Research Papers
João R. C. Ramos, Alexander G. Rath, Yvonne Genzel, Volker Sandig, Udo Reichl
A dynamic model linking cell growth to intracellular metabolism and extracellular by-product accumulation
http://dx.doi.org/10.1002/bit.27288
João R. C. Ramos, Thomas Bissinger, Yvonne Genzel, Udo Reichl
Impact of Influenza A Virus Infection on Growth and Metabolism of Suspension MDCK Cells Using a Dynamic Model
http://dx.doi.org/10.3390/metabo12030239
João R. C. Ramos, Gil P. Oliveira, Patrick Dumas, Rui Oliveira
Genome-scale modeling of Chinese hamster ovary cells by hybrid semi-parametric flux balance analysis
https://doi.org/10.1007/s00449-022-02795-9
João R. C. Ramos, José Pinto, Gil P. Oliveira, Ludovic Peeters, Patrick Dumas, Rui Oliveira
Deep hybrid modeling of a HEK293 process: combining Long Short-Term Memory (LSTM) networks with first principles equations
https://doi.org/10.1002/bit.28668
José Pinto, Mykaella Mestre, João R. C. Ramos, Rafael S. Costa, Gerald Striedner, Rui Oliveira
A General Deep Hybrid Model for Bioreactor Systems: Combining First Principles with Deep Neural Networks
https://doi.org/10.1016/j.compchemeng.2022.107952
José Pinto, Rafael S. Costa, Leonardo Alexandre, João R. C. Ramos, Rui Oliveira
SBML2HYB: a Python interface for SBML compatible hybrid modelling
https://doi.org/10.1093/bioinformatics/btad044
José Pinto, João R. C. Ramos, Rafael S. Costa, Sergio Rossell, Patrick Dumas, Rui Oliveira
Hybrid deep modeling of a CHO-K1 fed-batch process: combining First-Principles with deep neural networks
https://dx.doi.org/10.3389/fbioe.2023.1237963
José Pinto, João R. C. Ramos, Rafael S. Costa, Rui Oliveira
A General Hybrid Modeling Framework for Systems Biology Applications: Combining Mechanistic Knowledge with Deep Neural Networks under the SBML Standard
https://doi.org/10.3390/ai4010014
José Pinto, João R. C. Ramos, Rafael S. Costa, Rui Oliveira
Hybrid Deep Modeling of a GS115 (Mut+) Pichia pastoris Culture with State–Space Reduction
https://doi.org/10.3390/fermentation9070643
Roshanak Agharafeie, João R. C. Ramos, Jorge M. Mendes, Rui Oliveira
From Shallow to Deep Bioprocess Hybrid Modeling: Advances and Future Perspectives
https://doi.org/10.3390/fermentation9100922
Roshanak Agharafeie, João R. C. Ramos, Rui Oliveira, Jorge M. Mendes
Application of Hybrid Models in Biopharmaceutical Manufacturing
https://doi.org/10.1002/cite.202255039
Book Chapters
José Pinto, João Antunes, João R. C. Ramos, Rafael S. Costa, Rui Oliveira
Modeling and optimization of bioreactor processes
Chapter in: Current Developments in Biotechnology and Bioengineering: Advances in Bioprocess Engineering