Papers in peer-reviewed journals
- Francisca G. Vieira, Regina Bispo, Marta B. Lopes (2024). Integration of multi-omics data for the classification of glioma types and identification of novel biomarkers. Bioinformatics and Biology Insights, 18, doi:10.1177/11779322241249563
- Laila Musib, R. Coletti, Marta B. Lopes, Helena Mouriño, Eunice Carrasquinha (2024). Priority-Elastic net for binary disease outcome prediction based on multi-omics data. BioData Mining, 17(1):45, doi:10.1186/s13040-024-00401-0
- André Patrício, Rafael S. Costa, Rui Henriques (2024). Pattern-centric transformation of omics data grounded on discriminative gene associations aids predictive tasks in TCGA while ensuring interpretability. Biotechnology and Bioengineering, 121:2881–2892, doi:10.1002/bit.28758
- Jorge Orestes Cerdeira, Maria João Martins, Marcos Raydan (2023). The max-out min-in problem: A tool for data analysis. Computers & Operations Research, 154:106218, doi:10.1016/j.cor.2023.106218
- Sofia Martins, Roberta Coletti, Marta B. Lopes (2023). Disclosing transcriptomics network-based signatures of glioma heterogeneity using sparse methods. BioData Mining, 16:26, doi:10.1186/s13040-023-00341-1
- Natasa Krejić, Evelin Krulikovski, Marcos Raydan (2023). An augmented Lagrangian approach for cardinality constrained minimization applied to variable selection problems. Applied Numerical Mathematics, doi:10.1016/j.apnum.2023.12.006
- João F. Carrilho, Marta B. Lopes (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.
- Bruno Mera, Paulo Mateus, Alexandra M. Carvalho (2022). Model complexity in statistical manifolds: The role of curvature. IEEE Transactions on Information Theory, 68(9):5619-5636, doi:10.1109/TIT.2022.3176470
- Antje Jensch, Marta B. Lopes, Susana Vinga, Nicole Radde (2022). ROSIE: RObust Sparse ensemble for outlIEr detection and gene selection in cancer omics data. Statistical Methods in Medical Research, 31(5), 947-958, doi:10.1177/09622802211072456
- Eduarda P. Martins, Céline S. Gonçalves, Marta Pojo, Rita Carvalho, Ana S. Ribeiro, Vera Miranda-Gonçalves, Ricardo Taipa, Fernando Pardal, Afonso A. Pinto, Carlos Custódia, Cláudia C. Faria, Fátima Baltazar, Nuno Sousa, Joana Paredes, Bruno M. Costa (2022). Cadherin-3 is a novel oncogenic biomarker with prognostic value in glioblastoma. Molecular Oncology, 16(14):2611-2631, doi:10.1002/1878-0261.13162.
- João Santinha, Celso Matos, Mario Figueiredo, Nikolaos Papanikolaou (2021). Improving performance and generalizability in radiogenomics: a pilot study for prediction of IDH1/2 mutation status in gliomas with multicentric data. Journal of Medical Imaging, 8(3):031905, doi:10.1117/1.JMI.8.3.031905
- Marta B. Lopes, Eduarda P. Martins, Susana Vinga, Bruno M. Costa (2021). The Role of Network Science in Glioblastoma. Cancers, 13(5):1045, doi:10.3390/cancers13051045
- Marta B. Lopes, Susana Vinga (2020). Tracking intratumoral heterogeneity in glioblastoma via regularized classification of single-cell RNA-Seq data. BMC Bioinformatics, 21(1):59, doi:10.1186/s12859-020-3390-4
Book chapters
Papers in conference proceedings
- João Brandão, Marta B. Lopes, Eunice Carrasquinha (2024). Refining Gene Selection and Outlier Detection in Glioblastoma Based on a Consensus Approach for Regularized Survival Models. In: Rojas, I., Ortuño, F., Rojas, F., Herrera, L.J., Valenzuela, O. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2024. Lecture Notes in Computer Science, vol 14848. Springer, Cham, doi:10.1007/978-3-031-64629-4_2
- Roberta Coletti, Marta B. Lopes (2023). Multi-omics data integration and network inference for biomarker discovery in glioma. In: Moniz, N., Vale, Z., Cascalho, J., Silva, C., Sebastião, R. (eds) Progress in Artificial Intelligence. EPIA 2023. Lecture Notes in Computer Science, vol 14116. Springer, Cham, doi:10.1007/978-3-031-49011-8_20
- João Santinha, Celso Matos, Nickolas Papanikolaou, Mário A. T. Figueiredo (2022). Improving generalizability to out-of-distribution data in radiogenomic models to predict IDH mutation status in glioma patients. In 2022 IEEE International Symposium on Medical Measurements and Applications (MeMeA), Messina, Italy, 2022, pp. 1-5, doi:10.1109/MeMeA54994.2022.9856493
Preprints
- João F. Carrilho, Roberta Coletti, Bruno M. Costa, Marta B. Lopes. Multi-omics biomarker selection and outlier detection across WHO glioma classifications via robust sparse multinomial regression. medRxiv, doi:10.1101/2024.08.26.24312601
- Roberta Coletti, João Carrilho, Eduarda P. Martins, Céline S. Gonçalves, Bruno M. Costa, Marta B. Lopes. A novel tool for multi-omics network integration and visualization: A study of glioma heterogeneity. bioRxiv, doi:10.1101/2024.03.18.585500
- Nina Kastendiek, Roberta Coletti, Thilo Gross, Marta B. Lopes. Exploring glioma heterogeneity through omics networks: from gene network discovery to causal insights and patient stratification. bioRxiv, doi:10.1101/2024.07.02.601715
- Mónica Leiria de Mendonça, Roberta Coletti, Céline Gonçalves, Eduarda P. Martins, Bruno M. Costa, Susana Vinga, Marta B. Lopes. Updating TCGA glioma classification through integration of molecular profiling data following the 2016 and 2021 WHO guidelines. bioRxiv, doi:10.1101/2023.02.19.529134