Researcher Profile

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 

http://dx.doi.org/10.1016/B978-0-323-91167-2.00016-2

Softwares

• Mechanistic Dynamic Model of Growth and Central Carbon Metabolism of Suspension AGE1.HN Cells  implementation in MATLAB

(Demo 1, ODEs, 33 states, MATLAB)

• Mechanistic Dynamic Model of Growth, Central Carbon Metabolism and Influenza A Virus Production in Suspension MDCK Cells  implementation in MATLAB

(Demo 2, ODEs, 35 states, MATLAB)

• CHO hybrid semi-parametric flux balance analysis (HybridFBA) implementation code and toy example in MATLAB

(Demo 3, constraint-based model, MATLAB)

• SBML2HYB implementation in Python and examples

(Demo 4, SBML to hybrid model, Python)

• HYBMOD toolbox for hybrid modeling

(Demo 5, SBML to hybrid model, MATLAB)

• HYBMOD toolbox for hybrid modeling of bioreactor experiments

(Demo 6, hybrid modeling using neural networks and first principle equations, MATLAB)

• HYBMOD toolbox for hybrid modeling of bioreactor using LSTM

(Demo 7, hybrid modeling using neural networks and first principle equations, MATLAB)

Education

2025.  PhD in Bioprocess Engineering & Systems Biology, Otto-von-Guericke-Universität, Germany

2015. MSc. in Biotechnology, Nova University of Lisbon, Portugal

2013.  Bsc. in Biotechnology, Évora University, Portugal

Work

2021-2025 Research Assistant, Nova University of Lisbon

SILICOMEDIA project with GlaxoSmithKline Belgium: 

• Developed a hybrid genome-scale model of CHO cells to optimize feeding strategies. 

• Applied metabolic and AI-based modeling to improve recombinant protein production. 

• Collaborated in interdisciplinary academic–industry teams.

2015-2020 Doctoral Research, Max Planck Institute for Dynamics of Complex Technical Systems, Germany

My PhD research topic was ''Modeling the Dynamics of Cell Growth, Central Carbon Metabolism and Virus Production in Animal Cells'' under the supervision of Prof. Dr. Udo Reichl and Dr. Yvonne Genzel. I established dynamic models to describe cell growth or even virus infection for different cell lines and process conditions (batch, shaker flask and continuous). I gained profound knowledge into bioprocesses, establishing continuous models of bioprocess and parameter optimization.

The overall achievements were:

• Designed dynamic and mechanistic models of mammalian cell growth, virus infection, and metabolism. 

• Performed parameter estimation, data integration, and simulation for large-scale bioprocesses. 

• Presented work at international conferences.

Talks

• Ramos JRC, Oliveira R. Hybrid Flux Balance Analysis: Coupling Mechanistic and Empirical Constraints in a Common Linear Program. 2023, Metabolic Pathway Analysis 9th, Seoul, South Korea

• Ramos JRC, Oliveira R. Genome-scale hybrid modeling. 2023, Hybrid Modeling Summer School 5th, Lisbon, Portugal

• Ramos JRC, Bissinger T, Genzel Y, Reichl U. A dynamic model for cell growth, metabolism and virus production of MDCK suspension cells. 2020, Society of Mathematical Biology Annual Meeting, Virtual Meeting

Posters

• Ramos JRC, Bissinger T, Genzel Y, Reichl U. A Dynamic Model for Cell Growth, Metabolism & Virus Production of MDCK Suspension Cells. 2019, YCOPE 2019, Magdeburg, Germany

• Bissinger T, Ramos JRC, Ringeisen J., Genzel Y, Reichl U. Dynamics of intracellular metabolite pools in MDCK suspension cells during cell growth and influenza virus infection. 2018, Cell Culture Engineering XVI, Tampa, Florida, USA

• Bissinger T, Ramos JRC, Ringeisen J., Genzel Y, Reichl U. Intracellular Metabolic Pool Dynamics in MDCK Suspension Cells during Growth and Influenza Virus Infection. 2017, 25th ESACT Meeting, Lausanne, Switzerland

• Ramos JRC, Rath AG, Genzel Y, Rose T, Sandig V, Reichl U.A Dynamic Model of Growth and Metabolism of AGE1.HN Suspension Cells. 2016, 6th IFAC Conference on Foundations of Systems Biology in Engineering, Magdeburg, Germany