Combining first principles modelling and artificial neural networks: a general framework. - Rui Oliveira 002 (Comput. Chem. Eng., 2004)

Hybrid Metabolic Flux Analysis/Artificial Neural Network Modeling of Bioprocesses. - Ana P. Teixeira; Paula M. Alves; Rui Oliveira 002; Carlos Alves; Manuel J. T. Carrondo (HIS, 2005)

Hybrid elementary flux analysis/nonparametric modeling: application for bioprocess control. - Ana P. Teixeira; Carlos Alves; Paula M. Alves; Manuel J. T. Carrondo; Rui Oliveira 002 (BMC Bioinform., 2007)

Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures. - João M. L. Dias; Adrian Oehmen; Luísa S. Serafim; Paulo C. Lemos; Maria A. M. Reis; Rui Oliveira 002 (BMC Syst. Biol., 2008)

Stochastic simulation of protein expression in the baculovirus/insect cells system. - António Roldão; Manuel J. T. Carrondo; Paula M. Alves; Rui Oliveira 002 (Comput. Chem. Eng., 2008)

Modelling biochemical networks with intrinsic time delays: a hybrid semi-parametric approach. - Moritz von Stosch; Joana Peres; Sebastião Feyo de Azevedo; Rui Oliveira 002 (BMC Syst. Biol., 2010)

Hybrid metabolic flux analysis: combining stoichiometric and statistical constraints to model the formation of complex recombinant products. - Nuno Carinhas; Vicente Bernal; Ana P. Teixeira; Manuel J. T. Carrondo; Paula M. Alves; Rui Oliveira 002 (BMC Syst. Biol., 2011)

Projection to latent pathways (PLP): a constrained projection to latent variables (PLS) method for elementary flux modes discrimination. - Ana R. Ferreira; João M. L. Dias; Ana P. Teixeira; Nuno Carinhas; Rui M. C. Portela; Inês A. Isidro; Moritz von Stosch; Rui Oliveira 002 (BMC Syst. Biol., 2011)

Cell functional enviromics: Unravelling the function of environmental factors. - Ana P. Teixeira; João M. L. Dias; Nuno Carinhas; Marcos Sousa; José Clemente; António Cunha; Moritz von Stosch; Paula M. Alves; Manuel J. T. Carrondo; Rui Oliveira 002 (BMC Syst. Biol., 2011)

A novel identification method for hybrid (N)PLS dynamical systems with application to bioprocesses. - Moritz von Stosch; Rui Oliveira 002; Joana Peres; Sebastião Feyo de Azevedo (Expert Syst. Appl., 2011)

On the Effect of Thermodynamic Equilibrium on the Assembly Efficiency of Complex Multi-Layered Virus-Like Particles (VLP): the Case of Rotavirus VLP. - António Roldão; Maria Candida M. Mellado; J. C. Lima; Manuel J. T. Carrondo; Paula M. Alves; Rui Oliveira 002 (PLoS Comput. Biol., 2012)

Hybrid Modeling for Systems Biology: Theory and Practice. - Moritz von Stosch; Nuno Carinhas; Rui Oliveira 002 (Large-Scale Networks in Engineering and Life Sciences, 2014)

Hybrid semi-parametric modeling in process systems engineering: Past, present and future. - Moritz von Stosch; Rui Oliveira 002; Joana Peres; Sebastião Feyo de Azevedo (Comput. Chem. Eng., 2014)

Iterative learning control of polyhydroxybutyrate production in a sequencing batch reactor. - Seyong Jung; Jie Zhang 005; Rui Oliveira 002 (MMAR, 2015)

A principal components method constrained by elementary flux modes: analysis of flux data sets. - Moritz von Stosch; Cristiana Rodrigues de Azevedo; Mauro Luis; Sebastião Feyo de Azevedo; Rui Oliveira 002 (BMC Bioinform., 2016)

A general deep hybrid model for bioreactor systems: Combining first principles with deep neural networks. - José Pinto 007; Mykaella Mestre; J. Ramos; Rafael S. Costa; Gerald Striedner; Rui Oliveira 002 (Comput. Chem. Eng., 2022)

SBML2HYB: a Python interface for SBML compatible hybrid modeling. - José Pinto 007; Rafael S. Costa; Leonardo Alexandre; João Ramos; Rui Oliveira 002 (Bioinform., 2023)

Incorporating first-principles information into hybrid modeling structures: Comparing hybrid semi-parametric models with Physics-Informed Recurrent Neural Networks. - Peter Jul-Rasmussen; Monesh Kumar; José Pinto 007; Rui Oliveira 002; Xiaodong Li; Jakob Kjøbsted Huusom (Comput. Chem. Eng., 2025)