Isabel Rocha - RankMe

67 papers B 4C 4Misc 8Journal 29Unranked 22

Year	Rank	Type	Title / Venue / Authors
2023	J	`jnl`	The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber. PLoS Comput. Biol. Emanuel Cunha, Miguel Silva, Inês Chaves, Hüseyin Demirci, Davide Lagoa, Diogo Lima, Miguel Rocha, Isabel Rocha, Oscar Dias
2021	J	`jnl`	Inclusion of maintenance energy improves the intracellular flux predictions of CHO. PLoS Comput. Biol. Diana Széliová, Jerneja Stor, Isabella Thiel, Marcus Weinguny, Michael Hanscho, Gabriele Lhota, Nicole Borth, Jürgen Zanghellini, David E. Ruckerbauer, Isabel Rocha
2021	—	`conf`	Threats and Opportunities for the Clinical Investigation of High-risk Medical Devices in the Context of the New European Regulations. BIODEVICES 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
2020	—	`conf`	Xtrace: Novel Bioresorbable Device for Patent Foramen Ovale Closure. BIODEVICES Sara Abu Ajamieh, Diana Mîndroc-Filimon, Irene Mozo, Isabel Rocha
2019	J	`jnl`	Comparison of pathway analysis and constraint-based methods for cell factory design. BMC Bioinform. Vítor Vieira, Paulo Maia, Miguel Rocha, Isabel Rocha
2019	—	`conf`	Concept Design of a New Portable Medical Device for Lymphedema Monitoring: A EIT Health ClinMed Summer School Project. HEALTHINF Jordi Escuder Tisaire, Elena Martín Rodrigo, Sofia Ribeiro, Mariachiara Ricci, Juan Sebastian Cuellar, Dimitrios I. Zeugolis, Yves Bayon, Isabel Rocha
2019	J	`jnl`	SamPler - a novel method for selecting parameters for gene functional annotation routines. BMC Bioinform. Fernando Cruz, Davide Lagoa, João Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha, Oscar Dias
2018	J	`jnl`	Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes. PLoS Comput. Biol. Joana C. Xavier, Kiran Raosaheb Patil, Isabel Rocha
2018	J	`jnl`	Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z. BMC Syst. Biol. Bruno Pereira, Joana Miguel, Paulo Vilaça, Simão Soares, Isabel Rocha, Sónia Carneiro
2017	J	`jnl`	Genome-Wide Semi-Automated Annotation of Transporter Systems. IEEE ACM Trans. Comput. Biol. Bioinform. Oscar Dias, Daniel Gomes, Paulo Vilaça, João G. R. Cardoso, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha
2017	—	`conf`	Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction. GECCO (Companion) Paulo Maia, Isabel Rocha, Miguel Rocha
2016	Misc	`conf`	A Computation Tool for the Estimation of Biomass Composition from Genomic and Transcriptomic Information. PACBB Sophia Santos, Isabel Rocha
2016	Misc	`conf`	Development of an Integrated Framework for Minimal Cut Set Enumeration in Constraint-Based Models. PACBB Vítor Vieira, Paulo Maia, Isabel Rocha, Miguel Rocha
2016	J	`jnl`	Estimation of biomass composition from genomic and transcriptomic information. J. Integr. Bioinform. Sophia Santos, Isabel Rocha
2016	J	`jnl`	Stoichiometric Representation of Gene-Protein-Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction. PLoS Comput. Biol. Daniel Machado, Markus J. Herrgård, Isabel Rocha
2015	Misc	`conf`	A Text Mining Approach for the Extraction of Kinetic Information from Literature. PACBB Ana Alão Freitas, Hugo Costa, Miguel Rocha, Isabel Rocha
2015	J	`jnl`	Development and application of efficient pathway enumeration algorithms for metabolic engineering applications. Comput. Methods Programs Biomed. Filipe Liu, Paulo Vilaça, Isabel Rocha, Miguel Rocha
2015	J	`jnl`	Extracting kinetic information from literature with KineticRE. J. Integr. Bioinform. Ana Alão Freitas, Hugo Costa, Miguel Rocha, Isabel Rocha
2014	J	`jnl`	A kinetic model for curcumin production in Escherichia coli. Biosyst. Daniel Machado, Lígia R. Rodrigues, Isabel Rocha
2014	J	`jnl`	CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data. BMC Syst. Biol. Rafael Carreira, Pedro Evangelista, Paulo Maia, Paulo Vilaça, Marcellinus Pont, Jean-François Tomb, Isabel Rocha, Miguel Rocha
2014	Misc	`conf`	Evaluating Pathway Enumeration Algorithms in Metabolic Engineering Case Studies. PACBB Filipe Liu, Paulo Vilaça, Isabel Rocha, Miguel Rocha
2014	J	`jnl`	Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. Briefings Bioinform. José P. Faria, Ross A. Overbeek, Fangfang Xia, Miguel Rocha, Isabel Rocha, Christopher S. Henry
2014	J	`jnl`	Optimization of fed-batch fermentation processes with bio-inspired algorithms. Expert Syst. Appl. Miguel Rocha, Rui Mendes, Orlando Rocha, Isabel Rocha, Eugénio C. Ferreira
2013	—	`conf`	Algorithms to infer metabolic flux ratios from fluxomics data. BIBM Rafael Carreira, Miguel Rocha, Silas Granato Villas-Bôas, Isabel Rocha
2013	B	`conf`	An integrated framework for strain optimization. IEEE Congress on Evolutionary Computation Paulo Maia, Isabel Rocha, Miguel Rocha
2013	Misc	`conf`	Assignment of Novel Functions to Helicobacter pylori 26695's Genome. PACBB Tiago Resende, Daniela M. Correia, Isabel Rocha
2013	B	`conf`	Evolutionary computation for predicting optimal reaction knockouts and enzyme modulation strategies. IEEE Congress on Evolutionary Computation Pedro Evangelista, Miguel Rocha, Isabel Rocha
2013	J	`jnl`	Re-annotation of the genome sequence of Helicobacter pylori 26695. J. Integr. Bioinform. Tiago Resende, Daniela M. Correia, Miguel Rocha, Isabel Rocha
2012	J	`jnl`	An integrated computational environment for elementary modes analysis of biochemical networks. Int. J. Data Min. Bioinform. Paulo Maia, Paulo Vilaça, Isabel Rocha, Marcellinus Pont, Jean-François Tomb, Miguel Rocha
2012	Misc	`conf`	Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression. PACBB Emanuel J. V. Gonçalves, Isabel Rocha, Miguel Rocha
2012	J	`jnl`	Optimization Approaches for the J. Comput. Biol. Emanuel J. V. Gonçalves, Rui Pereira, Isabel Rocha, Miguel Rocha
2012	J	`jnl`	Random sampling of elementary flux modes in large-scale metabolic networks. Bioinform. Daniel Machado, Zita Soons, Kiran Raosaheb Patil, Eugénio C. Ferreira, Isabel Rocha
2011	J	`jnl`	A Study of the Short and Long-term Regulation of E. coli Metabolic Pathways. J. Integr. Bioinform. Anália Lourenço, Sónia Carneiro, José P. Pinto, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha
2011	Misc	`conf`	A Systematic Modeling Approach to Elucidate the Triggering of the Stringent Response in Recombinant PACBB Sónia Carneiro, Eugénio C. Ferreira, Isabel Rocha
2011	J	`jnl`	A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information. Biosyst. Paulo Vilaça, Isabel Rocha, Miguel Rocha
2011	J	`jnl`	Challenges in integrating Briefings Bioinform. Anália Lourenço, Sónia Carneiro, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha
2011	—	`conf`	Highlighting Metabolic Strategies Using Network Analysis over Strain Optimization Results. PRIB José Pedro Pinto, Isabel Rocha, Miguel Rocha
2011	Misc	`conf`	Interpreting the Regulatory Interplay in PACBB Anália Lourenço, Sónia Carneiro, José P. Pinto, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha
2011	—	`conf`	New insight into arrhythmia onset using HRV and BPV analysis. EMBC Gabriela Postolache, Mario Oliveira, Isabel Rocha, Pedro Silva Girão, Octavian Postolache
2011	J	`jnl`	Semantic annotation of biological concepts interplaying microbial cellular responses. BMC Bioinform. Rafael Carreira, Sónia Carneiro, Rui Pereira, Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira, Anália Lourenço
2010	—	`conf`	A software tool for network topology analysis under a metabolic engineering perspective. BCB José P. Pinto, Isabel Rocha, Miguel Rocha
2010	—	`conf`	Applying a Metabolic Footprinting Approach to Characterize the Impact of the Recombinant Protein Production in IWPACBB Sónia Carneiro, Silas Granato Villas-Bôas, Isabel Rocha, Eugénio C. Ferreira
2010	J	`jnl`	BioDR: Semantic indexing networks for biomedical document retrieval. Expert Syst. Appl. 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
2010	—	`conf`	Enhancing Elementary Flux Modes Analysis Using Filtering Techniques in an Integrated Environment. IWPACBB Paulo Maia, Marcellinus Pont, Jean-François Tomb, Isabel Rocha, Miguel Rocha
2010	J	`jnl`	Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations. Biosyst. Rafael S. Costa, Daniel Machado, Isabel Rocha, Eugénio C. Ferreira
2010	—	`conf`	Metaheuristics for Strain Optimization Using Transcriptional Information Enriched Metabolic Models. EvoBIO Paulo Vilaça, Paulo Maia, Isabel Rocha, Miguel Rocha
2010	—	`conf`	Model Transformation of Metabolic Networks using a Petri Net Based Framework. ACSD/Petri Nets Workshops Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugénio C. Ferreira
2010	J	`jnl`	OptFlux: an open-source software platform for in silico metabolic engineering. BMC Syst. Biol. Isabel Rocha, Paulo Maia, Pedro Evangelista, Paulo Vilaça, Simão Soares, José P. Pinto, Jens Nielsen, Kiran Raosaheb Patil, Eugénio C. Ferreira, Miguel Rocha
2009	J	`jnl`	@Note: A workbench for Biomedical Text Mining. J. Biomed. Informatics Anália Lourenço, Rafael Carreira, Sónia Carneiro, Paulo Maia, Daniel Glez-Peña, Florentino Fdez-Riverola, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha
2009	—	`conf`	A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems. IWANN (2) Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugénio C. Ferreira
2009	—	`conf`	A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models. IWANN (2) Pedro Evangelista, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha
2009	—	`conf`	Biomedical Text Mining Applied to Document Retrieval and Semantic Indexing. IWANN (2) 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
2009	—	`conf`	Evolutionary Approaches for Strain Optimization Using Dynamic Models under a Metabolic Engineering Perspective. EvoBIO Pedro Evangelista, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha
2009	—	`conf`	Large Scale Dynamic Model Reconstruction for the Central Carbon Metabolism of Escherichia coli . IWANN (2) Rafael S. Costa, Daniel Machado, Isabel Rocha, Eugénio C. Ferreira
2008	C	`conf`	A framework for the development of Biomedical Text Mining software tools. BIBE Anália Lourenço, Rafael Carreira, Sónia Carneiro, Paulo Maia, Daniel Glez-Peña, Florentino Fdez-Riverola, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha
2008	C	`conf`	A framework for the integrated analysis of metabolic and regulatory networks. BIBE Rui Mendes, Anália Lourenço, Sónia Carneiro, Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira
2008	—	`conf`	Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis. IWPACBB José P. Pinto, Oscar Dias, Anália Lourenço, Sónia Carneiro, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha
2008	C	`conf`	Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains. BIBE Paulo Maia, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha
2008	—	`conf`	Modelling Fed-Batch Fermentation Processes: An Approach Based on Artificial Neural Networks. IWPACBB Eduardo Valente, Isabel Rocha, Miguel Rocha
2008	J	`jnl`	Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinform. Miguel Rocha, Paulo Maia, Rui Mendes, José P. Pinto, Eugénio C. Ferreira, Jens Nielsen, Kiran Raosaheb Patil, Isabel Rocha
2007	—	`conf`	Evaluating Evolutionary Algorithms and Differential Evolution for the Online Optimization of Fermentation Processes. EvoBIO Miguel Rocha, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira
2007	—	`conf`	Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains. EPIA Workshops Miguel Rocha, Rui Mendes, Paulo Maia, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira
2007	C	`conf`	Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms. CIBCB Miguel Rocha, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira
2006	B	`conf`	A Comparison of Algorithms for the Optimization of Fermentation Processes. IEEE Congress on Evolutionary Computation Rui Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha
2005	B	`conf`	A new representation in evolutionary algorithms for the optimization of bioprocesses. Congress on Evolutionary Computation Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira
2005	J	`jnl`	Evolutionary programming as a platform for BMC Bioinform. Kiran Raosaheb Patil, Isabel Rocha, Jochen Förster, Jens Nielsen
2004	—	`conf`	Evolutionary Algorithms for Optimal Control in Fed-Batch Fermentation Processes. EvoWorkshops Miguel Rocha, José Neves, Isabel Rocha, Eugénio C. Ferreira