People
Rafael Costa
senior researcher
Email
rs.costa@fct.unl.pt
Phone number
-
ORCID
Ciência Vitae
Recent publications
- 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; 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
- A. Patrício, M. B Lopes, P. R. Costa, R. S. Costa, R. Henriques, S. Vinga. 2022. Time-Lagged Correlation Analysis of Shellfish Toxicity Reveals Predictive Links to Adjacent Areas, Species, and Environmental Conditions. Toxins, 14(10), DOI: 10.3390/toxins14100679
- 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
- Alexandre, L; Costa, RS; Henriques, R.. 2021. DI2: prior-free and multi-item discretization of biological data and its applications. BMC BIOINFORMATICS, DOI: 10.1186/s12859-021-04329-8
- Patrício, A; Costa, RS and Henriques, R. 2021. Predictability of COVID-19 Hospitalizations, Intensive Care Unit Admissions, and Respiratory Assistance in Portugal: Longitudinal Cohort Study. JOURNAL OF MEDICAL INTERNET RESEARCH, DOI: 10.2196/26075
- Alexandre, L; Costa, RS; Santos, LL; Henriques, R.. 2021. Mining pre-surgical patterns able to discriminate post-surgical outcomes in the oncological domain. IEEE Journal of Biomedical and Health Informatics, DOI: 10.1109/jbhi.2021.3064786
- Mochao, H; Barahona, P; Costa, RS. 2020. KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling. Database-The Journal of Biological Databases and Curation, DOI: 10.1093/database/baaa093
- Waltemath, D; Karr, JR; Bergmann, FT; Chelliah, V; Hucka, M; Krantz, M; Liebermeister, W; Mendes, P; Myers, CJ; Pir, P; Alaybeyoglu, B; Aranganathan, NK; Baghalian, K; Bittig, AT; Burke, PEP; Cantarelli, M; Chew, YH; Costa, RS; Cursons, J; et al. 2016. Toward Community Standards and Software for Whole-Cell Modeling. IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING, 63(10), DOI: 10.1109/tbme.2016.2560762
- Costa, RS; Hartmann, A; Gaspar, P; Neves, AR; Vinga, S. 2014. An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production. Molecular BioSystems, 10(3), DOI: 10.1039/c3mb70265k
- Machado, D; Costa, RS; Ferreira, EC; Rocha, I; Tidor, B. 2012. Exploring the gap between dynamic and constraint-based models of metabolism. METABOLIC ENGINEERING, 14(2), DOI: 10.1016/j.ymben.2012.01.003
- Machado, D; Costa, RS; Rocha, M; Ferreira, EC; Tidor, B; Rocha, I. 2011. Modeling formalisms in systems biology. AMB Express, 1(1), DOI: 10.1186/2191-0855-1-45