Researcher Profile
Researcher Profile
João Rodrigues Correia Ramos, PhD João R. C. Ramos, Joao R. C. Ramos, Joao Rodrigues Correia Ramos
Mail: joao.ramos[at]medizin.uni-freiburg.de ; jr.ramos[at]campus.fct.unl.pt
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Welcome to my website 😊 I am a Bioprocess Engineer | Computational Biologist | Hybrid Modeling Specialist
Born on a farm in Cape Verde, raised with curiosity and care, and trained across Portugal and Germany, I bring a systems-thinking approach to life — whether I’m growing vegetables, building neural networks, or modeling virus dynamics inside living cells.
As a bioprocess engineer and computational biologist, my work sits at the intersection of biology, data science, and systems optimization. During my time at FCT NOVA, my research focused on hybrid deep modeling of bioprocesses and using in silico media/feed design with hybrid semi-parametric modeling to optimize media formulations. This work directly contributed to over 50% gains in mammalian cell productivity. I specialize in statistical modeling, machine learning, and dynamic systems design, driven by a deep curiosity about how we can simulate and decode the inner workings of life itself.
At the Max Planck Institute, my focus was on the development of mechanistic dynamical models of cell growth, central carbon metabolism, and virus production in animal cells under varying conditions. My research included parameter optimization, intracellular analysis, and a strong focus on making biopharmaceutical processes more efficient and scalable.
Outside the lab, you can often find me programming (whether it's a web bot to automate a task or a model to predict bitcoin prices), watching series and anime, or riding my MTB on a trail. I'm almost always listening to music—even while working! To disconnect, I enjoy occasional camping, walks in nature, reading philosophy (stoicism is a favorite), and finding peace while watering the garden. I believe engineering is not just about precision — it’s also about care, consciousness, and designing for what truly matters.
These are my social profiles links, click to find more info, most included in this page.
Spin-off contribution: https://levacells.com/
Research Papers
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
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
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
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
Work
2026- Postdoctoral Researcher, Universitätsklinikum Freiburg
Mathematical modeling
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
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
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
Memberships, Scholarships and Awards
Memberships, Scholarships and Awards
2022 : Best Paper Award 2022 (https://doi.org/10.1007/s00449-022-02795-9)
2017 : ESACT Award “This is how we innovate”
2015 : Vice Representative of International Max Planck Research School (IMPRS) students
2013-2015: Bachelor and Master Thesis Scholarship from Fundação Lapa Dos Lobos
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