Centre of Biological Engineering / Centro de Engenharia Biológica

1	Sequeira, João C.; Salvador, Andreia F.; Rocha, Miguel Uncovering the role of conductive nanomaterials on anaerobic digestion / Explorando o papel de nanomateriais condutores na digestão anaeróbia
2	Babo, Ana Camila Ribeiro de; Dias, Oscar; Dijk, Aalt-Jan Van Integrating machine learning and mechanistic modeling towards adaptation of plants to climate change
3	Oliveira, Alexandre; Cunha, Emanuel; Silva, Miguel; Faria, Cristiana; Dias, Oscar Exploring Xylella fastidiosa’s metabolic traits using a GSM model of the phytopathogenic bacterium
4	Machado, Tiago; Dias, Oscar Development and analysis of mathematical models to study metabolic constraints and capacities in different photosynthetic types
5	Martins, Inês Tavares; Rocha, Miguel Predicting the impact of psychoactive compounds on human gut bacteria with metabolic modelling / Previsão do impacto de compostos psicoativos nas bactérias do intestino humano com modelação metabólica
6	Martins, Gilberto; Campos, Sara; Ferreira, Ana; Castro, Rita; Duarte, Maria Salomé; Cavaleiro, Ana Júlia A mathematical model for bioremediation of hydrocarbon-contaminated soils
7	Vieira, Vítor; Rocha, Miguel; Saez-Rodriguez, Julio Integrative pathway analysis approaches for cancer research and drug development / Abordagens integrativas de análise de vias para a investigação e desenvolvimento de fármacos para cancro
8	Marta Sampaio; Rocha, Miguel; Oscar Dias Exploring synergies between plant metabolic modelling and machine learning
9	Castro, Ana Rita Sousa; Pereira, M. Alcina; Magalhães, Adriano José Pereira de Definição das velocidades de escoamento e monitorização da qualidade da água ao longo do Sistema Adutor X/Y (ETA – extremo da rede) / Definition of flow velocities and monitoring of water quality along the aductor system X/Y
10	Monteiro, Maria A.; Rocha, Miguel A model validation pipeline for healthy tissue genome-scale metabolic models
11	Murphy, Denis J.; Goggin, Kirstie; Paterson, R. Russell M. Oil palm in the 2020s and beyond: challenges and solutions
12	Santos, David Miguel Ferreira dos; Dias, Oscar Dynamic genome-scale modelling of the Saccharomyces non-cerevisiae yeasts metabolism in wine fermentation
13	Magalhães, Beatriz T.; Lourenço, Anália; Azevedo, Nuno F. Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae
14	Adhikari, Mira; Isaac, Elizabeth L.; Paterson, R. Russell M.; Maslin, Mark A. A review of potential impacts of climate change on coffee cultivation and mycotoxigenic fungi
15	Gael Pérez-Rodríguez; Martín Pérez-Pérez; Florentino Fdez-Riverola; Lourenço, Anália Mining the sociome for Health Informatics: Analysis of therapeutic lifestyle adherence of diabetic patients in Twitter
16	Ribeiro, Catarina; Dias, Oscar; Zeidan, Ahmad Assessment of microbial community interactions using different tools
17	Paterson, R. Russell M. Oil palm survival under climate change in Malaysia with future basal stem rot assessments
18	Martins, Madalena; Silva, Carla; Cavaco-Paulo, Artur α-Chymotrypsin catalysed oligopeptide synthesis for hair modelling
19	Bastos, José Jorge Sampaio; Dias, Oscar; Stams, Alfons J.M. Modelling interspecies interactions of syntrophic communities of Syntrophobacter fumaroxidans and Methanospirillum hungatei
20	Maia, Paulo; Pérez-Rodríguez, Gael; Pérez-Pérez, Martín; Fdez-Riverola, Florentino; Lourenço, Anália; Azevedo, Nuno F. Application of agent-based modelling to assess single-molecule transport across the cell envelope of E. coli
21	Castro, Tarsila G.; Munteanu, Florentina-Daniela; Cavaco-Paulo, Artur Electrostatics of tau protein by molecular dynamics
22	Janek, Tomasz; Rodrigues, Lígia R.; Czyznikowska, Zaneta Study of metal-lipopeptide complexes and their self-assembly behavior, micelle formation, interaction with bovine serum albumin and biological properties
23	Pinu, Farhana R.; Granucci, Ninna; Daniell, James; Han, Ting-Li; Carneiro, Sónia; Rocha, Isabel; Nielsen, Jens; Villas-Boas, Silas G. Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test
24	Rosca, Mihaela; Hlihor, Raluca-Maria; Cozma, P.; Dragoi, E.N.; Diaconu, M.; Silva, Bruna; Tavares, Teresa; Gavrilescu, M. Comparison of Rhodotorula sp. and Bacillus megaterium in the removal of cadmium ions from liquid effluents
25	Pérez-Rodríguez, Gael; Dias, Sónia; Pérez-Pérez, Martín; Fdez-Riverola, Florentino; Azevedo, Nuno F.; Lourenço, Anália Agent-based model of diffusion of N-acyl homoserine lactones in a multicellular environment of Pseudomonas aeruginosa and Candida albicans
26	Gonçalves, Emanuel; Sciacovelli, Marco; Costa, Ana S.H.; Tran, Maxine Gia Binh; Johnson, Timothy Isaac; Machado, Daniel; Frezza, Christian; Saez-Rodriguez, Julio Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells
27	Martins, Gilberto; Ferreira, Ana; Castro, A. Rita; Yanbo, Wu; Langenhoff, Alette A.M.; Cavaleiro, Ana Júlia Bioremediation of petroleum-contaminated soils: mathematical modelling as a tool for the simulation of alternative strategies
28	Lopes, Hélder; Rocha, Isabel Genome-scale modeling of yeast: chronology, applications and critical perspectives
29	Janek, Tomasz; Rodrigues, Lígia R.; Gudiña, Eduardo J.; Czyznikowska, Zaneta Structure and mode of action of cyclic lipopeptide pseudofactin II with divalent metal ions
30	Pérez-Rodríguez, G.; Pérez-Pérez, M.; Fdez-Riverola, F.; Lourenço, Anália High performance computing for three-dimensional agent-based molecular models
31	Villaverde, Alejandro F.; Bongard, Sophia; Mauch, Klaus; Balsa-Canto, Eva; Banga, Julio R. Metabolic engineering with multi-objective optimization of kinetic models
32	Coelho, Eduardo; Vilanova, Mar; Genisheva, Zlatina; Oliveira, José Maria; Teixeira, José A.; Domingues, Lucília Systematic approach for the development of fruit wines from industrially processed fruit concentrates, including optimization of fermentation parameters, chemical characterization and sensory evaluation
33	Fuciños, Clara; Fuciños, Pablo; Fajardo, Paula; Amado, Isabel R.; Pastrana, Lorenzo M.; Rúa, María L. Evaluation of antimicrobial effectiveness of pimaricin-loaded thermosensitive nanohydrogels in grape juice
34	Sousa, Ana Margarida; Pereira, Maria Olívia; Azevedo, N.F.; Lourenço, Anália Designing an ontology tool for the unification of biofilms data
35	Fuciños, Clara; Fuciños, Pablo; Pastrana, Lorenzo M.; Rúa, María L. Functional characterization of poly(N-isopropylacrylamide) nanohydrogels for the controlled release of food preservatives
36	Oliveira, Felisbela; Sousa-Gallagher, M.J.; Mahajan, P.V.; Teixeira, José A. Development of shelf-life kinetic model for modified atmosphere packaging of fresh sliced mushrooms
37	Neri, David F.M.; Balcão, Victor M.; Costa, Rafael S.; Rocha, Isabel; Ferreira, Eugénio C.; Torres, Duarte P.M.; Rodrigues, Lígia R.; Carvalho Jr., L.B.; Teixeira, José A. Galacto-oligosaccharides production during lactose hydrolysis by free Aspergillus oryzae β-galactosidase and immobilized on magnetic polysiloxane-polyvinyl alcohol
38	Costa, Rafael S.; Machado, Daniel; Rocha, Isabel; Ferreira, Eugénio C. Integration of proteomic data for predicting dynamic behaviour in an E. coli central carbon network after genetic perturbations
39	Quintelas, Cristina; Fonseca, B.; Silva, Bruna; Figueiredo, Hugo; Tavares, Teresa Treatment of chromium(VI) solutions in a pilot-scale bioreactor through a biofilm of arthrobacter viscosus supported on GAC
40	Valente, Eduardo; Rocha, Isabel; Rocha, Miguel Modelling fed-batch fermentation processes: An approach based on artificial neural networks
41	Costa, Rafael S.; Rocha, Isabel; Ferreira, Eugénio C. Mathematical modeling of recombinant Escherichia coli aerobic batch fermentations
42	Simões, Manuel; Pereira, Maria Olívia; Vieira, Maria João Kinetics of Pseudomonas fluorescens inactivation with ortho-phtalaldehyde
43	Mota, Manuel; Yelshin, A.; Fidaleo, Marcello; Flickinger, Michael C. Modelling diffusivity in porous polymeric membranes with an intermediate layer containing microbial cells
44	Martins, Gilberto; Rodrigues, Alexandrina L.; Brito, António G.; Nogueira, Regina Modelling of biofilm growth on humic substances
45	Guimarães, P.M.R.; Parrou, J. L.; Le Berre, V.; François, J.; Teixeira, José A.; Domingues, Lucília Adaptive evolution of a recombinant lactose-consuming Saccharomyces cerevisiae strain
46	Madeira, Pedro P.; Xu, Xin; Teixeira, José A.; Macedo, Eugénia A. Prediction of protein partition in polymer/salt aqueous two-phase systems using the modified Wilson model
47	Dias, R.P.; Teixeira, José A.; Mota, Manuel; Yelshin, A. Preparation of controlled particulate mixtures with glass beads of different sizes
48	Mota, Manuel; Teixeira, José A.; Bowen, W.R.; Yelshin, A. Binary spherical particle mixed beds: porosity and permeability relationship measurement
49	Santos, Mariana; Teixeira, José A.; Rodrigues, Alírio Production of dextransucrase, dextran and fructose from sucrose using Leuconostoc mesenteroides NRRL B512(f)
50	Mota, Manuel; Teixeira, José A.; Yelshin, A. Image analysis of packed beds of spherical particles of different sizes
51	Gabriel, D.; Ferreira, Eugénio C.; Valero, F.; Lafuente, J. Calibration of a simplified model describing an urban waste water treatment pilot plant based on N/D and BEPR criteria

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