People
Rafael Costa
senior researcher
Email
rs.costa@fct.unl.pt
Research Lab
Phone number
-
ORCID
Ciência Vitae
Recent publications
- Wettinger, SB; Karaduzovic-Hadziabdic, K; Attard, R; Farrugia, R; Wolford, BN; Chierici, M; Jurman, G; Alexiou, P; Peñalvo, JL; Costa, RS; Basílio, J; Sabovcik, F; Vitorino, R; Schmid, JA; Shigdel, R; Vilne, B; Hatzigeorgiou, AG; Sopic, M; Devaux, Y; Magni, P; Tellez-Plaza, M; Kreil, DP; Gruca, A. 2025. Bottlenecks in advancing and applying multiomic data integration-common data resources as rate-limiting drivers-the high-impact use case of atherosclerotic cardiovascular disease. BRIEFINGS IN BIOINFORMATICS, 26, DOI: 10.1093/bib/bbaf526
- Alexandre, L; Costa, RS; Henriques, R. 2025. Integrating statistical significance and discriminative power in pattern discovery. KNOWLEDGE-BASED SYSTEMS, 316, DOI: 10.1016/j.knosys.2025.113356
- Patrício, A; Costa, RS; Henriques, R. 2024. Pattern-centric transformation of omics data grounded on discriminative gene associations aids predictive tasks in TCGA while ensuring interpretability. BIOTECHNOLOGY AND BIOENGINEERING, DOI: 10.1002/bit.28758
- Alexandre, L; Costa, RS; Henriques, R. 2024. TriSig: Evaluating the statistical significance of triclusters. PATTERN RECOGNITION, 149, DOI: 10.1016/j.patcog.2023.110231
- Daniel MGonçalves; Rui Henriques; Rafael S Costa. 2023. Predicting metabolic fluxes from omics data via machine learning: Moving from knowledge-driven towards data-driven approaches. Computational and Structural Biotechnology Journal, 21, DOI: 10.1016/j.csbj.2023.10.002
- José Pinto, João R. C. Ramos, Rafael S. Costa, Sergio Rossell, Patrick Dumas, Rui Oliveira. 2023. Hybrid deep modeling of a CHO-K1 fed-batch process: combining First-Principles with deep neural networks. Frontiers in Bioengineering and Biotechnology, DOI: 10.3389/fbioe.2023.1237963
- José Pinto; João R. C. Ramos; Rafael S. Costa; Rui Oliveira. 2023. Hybrid deep modelling of a GS115 (Mut+) Pichia pastoris culture with state-space reduction. Fermentation, 9(7), DOI: 10.3390/fermentation9070643
- José Pinto; João R. C. Ramos; Rafael S. Costa; Rui Oliveira. 2023. A General Hybrid Modeling Framework for Systems Biology Applications: Combining Mechanistic Knowledge with Deep Neural Networks under the SBML Standard. AI, 4(1), DOI: 10.3390/ai4010014
- José Pinto; Rafael Costa; Leonardo Alexandre; João Ramos; Rui Oliveira. 2023. SBML2HYB: a Python interface for SBML compatible hybrid modelling. Bioinformatics (Oxford, England), DOI: 10.1093/bioinformatics/btad044
- José Pinto; João Antunes; João Ramos; Rafael S. Costa; Rui Oliveira. 2022. Modeling and optimization of bioreactor processes. Current Developments in Biotechnology and Bioengineering: Advances in Bioprocess Engineering, N/D, DOI: 10.1016/B978-0-323-91167-2.00016-2
- Leonardo Alexandre; Rafael S Costa; Rui Henriques. 2022. DISA tool: Discriminative and informative subspace assessment with categorical and numerical outcomes. PLoS One, 17, DOI: 10.1371/journal.pone.0276253
- J Pinto, M Mestre, J Ramos, R S Costa, G Striedner, R Oliveira. 2022. A general deep hybrid model for bioreactor systems: combining first Principles equations with deep neural networks. Computers and Chemical Engineering, 165, DOI: 10.1016/j.compchemeng.2022.107952
- H Mochão, D Gonçalves, L Alexandre, C Castro, D Valério, P Barahona, D Moreira-Gonçalves, P Matos da Costa, R Henriques, L L Santos, R S Costa. 2022. IPOscore: an interactive web-based platform for postoperative surgical complications analysis and prediction in the oncology domain. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE, 219, DOI: 10.1016/j.cmpb.2022.106754
- Pedro Rodrigues, Rafael S.Costa, Rui Henriques. 2022. Enrichment analysis on regulatory subspaces: a novel direction for the superior description of cellular responses to SARS-CoV-2. COMPUTERS IN BIOLOGY AND MEDICINE, 146, DOI: 10.1016/j.compbiomed.2022.105443