Vinga, S. (2021). Learning Biomedical Networks: Toward Data-Informed Clinical Decision and Therapy. In: Pham T.D., Yan H., Ashraf M.W., Sjoberg F. (eds) Advances in Artificial Intelligence, Computation, and Data Science. Computational Biology. Springer, Cham, DOI:0.1007/978-3-030-69951-2_3

  2. Diegues, I.; Vinga, S.; Lopes, M.B. (2020). Identification of common gene signatures in microarray and RNA-sequencing data using network-based regularization. In: Rojas I., Valenzuela O., Rojas F., Herrera L., Ortuño F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2020. Lecture Notes in Computer Science, vol 12108. Springer, Cham, DOI:10.1007/978-3-030-45385-5_2

  3. Carrasquinha, E.; Veríssimo, A.; Lopes, M.B.; Vinga, S. (2020). Network-based variable selection for survival outcomes in oncological data. In: Rojas I., Valenzuela O., Rojas F., Herrera L., Ortuño F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2020. Lecture Notes in Computer Science, vol 12108. Springer, Cham, DOI:10.1007/978-3-030-45385-5_49

  4. Veríssimo, A.; Lopes, M.B.; Carrasquinha, E.; Vinga, S. (2020). Random sample consensus for the robust identification of outliers in cancer data. In: Cazzaniga P., Besozzi D., Merelli I., Manzoni L. (eds) Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2019. Lecture Notes in Computer Science, vol 12313. Springer, Cham, DOI:10.1007/978-3-030-63061-4_11

  5. Villa-Brito, J.; Lopes, M.B.; Carvalho, A.; Vinga, S. (2020). Unravelling Breast and Prostate Common Gene Signatures by Bayesian Network Learning. In: Raposo M., Ribeiro P., Sério S., Staiano A., Ciaramella A. (eds) Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2018. Lecture Notes in Computer Science, vol 11925. Springer, Cham, DOI:10.1007/978-3-030-34585-3_25

  6. Lopes, M.B.; Veríssimo, A.; Carrasquinha, E.; Vinga, S. (2019) On the role of hub and orphan genes in the diagnosis of breast invasive carcinoma. In: Nicosia G., Pardalos P., Umeton R., Giuffrida G., Sciacca V. (eds) Machine Learning, Optimization, and Data Science. LOD 2019. Lecture Notes in Computer Science, vol 11943. Springer, Cham, DOI:10.1007/978-3-030-37599-7_52

  7. Carrasquinha, E.; Veríssimo, A.; Lopes, M.B.; Vinga, S. (2019). Variable selection and outlier detection in regularized survival models: application to melanoma gene expression data. In: Nicosia G., Pardalos P., Giuffrida G., Umeton R., Sciacca V. (eds) Machine Learning, Optimization, and Data Science. LOD 2018. Lecture Notes in Computer Science, vol 11331. Springer, Cham, DOI:10.1007/978-3-030-13709-0_36

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ARTICLES IN INTERNATIONAL PEER-REVIEWED JOURNALS

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  1. Peixoto, C.; Lopes, M.B., Martins, M., Casimiro, S.; Sobral, D. et al. (2023). Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization. BMC Bioinformatics, 24(1): 17, DOI: 10.1186/s12859-022-05104-z

  2. Carrilho, J.; Lopes, M.B (2022). Classification and biomarker selection in lower-grade glioma using robust sparse logistic regression applied to RNA-seq data. Brazilian Journal of Biometrics, 40: 371:381, DOI: 10.28951/bjb.v40i4.634

  3. Cruz, R.C.; Costa, P.R.; Krippahl, L.; Lopes, M.B (2022). Forecasting biotoxin contamination in mussels across production areas of the Portuguese coast with Artificial Neural Networks. Knowledge-Based Systems, 257: 109895, DOI: 10.1016/j.knosys.2022.109895

  4. Patrício A.; Lopes, M.B.; Costa, P.R.; Costa, R.S.; Henriques, R.; Vinga, S. (2022). Time-Lagged Correlation Analysis of Shellfish Toxicity Reveals Predictive Links to Adjacent Areas, Species, and Environmental Conditions. Toxins, 14(10): 679, DOI: 10.3390/toxins14100679

  5. Jensch, A.; Lopes, M.B.; Vinga, S.; Radde N. (2022). ROSIE: RObust Sparse ensemble for outlIEr detection and gene selection in cancer omics data. Statistical Methods in Medical Research, 1-12, DOI:10.1177/09622802211072456

  6. Lopes, M.B.; Martins, E.P.; Vinga, S.; Costa, B.M. (2021). The Role of Network Science in Glioblastoma. Cancers, 13(5): 1045, DOI:10.3390/cancers13051045

  7. Cruz, R.C.; Costa, P.R.; Vinga, S.; Krippahl, L.; Lopes, M.B. (2021). 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, DOI:10.3390/jmse9030283

  8. Marcos-Zambrano, L.J.; Karaduzovic-Hadziabdic, K.; Loncar Turukalo, T.; Przymus, P.; Trajkovik, V.; et al. (2021). Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment. Frontiers in Microbiology 12: 634511, DOI:10.3389/fmicb.2021.634511

  9. Moreno-Indias, I.; Lahti, L.; Nedyalkova, M.; Elbere, I.; Roshchupkin, G.; Adilovic, M.; Aydemir, O.; et al. (2021). Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Frontiers in Microbiology, 12: 635781, DOI:10.3389/fmicb.2021.635781

  10. Peixoto, C.; Lopes, M.B.; Martins, M.; Costa, L.; Vinga, S. (2020). TCox: correlation-based regularization applied to colorectal cancer survival data. Biomedicines, 8(11): 488, DOI:10.3390/biomedicines8110488

  11. Lopes, M.B., Vinga, S. (2020) Tracking intratumoral heterogeneity in glioblastoma via regularized classification of single-cell RNA-Seq data. BMC Bioinformatics, 21: 50, DOI:10.1186/s12859-020-3390-4

  12. Lopes, M.B.; Casimiro, S.; Vinga, S. (2019). Twiner: correlation-based regularization for identifying common cancer gene signatures. BMC Bioinformatics, 20: 356, DOI:10.1186/s12858-019-2937-8

  13. Segaert, P.; Lopes, M.B.; Vinga, S.; Rousseeuw, P.J. (2018). Robust identification of target genes and outliers in triple-negative breast cancer data. Statistical methods in medical research, 28(10-11): 3042-56, DOI:10.1177/0962280218794722

  14. Lopes, M.B.; Veríssimo, A.; Carrasquinha, E.; Casimiro, S.; Beerenwinkel N.; Vinga, S. (2018). Ensemble outlier detection and gene selection in triple-negative breast cancer data. BMC bioinformatics, 9: 168, DOI:10.1186/s12859-018-2149-7

  15. Lopes, M.B.; Amorim, A.; Calado, C.R.C.; Costa, P.R. (2018). 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): 147-147, DOI:10.3390/jmse6040147

  16. Lopes, M.B.; Calado, C.R.C. (2018). 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): 3056-3066, DOI:10.1002/jctb.5666

  17. Carrasquinha, E.; Veríssimo, A.; Lopes, M.B.; Vinga, S. (2018). Identification of influential observations in high-dimensional cancer survival data through the rank product test. BioData Mining, 11: 1, DOI:10.1186/s13040-018-0162-z

  18. Sampaio, P.N.; Sales, K.C.; Rosa, F.O.; Lopes, M.B.; Calado, C.R.C. (2017). High-throughput FTIR-based bioprocess analysis of recombinant cyprosin production. Journal of Industrial Microbiology and Biotechnology, 44 (1): 49-61, DOI:10.1007/s10295-016-1865-0

  19. Sales, K.C.; Rosa, F.; Cunha, B.R.; Sampaio, P.N.; Lopes, M.B.; Calado, C.R.C. (2017). Metabolic profiling of recombinant Escherichia coli cultivations based on high-throughput FT-MIR spectroscopic analysis. Biotechnology Progress, 33 (2): 285-298, DOI:10.1002/btpr.2378

  20. Lopes, M.B.; Calado, C.R.C.; Figueiredo, M.A.T.; Bioucas-Dias, J.M. (2016). Does nonlinear modeling play a role in plasmid bioprocess monitoring using Fourier Transform Infrared spectra? Applied Spectroscopy, 71(6): 1148-1156, DOI:10.1177/0003702816670913

  21. Rosa, F.; Sales, K.C.; Carmelo, J.G.; Fernandes-Platzgummer, A.; da Silva, C.L.; Lopes, M.B.; Calado, C.R.C. (2016). 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): 447-455, DOI:10.1002/btpr.2215

  22. 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. (2015). 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): 255-261, DOI:10.1002/jctb.4431

  23. Rosa, F.; Sales, K.C.; Cunha, B.R.; Couto, A.; Lopes, M.B.; Calado, C.R.C. (2015). 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): 8097-8108, DOI:10.1007/s00216-015-8983-9

  24. Sales, K.C.; Rosa, F.; Sampaio, P.N.; Fonseca, L.P.; Lopes, M.B.; Calado, C.R.C. (2015). In situ near-infrared (NIR) versus high-throughput mid-infrared (MIR) spectroscopy to monitor biopharmaceutical production. Applied spectroscopy, 69 (6): 760-772, DOI:10.1366/14-07588

  25. Lopes, M.B.; Martins, G.; Calado, C.R.C. (2014). Kinetic modeling of plasmid bioproduction in Escherichia coli DH5a cultures over different carbon-source compositions. Journal of Biotechnology, 186: 38-48, DOI:10.1016/j.jbiotec.2014.06.022

  26. Sampaio, P.N.; Sales, K.C.; Rosa, F.O.; Lopes, M.B.; Calado, C.R.C. (2014). In situ near infrared spectroscopy monitoring of cyprosin production by recombinant Saccharomyces cerevisiae strains. Journal of Biotechnology, 188: 148-157, DOI:10.1016/j.jbiotec.2014.07.454

  27. Lopes, M.B.; Wolff, J.-C.; Bioucas-Dias, J.M.; Figueiredo, M.A.T. (2011). Study on the effect of pixel resolution and blending grade on near-infrared hyperspectral unmixing of tablets. Applied Spectroscopy, 65 (2): 193-200, DOI:10.1366/10-06079

  28. Lopes, M.B.; Wolff, J.-C.; Bioucas-Dias, J.M.; Figueiredo, M.A.T. (2010). Quantification of components in non-homogenous pharmaceutical tablets using near infrared reflectance imaging. Journal of Near Infrared Spectroscopy, 18 (5): 333-340, DOI:10.1255/jnirs.897

  29. Lopes, M.B.; Wolff, J.-C.; Bioucas-Dias, J.M.; Figueiredo, M.A.T. (2010). '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): 8753-8754, DOI:10.1021/ac102443w

  30. Lopes, M.B.; Wolff, J.-C.; Bioucas-Dias, J.M.; Figueiredo, M.A.T. (2010). Near-infrared hyperspectral unmixing based on a minimum volume criterion for fast and accurate chemometric characterization of counterfeit tablets. Analytical Chemistry, 82 (4): 1462-1469, DOI:10.1021/ac902569e

  31. Lopes, M.B.; Wolff, J.-C.; Bioucas-Dias, J.M.; Figueiredo, M.A.T. (2009). Determination of the composition of counterfeit Heptodin™ tablets by near infrared chemical imaging and classical least squares estimation. Analytica Chimica Acta, 641 (1-2): 46-51, DOI:10.1016/j.aca.2009.03.034

  32. Lopes, M.B.; Wolff, J.-C. (2009). Investigation into classification/sourcing of suspect counterfeit Heptodin™ tablets by near infrared chemical imaging. Analytica Chimica Acta, 633 (1): 149-155, DOI:10.1016/j.aca.2008.11.036

  33. Brás, L.P.; Lopes, M.B.; Ferreira, A.P.; Menezes, J.C. (2008). A bootstrap-based strategy for spectral interval selection in PLS regression. Journal of Chemometrics, 22 (11-12): 695-700, DOI:10.1002/cem.1153

  34. Cabral, H.N.; Vasconcelos, R.; Vinagre, C. ; França, S.; Fonseca, V.; Maia, A.; Reis-Santos, P.; Lopes, M.B.; Ruano, M.; Campos, J.; Freitas, V.; Santos, P.T.; Costa, M.J. (2007). Relative importance of estuarine flatfish nurseries along the Portuguese coast. Journal of Sea Research, 57 (2-3): 209-217, DOI:10.1016/j.seares.2006.08.007

  35. Lopes, M.B.; Murta, A.G.; Cabral, H.N. (2006). Discrimination of snipefish Macroramphosus species and boarfish Capros aper morphotypes through multivariate analysis of body shape. Helgoland Marine Research, 60 (1): 18-24, DOI:10.1007/s10152-005-0010-7

  36. Lopes, M.B.; Murta, A.G.; Cabral, H.N. (2006). 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): 363-378, DOI:10.1111/j.1095-8649.2006.01093.x

  37. Cabral, H.N.; Lopes, M.B.; Loeper, R. (2002). Trophic niche overlap between flatfishes in a nursery area on the Portuguese coast. Scientia Marina, 66 (3): 293-300, DOI:10.3989/scimar.2002.66n3293

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ARTICLES IN CONFERENCE PROCEEDINGS

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  1. Sampaio, P.N.; Cunha, B.; Rosa, F.; Sales, K.; Lopes, M.B.; Calado, C.R.C. (2015). Molecular fingerprint of human gastric cell line infected by Helicobacter pylori, DOI:10.1109/ENBENG.2015.7088877

  2. Lopes, M.B.; Sales, K.C.; Lopes, V.V.; Calado, C.R.C. (2013). Real-time plasmid monitoring of batch and fed-batch Escherichia coli cultures by NIR spectroscopy, DOI:10.1109/ENBENG.2013.6518394

  3. Lopes, M.B.; Scholtz, T.; Silva, D.; Santos, I.; Silva, T.; Sampaio, P.; Couto, A.; Lopes, V.V.; Calado, C.R.C. (2012). Modelling, monitoring and control of plasmid bioproduction in Escherichia coli cultures, DOI:10.1109/ENBENG.2012.6331370

  4. Lopes, M.B.; Bioucas-Dias, J.M.; Figueiredo, M.A.T.; Wolff, J.-C.; Mistry, N.; Warrack, J. (2011). Comparison of near infrared and Raman hyperspectral unmixing performances for chemical identification of pharmaceutical tablets, DOI:10.1109/WHISPERS.2011.6080869

  5. Lopes, M.B.; Bioucas-Dias, J.M.; Figueiredo, M.A.T.; Wolff, J.-C. (2009). Spectral unmixing via minimum volume simplices: Application to near infrared spectra of counterfeit tablets, DOI:10.1109/WHISPERS.2009.5289081

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ARTICLES IN NATIONAL JOURNALS

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  1. Santos, H.; Sousa, D.; Caldeira, P.; Lopes, M.B.; Açucena, F.; Ramos, A.; Moniz, M.; Lopes, A.; Guerreiro, H. (2008). Survival and prognosis of patients with percutaneous endoscopic gastrostomy. Revista APNEP, 2: 157-159 (in portuguese)

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ARTICLES IN SCIENTIFIC NEWSLETTERS

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  1. Lopes, M.B.; Wolff, J.-C.; Bioucas-Dias, J.M.; Figueiredo, M.A.T. (2011). Investigating counterfeit medicines - the near infrared chemical imaging picture. NIR News, 22: 10-18, DOI:10.1255/nirn.1243

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PREPRINTS

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  1. Veríssimo, A.; Carrasquinha, E.; Lopes, M.B.; Oliveira, A.L.; Sagot, M.-F.; Vinga, S. (2018). Sparse network-based regularization for the analysis of patientomics high-dimensional survival data. bioRxiv, DOI:10.1101/403402

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STATISTICAL SOFTWARE

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  1. Veríssimo, A.; Vinga, S.; Carrasquinha, E.; Lopes, M.B. (2018). glmSparseNet - Network centrality metrics for elastic-net regularized models. Bioconductor R package 

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COMMUNICATIONS

ORAL COMMUNICATIONS

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  1. Cruz, R.C., Costa P.R., Krippahl L., Lopes M.B. (2022). Predicting biotoxin shellfish contamination with artificial neural networks: towards a forecasting system for shellfish safety. Littoral 2022, Caparica, Portugal, Sep 12-16

  2. Lopes M.B. (2022). Identification of driver genes in glioblastoma via regularized classification. 17th Conference of the International Federation of Classification Societies, Faculty of Economy, University of Porto, Porto, July 19-23

  3. Lopes M.B. (2022). Biomarker discovery in cancer transcriptomic data using network-based regularization. ML4Microbiome Workshop, Faculty of Natural Sciences, University of Tirana, Albania, May 24

  4. Cruz, R.C.; Costa, P.R.; Krippahl, L.; Lopes, M.B. (2022). Forecasting mussel contamination by marine biotoxins using long short-term memory networks. GlobalHAB Workshop, Glasgow, Scotland, May 9-13

  5. Lopes M.B. (2021). Inteligência artificial em aplicações biomédicas e ambientais. 1st Conferência de Inteligência Artificial e Machine Learning, Pemba, Cabo Delgado, Moçambique, July 27 (virtual)

  6. Lopes M.B. (2020) Statistics and machine learning in biomedical and environmental sciences. Workshop on Data Science and Big Data, NOVA LINCS/NOVA MATH, NOVA School of Science and Technology, March 4

  7. Lopes, M.B.; Veríssimo, A.; Carrasquinha, E.; Vinga, S. (2019). 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, September 13-16

  8. Lopes, M.B.; Veríssimo, A.; Casimiro, S.; Carrasquinha, E.; Vinga S. (2018). 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, July 9-11

  9. Lopes, M.B.; Veríssimo, A.; Carrasquinha, E.; Vinga, S. (2017). 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, Lisbon, Portugal, July 12-14

  10. Lopes, M.B.; Silva, D.; Couto, A.; Lopes, V.V.; Calado, C.R.C. (2012). On-line monitoring of plasmid production in an Escherichia coli bioprocess by near infrared spectroscopy. European Symposium on Biochemical Engineering Science (ESBES 2012), Istanbul, Turkey, September 23-26

  11. Lopes, M.B.; Wolff, J.-C.; Mistry, N.; Warrack, J.; Bioucas-Dias, J.M.; Figueiredo M.A.T. (2011). Comparison of near infrared and Raman hyperspectral unmixing performances for chemical identification of pharmaceutical tablets. Third IEEE Workshop on Hyperspectral Image and Signal Processing: Evolution in Remote Sensing (WHISPERS 2011), Lisbon, Portugal, June 5-9

  12. Lopes, M.B.; Wolff, J.-C.; Bioucas-Dias, J.M.; Figueiredo, M.A.T. (2008). Determination of the composition of counterfeit drugs by near-infrared chemical imaging. The 35th Federation of Analytical Chemistry and Spectroscopy Societies Conference (FACSS 2008), Reno, USA, September 28 - October 2

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POSTER COMMUNICATIONS

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  1. Patrício, A.; Henriques, R.; Costa, P.R.; Vinga, S.; Lopes, M.B. (2022). Time-lagged correlation analysis of bivalve toxicity across spatial, species and context dimensions. GlobalHAB Workshop, Glasgow, Scotland, May 9-13

  2. Veríssimo, A.; Lopes, M.B.; Carrasquinha, E.; Vinga, S. (2019). Performance and stability analysis of sparse network-based survival models. Workshop on Statistical Challenges in Medical Data Science. Monte Verità, Ascona, Switzerland, July 16-21

  3. Peixoto, C.; Lopes, M.B.; Martins, M.; Veríssimo, A.; Costa, L.; Vinga, S. (2019). Sparse models and network-based regularizers for the analysis of RNA-seq data from colorectal cancer. EMBO Workshop - Precision Health: Molecular Basis, Technology and Digital Health. EMBL, Heidelberg, Germany, November 13-16 

  4. Carrasquinha, E.; Lopes, M.B.; Veríssimo, A.; Casimiro, S.; Beerenwinkel, N.; Vinga, S. (2018). Ensemble outlier detection in cancer gene expression data. The 17th European Conference on Computational Biology (ECCB 2018), Athens, Greece, September 8-12

  5. Carrasquinha, E.; Veríssimo, A.; Lopes, M.B.; Vinga, S. (2018). Survival analysis of high-dimensional cancer gene expression data. The European Conference on Mathematical and Theoretical Biology (ECMTB 2018), Lisbon, Portugal, July 23-27

  6. Veríssimo, A.; Carrasquinha, E.; Lopes, M.B.; Oliveira, A.L.; Sagot, M.-F.; Vinga, S. (2017). Regularized survival analysis and feature clustering of TCGA breast cancer data. From Single- to Multiomics: Applications and Challenges in Data Integration, Heidelberg, Germany, November 12-14

  7. Veríssimo, A.; Lopes, M.B.; Carrasquinha, E.; Oliveira, A.L.; Sagot, M.-F.; Vinga, S. (2017). Random Sample Consensus (RANSAC) for the robust identification of outliers in transcriptomic data. Intelligent Systems for Molecular Biology / European Conference on Computational Biology (ISMB/ECCB 2017), Prague, Czech Republic, July 21-25

  8. Veríssimo, A.; Carrasquinha, E.; Lopes, M.B.; Sagot, M-F.; Oliveira, A.L.; Vinga, S. (2017). Network-based sparse modeling of breast invasive carcinoma survival data. Signal Processing with Adaptive Sparse Structured Representations (SPARS 2017), Lisbon, Portugal, June 5-8

  9. Veríssimo, A.; Carrasquinha, E.; Lopes, M.B.; Sagot, M.-F.; Oliveira, A.L.; Vinga, S. (2017). Network-based regularized optimization for cancer survival data analysis. Ascona Workshop 17, Statistical Challenges in Single-Cell Biology, ETH Zurich, Switzerland, April 30 - May 5

  10. Sampaio, P.N.; Sales, K.C.; Lopes, M.B.; Calado, C.R.C. (2013). In-situ prediction of a recombinant aspartic protease production in bioreactor with near infrared spectroscopy and partial least squares regression. The Portuguese Congress of Microbiology and Biotechnology (MicroBiotec 2013), Aveiro, Portugal, December 6-8

  11. Sales, K.C.; Rosa, F.O.; Lopes, M.B.; Sampaio, P.N.; Calado, C.R.C. (2013). Near-infrared (NIR) versus mid-infrared (MIR) spectroscopy to monitor the bioproduction of heterologous products. The Portuguese Congress of Microbiology and Biotechnology (MicroBiotec 2013), Aveiro, Portugal, December 6-8

  12. Cunha, B.R.; Sales, K.C.; Rosa, F.O.; Lopes, M.B.; Sampaio, P.N.; Calado, C.R.C. (2013). Evaluation of anti-bacterial agents using high-throughput FTIR spectroscopy. The Portuguese Congress of Microbiology and Biotechnology (MicroBiotec 2013), Aveiro, Portugal, December 6-8

  13. Lopes, M.B.; Sales, K.C.; Rosa, F.O.; Sampaio, P.N.; Calado, C.R.C. (2013). Tracking the effect of the culture design in the in-situ NIR monitoring of plasmid bioprocesses. The Portuguese Congress of Microbiology and Biotechnology (MicroBiotec 2013), Aveiro, Portugal, December 6-8

  14. Lopes, M.B.; Sales, K.C.; Lopes, V.V.; Calado, C.R.C. (2013). Real-time plasmid monitoring of batch and fed-batch Escherichia coli cultures by NIR spectroscopy. Third IEEE-EMBS Portuguese Bioengineering Meeting (ENBENG 2013), Braga, Portugal, February 20-22

  15. Lopes, M.B.; Scholz, T.; Santos, T.; Felício-Silva, D.; Sampaio, P.N.; Couto, A.; Lopes, V.V.; Calado, C.R.C. (2012). Modelling, monitoring and control of plasmid bioproduction in Escherichia coli cultures. The Second IEEE-EMBS Portuguese Bioengineering Meeting (ENBENG 2012), Coimbra, Portugal, February 23-25

  16. Lopes, M.B.; Bioucas-Dias, J.M.; Wolff, J.-C.; Figueiredo, M.A.T. (2009). Spectral unmixing via minimum volume simplices: application to near infrared spectra of counterfeit tablets. First IEEE Workshop on Hyperspectral Image and Signal Processing: Evolution in Remote Sensing (WHISPERS 2009), Grenoble, France, August 26-28

  17. Lopes, M.B.; Wolff, J.-C. (2008). Sourcing counterfeit tablets using NIR-CI: a case study. The 11th Conference on Chemometrics in Analytical Chemistry (CAC 2008), Montpellier, France, June 30 - July 4

  18. Lopes, M.B.; Ferreira, A.P.; Menezes, J.C. (2007). Near-infrared spectroscopy as an important tool for at-line monitoring and control of industrial Streptomyces fermentations: two case studies. The 13th International Conference on Near Infrared Spectroscopy (13th ICNIRS), Umea, Sweden, June 17-21

  19. Lopes, M.B.; Brás, L.P.; Ferreira, A.P.; Menezes, J.C. (2007). A bootstrap-based strategy for spectral interval selection in partial least squares regression. The 10th Scandinavian Symposium on Chemometrics (SSC10), Lappeenranta, Finland, June 11-15

  20. Santos, H.; Lopes, M.B.; Afonso, G.; Bretes, L.; Guerreiro, H.; Silva, J.C. (2007). Colon and rectal cancer - Analysis of prognostic factors. XXVII Congresso Nacional de Gastrenterologia e Endoscopia Digestiva, Vilamoura, Portugal, June 6-9

  21. Cabral, H.N.; Vasconcelos, R.; Vinagre, C. ; França, S.; Fonseca, V.; Maia, A.; Reis-Santos, P. (2005). Anthropogenic pressures in estuarine flatfish nurseries along the Portuguese coast. The 6th International Flatfish Symposium, Kyoto, Japan, October 20-25

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ACADEMIC

SUPERVISION

NUNO EUSÉBIO

Identification of colorectal cancer genetic biomarkers via regularised classification models

Master's Dissertation in Analysis and Engineering of Big Data

NOVA School of Science and Technology (supervision)

2022

SOFIA MARTINS

Disclosing transcriptomics signatures of gliomas using sparse methods

Master's Dissertation in Biomedical Engineering

NOVA School of Science and Technology (supervision)

TIAGO MADEIRA

Inferring breast cancer subtypes based on patients mutation profiles

Master's Dissertation in Computer Science
NOVA School of Science and Technology (co-supervision)

RAFAELA CRUZ

Multivariate time-series forecasting of shellfish contamination by marine biotoxins

Master's Dissertation in Analysis and Engineering of Big Data

NOVA School of Science and Technology (supervision)

JOÃO COSTA

Remote sensing based estimation and forecasting of shellfish contamination with marine biotoxins

Master's Dissertation in Computer Science

NOVA School of Science and Technology (co-supervision)

ANTÓNIO COELHO

Telecom churn prediction: a big data approach

Master's Dissertation in Analysis and Engineering of Big Data
NOVA School of Science and Technology (supervision)

2021

ANDRÉ PEREIRA

Multivariate time-series forecasting of seafood safety

Master's Dissertation in Information Systems and Computer Engineering
Instituto Superior Técnico, Universidade de Lisboa (co-supervision)

2019 

INÊS DIEGUES

Identification of cancers common gene signatures through regularised classification

Master's Dissertation in Biomedical Engineering
Instituto Superior Técnico, Universidade de Lisboa (co-supervision)

2014

KEVIN SALES

Fourier Transform Infrared Spectroscopy, a powerful tool to monitor biopharmaceutical production

Master's Dissertation in Biomedical Engineering
Faculdade de Engenharia, Universidade Católica Portuguesa (co-supervision)

FILIPA ROSA

Infrared Spectroscopy: A groundbreaking tool for monitoring mammalian cells' processes

Master's Dissertation in Biomedical Engineering
Faculdade de Engenharia, Universidade Católica Portuguesa (co-supervision)

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WORKSHOPS AND COURSES

Home: Workshops and courses

17 - 18 May 2019

THE WIZARDRY OF ARTIFICIAL INTELLIGENCE: AI AND MACHINE LEARNING IN CANCER IMAGING

Champalimaud Foundation, Lisboa, Portugal

15 - 16 May 2019

COPERNICUS MARINE SERVICE TRAINING

Mercator Ocean International, Lisboa, Portugal

27 - 29 August 2018

NEW DIRECTIONS IN SINGLE CELL ANALYSIS

European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

15 - 16 June 2007

HYPERSPECTRAL IMAGING

Technobothnia Research Centre, Vaasa, Finland

3 - 4 April 2018

ADVANCED R PROGRAMMING

Data Programmers, European Molecular Biology Laboratory (EMBL)

Heidelberg, Germany

10 - 14 April 2006

ADVANCED COURSE ON EPIDEMIOLOGY OF INFECTIOUS DISEASES

Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal

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KNOWLEDGE TRANSFER

2019 - 

MEMBER OF THE HIGHSEEDTECH NETWORK

for the creation of value from knowledge through technology entrepreneurship and open innovation.

2012

PARTICIPATION IN THE COHiTEC PROGRAM - TURNING SCIENCE INTO BUSINESS (COTEC PORTUGAL)

Project title: A vaccine against Helicobacter pylori.

CONTACT

Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal

marta.lopes@fct.unl.pt

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