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2020 – today
- 2023
[j29]Emanuel Cunha
, Miguel Silva, Inês Chaves, Hüseyin Demirci, Davide Lagoa, Diogo Lima, Miguel Rocha, Isabel Rocha, Oscar Días:
The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber. PLoS Comput. Biol. 19(9) (2023)- 2021
- [j28]Diana Széliová, Jerneja Stor, Isabella Thiel, Marcus Weinguny, Michael Hanscho, Gabriele Lhota, Nicole Borth, Jürgen Zanghellini, David E. Ruckerbauer, Isabel Rocha:
Inclusion of maintenance energy improves the intracellular flux predictions of CHO. PLoS Comput. Biol. 17(6) (2021) - [c38]Lionel Pazart, Sylvia Pelayo, Thierry Chevallier, Gabriel Gruionu, Philippe Mabo, Yves Bayon, Frédéric Barbot, Thomas Lihoreau, Catherine Roussel, Nicos Maglaveras, Eirini Lekka, Hugo Alexandre Ferreira, Isabel Rocha, Liesbet Geris, C. Lavet:
Threats and Opportunities for the Clinical Investigation of High-risk Medical Devices in the Context of the New European Regulations. BIODEVICES 2021: 274-284 - 2020
- [c37]Sara Abu Ajamieh, Diana Mîndroc-Filimon, Irene Mozo, Isabel Rocha:
Xtrace: Novel Bioresorbable Device for Patent Foramen Ovale Closure. BIODEVICES 2020: 344-349
2010 – 2019
- 2019
- [j27]Vítor Vieira, Paulo Maia, Miguel Rocha, Isabel Rocha:
Comparison of pathway analysis and constraint-based methods for cell factory design. BMC Bioinform. 20(1): 350:1-350:15 (2019) - [j26]Fernando Cruz, Davide Lagoa, João Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha, Oscar Días:
SamPler - a novel method for selecting parameters for gene functional annotation routines. BMC Bioinform. 20(1): 454:1-454:11 (2019) - [c36]Jordi Escuder Tisaire, Elena Martín Rodrigo, Sofia Ribeiro, Mariachiara Ricci, Juan Sebastian Cuellar, Dimitrios I. Zeugolis, Yves Bayon, Isabel Rocha:
Concept Design of a New Portable Medical Device for Lymphedema Monitoring: A EIT Health ClinMed Summer School Project. HEALTHINF 2019: 611-620 - 2018
- [j25]Bruno Pereira, Joana Miguel, Paulo Vilaça, Simão Soares, Isabel Rocha, Sónia Carneiro:
Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z. BMC Syst. Biol. 12(1): 61:1-61:12 (2018) - [j24]Joana C. Xavier, Kiran Raosaheb Patil, Isabel Rocha:
Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes. PLoS Comput. Biol. 14(11) (2018) - 2017
- [j23]Oscar Días, Daniel Gomes, Paulo Vilaça, João G. R. Cardoso, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha:
Genome-Wide Semi-Automated Annotation of Transporter Systems. IEEE ACM Trans. Comput. Biol. Bioinform. 14(2): 443-456 (2017) - [c35]Paulo Maia, Isabel Rocha, Miguel Rocha:
Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction. GECCO (Companion) 2017: 1661-1668 - 2016
- [j22]Sophia Santos, Isabel Rocha:
Estimation of biomass composition from genomic and transcriptomic information. J. Integr. Bioinform. 13(2) (2016) - [j21]Daniel Machado, Markus J. Herrgård, Isabel Rocha:
Stoichiometric Representation of Gene-Protein-Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction. PLoS Comput. Biol. 12(10) (2016) - [c34]Sophia Santos, Isabel Rocha:
A Computation Tool for the Estimation of Biomass Composition from Genomic and Transcriptomic Information. PACBB 2016: 161-169 - [c33]Vítor Vieira, Paulo Maia, Isabel Rocha, Miguel Rocha:
Development of an Integrated Framework for Minimal Cut Set Enumeration in Constraint-Based Models. PACBB 2016: 193-201 - 2015
- [j20]Filipe Liu, Paulo Vilaça, Isabel Rocha, Miguel Rocha:
Development and application of efficient pathway enumeration algorithms for metabolic engineering applications. Comput. Methods Programs Biomed. 118(2): 134-146 (2015) - [j19]Ana Alão Freitas, Hugo Costa, Miguel Rocha, Isabel Rocha:
Extracting kinetic information from literature with KineticRE. J. Integr. Bioinform. 12(4) (2015) - [c32]Ana Alão Freitas, Hugo Costa, Miguel Rocha, Isabel Rocha:
A Text Mining Approach for the Extraction of Kinetic Information from Literature. PACBB 2015: 89-98 - 2014
- [j18]José P. Faria, Ross A. Overbeek, Fangfang Xia, Miguel Rocha, Isabel Rocha, Christopher S. Henry:
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. Briefings Bioinform. 15(4): 592-611 (2014) - [j17]Daniel Machado, Lígia R. Rodrigues, Isabel Rocha:
A kinetic model for curcumin production in Escherichia coli. Biosyst. 125: 16-21 (2014) - [j16]Rafael Carreira, Pedro Evangelista, Paulo Maia, Paulo Vilaça, Marcellinus Pont, Jean-François Tomb, Isabel Rocha, Miguel Rocha:
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data. BMC Syst. Biol. 8: 123 (2014) - [j15]Miguel Rocha, Rui Mendes, Orlando Rocha, Isabel Rocha, Eugénio C. Ferreira:
Optimization of fed-batch fermentation processes with bio-inspired algorithms. Expert Syst. Appl. 41(5): 2186-2195 (2014) - [c31]Filipe Liu, Paulo Vilaça, Isabel Rocha, Miguel Rocha:
Evaluating Pathway Enumeration Algorithms in Metabolic Engineering Case Studies. PACBB 2014: 215-223 - 2013
- [j14]Tiago Resende, Daniela M. Correia, Miguel Rocha, Isabel Rocha:
Re-annotation of the genome sequence of Helicobacter pylori 26695. J. Integr. Bioinform. 10(3) (2013) - [c30]Rafael Carreira, Miguel Rocha, Silas Granato Villas-Bôas, Isabel Rocha:
Algorithms to infer metabolic flux ratios from fluxomics data. BIBM 2013: 205-209 - [c29]Paulo Maia, Isabel Rocha, Miguel Rocha:
An integrated framework for strain optimization. IEEE Congress on Evolutionary Computation 2013: 198-205 - [c28]Pedro Evangelista, Miguel Rocha, Isabel Rocha:
Evolutionary computation for predicting optimal reaction knockouts and enzyme modulation strategies. IEEE Congress on Evolutionary Computation 2013: 1225-1232 - [c27]Tiago Resende, Daniela M. Correia, Isabel Rocha:
Assignment of Novel Functions to Helicobacter pylori 26695's Genome. PACBB 2013: 29-36 - 2012
- [j13]Daniel Machado, Zita Soons, Kiran Raosaheb Patil, Eugénio C. Ferreira, Isabel Rocha:
Random sampling of elementary flux modes in large-scale metabolic networks. Bioinform. 28(18): 515-521 (2012) - [j12]Paulo Maia, Paulo Vilaça, Isabel Rocha, Marcellinus Pont, Jean-François Tomb, Miguel Rocha:
An integrated computational environment for elementary modes analysis of biochemical networks. Int. J. Data Min. Bioinform. 6(4): 382-395 (2012) - [j11]Emanuel J. V. Gonçalves, Rui Pereira, Isabel Rocha, Miguel Rocha:
Optimization Approaches for the In Silico Discovery of Optimal Targets for Gene Over/Underexpression. J. Comput. Biol. 19(2): 102-114 (2012) - [c26]Emanuel J. V. Gonçalves, Isabel Rocha, Miguel Rocha:
Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression. PACBB 2012: 251-258 - 2011
- [j10]Anália Lourenço, Sónia Carneiro, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha:
Challenges in integrating Escherichia coli molecular biology data. Briefings Bioinform. 12(2): 91-103 (2011) - [j9]Paulo Vilaça, Isabel Rocha, Miguel Rocha:
A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information. Biosyst. 103(3): 435-441 (2011) - [j8]Rafael Carreira, Sónia Carneiro, Rui Pereira, Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira, Anália Lourenço:
Semantic annotation of biological concepts interplaying microbial cellular responses. BMC Bioinform. 12: 460 (2011) - [j7]Anália Lourenço, Sónia Carneiro, José P. Pinto, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha:
A Study of the Short and Long-term Regulation of E. coli Metabolic Pathways. J. Integr. Bioinform. 8(3) (2011) - [c25]Gabriela Postolache, Mario Oliveira, Isabel Rocha, Pedro Silva Girão, Octavian Postolache:
New insight into arrhythmia onset using HRV and BPV analysis. EMBC 2011: 2691-2694 - [c24]Anália Lourenço, Sónia Carneiro, José P. Pinto, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha:
Interpreting the Regulatory Interplay in E. coli Metabolic Pathways. PACBB 2011: 303-312 - [c23]Sónia Carneiro, Eugénio C. Ferreira, Isabel Rocha:
A Systematic Modeling Approach to Elucidate the Triggering of the Stringent Response in Recombinant E. coli Systems. PACBB 2011: 313-320 - [c22]José Pedro Pinto, Isabel Rocha, Miguel Rocha:
Highlighting Metabolic Strategies Using Network Analysis over Strain Optimization Results. PRIB 2011: 109-120 - 2010
- [j6]Rafael S. Costa, Daniel Machado, Isabel Rocha, Eugénio C. Ferreira:
Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations. Biosyst. 100(2): 150-157 (2010) - [j5]Isabel Rocha, Paulo Maia, Pedro Evangelista, Paulo Vilaça, Simão Soares, José P. Pinto, Jens Nielsen, Kiran Raosaheb Patil, Eugénio C. Ferreira, Miguel Rocha:
OptFlux: an open-source software platform for in silico metabolic engineering. BMC Syst. Biol. 4: 45 (2010) - [j4]Anália Lourenço, Rafael Carreira, Daniel Glez-Peña, José Ramón Méndez, Sónia Carneiro, Luis Mateus Rocha, Fernando Díaz, Eugénio C. Ferreira, Isabel Rocha, Florentino Fdez-Riverola, Miguel Rocha:
BioDR: Semantic indexing networks for biomedical document retrieval. Expert Syst. Appl. 37(4): 3444-3453 (2010) - [c21]Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugénio C. Ferreira:
Model Transformation of Metabolic Networks using a Petri Net Based Framework. ACSD/Petri Nets Workshops 2010: 103-117 - [c20]José P. Pinto, Isabel Rocha, Miguel Rocha:
A software tool for network topology analysis under a metabolic engineering perspective. BCB 2010: 569-578 - [c19]Paulo Vilaça, Paulo Maia, Isabel Rocha, Miguel Rocha:
Metaheuristics for Strain Optimization Using Transcriptional Information Enriched Metabolic Models. EvoBIO 2010: 205-216 - [c18]Sónia Carneiro, Silas Granato Villas-Bôas, Isabel Rocha, Eugénio C. Ferreira:
Applying a Metabolic Footprinting Approach to Characterize the Impact of the Recombinant Protein Production in Escherichia coli. IWPACBB 2010: 193-200 - [c17]Paulo Maia, Marcellinus Pont, Jean-François Tomb, Isabel Rocha, Miguel Rocha:
Enhancing Elementary Flux Modes Analysis Using Filtering Techniques in an Integrated Environment. IWPACBB 2010: 217-224
2000 – 2009
- 2009
- [j3]Anália Lourenço, Rafael Carreira, Sónia Carneiro, Paulo Maia, Daniel Glez-Peña, Florentino Fdez-Riverola, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha:
@Note: A workbench for Biomedical Text Mining. J. Biomed. Informatics 42(4): 710-720 (2009) - [c16]Pedro Evangelista, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha:
Evolutionary Approaches for Strain Optimization Using Dynamic Models under a Metabolic Engineering Perspective. EvoBIO 2009: 140-151 - [c15]Anália Lourenço, Sónia Carneiro, Eugénio C. Ferreira, Rafael Carreira, Luis M. Rocha, Daniel Glez-Peña, José Ramón Méndez, Florentino Fdez-Riverola, Fernando Díaz, Isabel Rocha, Miguel Rocha:
Biomedical Text Mining Applied to Document Retrieval and Semantic Indexing. IWANN (2) 2009: 954-963 - [c14]Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugénio C. Ferreira:
A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems. IWANN (2) 2009: 1063-1070 - [c13]Pedro Evangelista, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha:
A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models. IWANN (2) 2009: 1071-1078 - [c12]Rafael S. Costa, Daniel Machado, Isabel Rocha, Eugénio C. Ferreira:
Large Scale Dynamic Model Reconstruction for the Central Carbon Metabolism of Escherichia coli . IWANN (2) 2009: 1079-1083 - 2008
- [j2]Miguel Rocha, Paulo Maia, Rui Mendes, José P. Pinto, Eugénio C. Ferreira, Jens Nielsen, Kiran Raosaheb Patil, Isabel Rocha:
Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinform. 9 (2008) - [c11]Anália Lourenço, Rafael Carreira, Sónia Carneiro, Paulo Maia, Daniel Glez-Peña, Florentino Fdez-Riverola, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha:
A framework for the development of Biomedical Text Mining software tools. BIBE 2008: 1-6 - [c10]Paulo Maia, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha:
Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains. BIBE 2008: 1-6 - [c9]Rui Mendes, Anália Lourenço, Sónia Carneiro, Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira:
A framework for the integrated analysis of metabolic and regulatory networks. BIBE 2008: 1-6 - [c8]Eduardo Valente, Isabel Rocha, Miguel Rocha:
Modelling Fed-Batch Fermentation Processes: An Approach Based on Artificial Neural Networks. IWPACBB 2008: 30-39 - [c7]José P. Pinto, Oscar Días, Anália Lourenço, Sónia Carneiro, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha:
Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis. IWPACBB 2008: 92-101 - 2007
- [c6]Miguel Rocha, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira:
Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms. CIBCB 2007: 331-337 - [c5]Miguel Rocha, Rui Mendes, Paulo Maia, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira:
Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains. EPIA Workshops 2007: 473-484 - [c4]Miguel Rocha, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira:
Evaluating Evolutionary Algorithms and Differential Evolution for the Online Optimization of Fermentation Processes. EvoBIO 2007: 236-246 - 2006
- [c3]Rui Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha:
A Comparison of Algorithms for the Optimization of Fermentation Processes. IEEE Congress on Evolutionary Computation 2006: 2018-2025 - 2005
- [j1]Kiran Raosaheb Patil, Isabel Rocha, Jochen Förster, Jens Nielsen:
Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinform. 6: 308 (2005) - [c2]Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira:
A new representation in evolutionary algorithms for the optimization of bioprocesses. Congress on Evolutionary Computation 2005: 484-490 - 2004
- [c1]Miguel Rocha, José Neves, Isabel Rocha, Eugénio C. Ferreira:
Evolutionary Algorithms for Optimal Control in Fed-Batch Fermentation Processes. EvoWorkshops 2004: 84-93
Coauthor Index
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