Rui Manuel Freitas Oliveira
AuthID: R-000-FXV
1
TITLE: SBML2HYB: a Python interface for SBML compatible hybrid modeling Full Text
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
INDEXED IN: 
Scopus 
WOS
Scopus WOS2
TITLE: A General Hybrid Modeling Framework for Systems Biology Applications: Combining Mechanistic Knowledge with Deep Neural Networks under the SBML Standard Full Text
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
INDEXED IN: WOS
WOS3
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
INDEXED IN: Scopus WOS
Scopus WOS4
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 WOS5
TITLE: Hybrid deep modeling of a CHO-K1 fed-batch process: combining first-principles with deep neural networks
AUTHORS: Pinto, Jose; Ramos, Joao R. C.; Costa, Rafael S.; Rossell, Sergio; Dumas, Patrick; Oliveira, Rui;
PUBLISHED: 2023, SOURCE: FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY, VOLUME: 11
AUTHORS: Pinto, Jose; Ramos, Joao R. C.; Costa, Rafael S.; Rossell, Sergio; Dumas, Patrick; Oliveira, Rui;
PUBLISHED: 2023, SOURCE: FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY, VOLUME: 11
INDEXED IN: Scopus WOS
Scopus WOS6
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
INDEXED IN: Scopus WOS
Scopus WOS7
TITLE: Indole-Containing Pyrazino[2,1-b]quinazoline-3,6-diones Active against Plasmodium and Trypanosomatids
AUTHORS: Long, S; Duarte, D; Carvalho, C; Oliveira, R; Santarem, N; Palmeira, A ; Resende, DISP; Silva, AMS; Moreira, R; Kijjoa, A; da Silva, AC ; Nogueira, F; Sousa, E ; Pinto, MMM;
PUBLISHED: 2022, SOURCE: ACS MEDICINAL CHEMISTRY LETTERS, VOLUME: 13, ISSUE: 2
AUTHORS: Long, S; Duarte, D; Carvalho, C; Oliveira, R; Santarem, N; Palmeira, A ; Resende, DISP; Silva, AMS; Moreira, R; Kijjoa, A; da Silva, AC ; Nogueira, F; Sousa, E ; Pinto, MMM;
PUBLISHED: 2022, SOURCE: ACS MEDICINAL CHEMISTRY LETTERS, VOLUME: 13, ISSUE: 2
8
TITLE: Rewired glycosylation activity promotes scarless regeneration and functional recovery in spiny mice after complete spinal cord transection
AUTHORS: Nogueira Rodrigues, J; Leite, SC; Pinto Costa, R; Sousa, SC; Luz, LL; Sintra, MA; Oliveira, R; Monteiro, AC; Pinheiro, GG; Vitorino, M; Silva, JA ; Simao, S; Fernandes, VE; Provaznik, J; Benes, V; Cruz, CD ; Safronov, BV; Magalhaes, A; Reis, CA; Vieira, J ; ...More
PUBLISHED: 2022, SOURCE: DEVELOPMENTAL CELL, VOLUME: 57, ISSUE: 4
AUTHORS: Nogueira Rodrigues, J; Leite, SC; Pinto Costa, R; Sousa, SC; Luz, LL; Sintra, MA; Oliveira, R; Monteiro, AC; Pinheiro, GG; Vitorino, M; Silva, JA ; Simao, S; Fernandes, VE; Provaznik, J; Benes, V; Cruz, CD ; Safronov, BV; Magalhaes, A; Reis, CA; Vieira, J ; ...More
PUBLISHED: 2022, SOURCE: DEVELOPMENTAL CELL, VOLUME: 57, ISSUE: 4
9
TITLE: A general deep hybrid model for bioreactor systems: Combining first principles with deep neural networks Full Text
AUTHORS: Pinto, Jose; Mestre, Mykaella; Ramos, J.; Costa, Rafael S.; Striedner, Gerald; Oliveira, Rui;
PUBLISHED: 2022, SOURCE: COMPUTERS & CHEMICAL ENGINEERING, VOLUME: 165
AUTHORS: Pinto, Jose; Mestre, Mykaella; Ramos, J.; Costa, Rafael S.; Striedner, Gerald; Oliveira, Rui;
PUBLISHED: 2022, SOURCE: COMPUTERS & CHEMICAL ENGINEERING, VOLUME: 165
INDEXED IN: Scopus WOS
Scopus WOS10
TITLE: Genome-scale modeling of Chinese hamster ovary cells by hybrid semi-parametric flux balance analysis Full Text
AUTHORS: Ramos, Joao R. C.; Gil Poiares-Oliveira ; Dumas, Patrick; Oliveira, Rui;
PUBLISHED: 2022, SOURCE: BIOPROCESS AND BIOSYSTEMS ENGINEERING, VOLUME: 45, ISSUE: 11
AUTHORS: Ramos, Joao R. C.; Gil Poiares-Oliveira ; Dumas, Patrick; Oliveira, Rui;
PUBLISHED: 2022, SOURCE: BIOPROCESS AND BIOSYSTEMS ENGINEERING, VOLUME: 45, ISSUE: 11
