Rui Manuel Freitas Oliveira
AuthID: R-000-FXV
1
TITLE: Incorporating first-principles information into hybrid modeling structures: Comparing hybrid semi-parametric models with Physics-Informed Recurrent Neural Networks
AUTHORS: Jul Rasmussen, Peter; Kumar, Monesh; Pinto, Jose; Oliveira, Rui; Liang, Xiaodong; Huusom, Jakob Kjobsted;
PUBLISHED: 2025, SOURCE: COMPUTERS & CHEMICAL ENGINEERING, VOLUME: 199
AUTHORS: Jul Rasmussen, Peter; Kumar, Monesh; Pinto, Jose; Oliveira, Rui; Liang, Xiaodong; Huusom, Jakob Kjobsted;
PUBLISHED: 2025, SOURCE: COMPUTERS & CHEMICAL ENGINEERING, VOLUME: 199
2
TITLE: A Physics-Informed Neural Network (PINN) framework for generic bioreactor modelling
AUTHORS: Thirugnanasambandam, Monesh Kumar; Pinto, Jose; Moskovkina, Ekaterina; Costa, Rafael S.; Oliveira, Rui;
PUBLISHED: 2025, SOURCE: COMPUTERS & CHEMICAL ENGINEERING, VOLUME: 203
AUTHORS: Thirugnanasambandam, Monesh Kumar; Pinto, Jose; Moskovkina, Ekaterina; Costa, Rafael S.; Oliveira, Rui;
PUBLISHED: 2025, SOURCE: COMPUTERS & CHEMICAL ENGINEERING, VOLUME: 203
3
TITLE: A Review of Intelligent Modeling for Microalgae Systems: Integrating Data Mining, Machine Learning, and Hybrid Approaches
AUTHORS: Geovani R Freitas; Sara Badenes; Rui Oliveira; F. G. Martins;
PUBLISHED: 2025, SOURCE: Processes, VOLUME: 13, ISSUE: 9
AUTHORS: Geovani R Freitas; Sara Badenes; Rui Oliveira; F. G. Martins;
PUBLISHED: 2025, SOURCE: Processes, VOLUME: 13, ISSUE: 9
4
TITLE: Deep hybrid modeling of a HEK293 process: Combining long short-term memory networks with first principles equations Full Text
AUTHORS: Ramos, Joao R. C.; Pinto, Jose; Gil Poiares-Oliveira ; Peeters, Ludovic; Dumas, Patrick; Oliveira, Rui;
PUBLISHED: 2024, SOURCE: BIOTECHNOLOGY AND BIOENGINEERING, VOLUME: 121, ISSUE: 5
AUTHORS: Ramos, Joao R. C.; Pinto, Jose; Gil Poiares-Oliveira ; Peeters, Ludovic; Dumas, Patrick; Oliveira, Rui;
PUBLISHED: 2024, SOURCE: BIOTECHNOLOGY AND BIOENGINEERING, VOLUME: 121, ISSUE: 5
5
TITLE: SBML2HYB: a Python interface for SBML compatible hybrid modeling
AUTHORS: Pinto, Jose; Costa, Rafael S.; Alexandre, Leonardo; Ramos, Joao; Oliveira, Rui;
PUBLISHED: 2023, SOURCE: BIOINFORMATICS, VOLUME: 39, ISSUE: 1
AUTHORS: Pinto, Jose; Costa, Rafael S.; Alexandre, Leonardo; Ramos, Joao; Oliveira, Rui;
PUBLISHED: 2023, SOURCE: BIOINFORMATICS, VOLUME: 39, ISSUE: 1
6
TITLE: A General Hybrid Modeling Framework for Systems Biology Applications: Combining Mechanistic Knowledge with Deep Neural Networks under the SBML Standard
AUTHORS: Pinto, Jose; Ramos, Joao R. C.; Costa, Rafael S.; Oliveira, Rui;
PUBLISHED: 2023, SOURCE: AI, VOLUME: 4, ISSUE: 1
AUTHORS: Pinto, Jose; Ramos, Joao R. C.; Costa, Rafael S.; Oliveira, Rui;
PUBLISHED: 2023, SOURCE: AI, VOLUME: 4, ISSUE: 1
7
TITLE: Hybrid Deep Modeling of a GS115 (Mut+) Pichia pastoris Culture with State-Space Reduction
AUTHORS: Pinto, Jose; Ramos, Joao R. C.; Costa, Rafael S.; Oliveira, Rui;
PUBLISHED: 2023, SOURCE: FERMENTATION-BASEL, VOLUME: 9, ISSUE: 7
AUTHORS: Pinto, Jose; Ramos, Joao R. C.; Costa, Rafael S.; Oliveira, Rui;
PUBLISHED: 2023, SOURCE: FERMENTATION-BASEL, VOLUME: 9, ISSUE: 7
8
TITLE: Upcycling of food waste streams to valuable biopigments pyocyanin and 1-hydroxyphenazine Full Text
AUTHORS: Pantelic, Lena; Bogojevic, Sanja Skaro; Vojnovic, Sandra; Oliveira, Rui; Lazic, Jelena; Ilic Tomic, Tatjana; Milivojevic, Dusan; Nikodinovic Runic, Jasmina;
PUBLISHED: 2023, SOURCE: ENZYME AND MICROBIAL TECHNOLOGY, VOLUME: 171
AUTHORS: Pantelic, Lena; Bogojevic, Sanja Skaro; Vojnovic, Sandra; Oliveira, Rui; Lazic, Jelena; Ilic Tomic, Tatjana; Milivojevic, Dusan; Nikodinovic Runic, Jasmina;
PUBLISHED: 2023, SOURCE: ENZYME AND MICROBIAL TECHNOLOGY, VOLUME: 171
INDEXED IN: 
Scopus 
WOS
Scopus WOS9
TITLE: From Shallow to Deep Bioprocess Hybrid Modeling: Advances and Future Perspectives
AUTHORS: Agharafeie, Roshanak; Ramos, Joao Rodrigues Correia; Mendes, Jorge M. ; Oliveira, Rui;
PUBLISHED: 2023, SOURCE: FERMENTATION-BASEL, VOLUME: 9, ISSUE: 10
AUTHORS: Agharafeie, Roshanak; Ramos, Joao Rodrigues Correia; Mendes, Jorge M. ; Oliveira, Rui;
PUBLISHED: 2023, SOURCE: FERMENTATION-BASEL, VOLUME: 9, ISSUE: 10
10
TITLE: A General SBML Compatible Hybrid Modeling Framework: Combining Biochemical Mechanisms with Deep Neural Networks for Systems Biology Applications
AUTHORS: José Pinto; João R C Ramos; Rafael S Costa; Rui Oliveira;
PUBLISHED: 2023
AUTHORS: José Pinto; João R C Ramos; Rafael S Costa; Rui Oliveira;
PUBLISHED: 2023
