Search filters

List of works by Isabel Rocha

@Note: a workbench for biomedical text mining

scientific article published on 22 April 2009

A Comparative Analysis of Dynamic Models of the Central Carbon Metabolism of Escherichia coli

scholarly article by Ana Patrícia Lima et al published 2016 in IFAC Proceedings Volumes

A Computation Tool for the Estimation of Biomass Composition from Genomic and Transcriptomic Information

article

A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems

A Dynamical Model for the Fermentative Production of Fructooligosaccharides

A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models

A Systematic Modeling Approach to Elucidate the Triggering of the Stringent Response in Recombinant E. coli Systems

scholarly article by Sónia Carneiro et al published 2011 in Advances in Intelligent and Soft Computing

A Text Mining Approach for the Extraction of Kinetic Information from Literature

A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information.

scientific article published on 7 December 2010

A framework for the development of Biomedical Text Mining software tools

A framework for the integrated analysis of metabolic and regulatory networks

article published in 2008

A kinetic model for curcumin production in Escherichia coli.

scientific article published on 16 September 2014

A software tool for network topology analysis under a metabolic engineering perspective

Algorithms to infer metabolic flux ratios from fluxomics data

An integrated computational environment for elementary modes analysis of biochemical networks

scientific article published in January 2012

An integrated framework for strain optimization

Analyzing and Designing Cell Factories with OptFlux

scientific article published in January 2018

Applying a Metabolic Footprinting Approach to Characterize the Impact of the Recombinant Protein Production in Escherichia coli

scholarly article by Sónia Carneiro et al published 2010 in Advances in Intelligent and Soft Computing

Assessment of physiological conditions in E. coli fermentations by epifluorescent microscopy and image analysis.

scientific article published in May 2009

Assignment of Novel Functions to Helicobacter pylori 26695’s Genome

BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

article

BioDR: Semantic indexing networks for biomedical document retrieval

Biomedical Text Mining Applied to Document Retrieval and Semantic Indexing

CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data

scientific article

Challenges in integrating Escherichia coli molecular biology data

scientific article

Comparison of adsorption equilibrium of fructose, glucose and sucrose on potassium gel-type and macroporous sodium ion-exchange resins

scientific article published on 23 June 2009

Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression

article

Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation

scientific article

Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modelling.

scientific article

Current state and challenges for dynamic metabolic modeling

scientific article

Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis

Design and application of genome-scale reconstructed metabolic models.

scientific article published in January 2008

Development and application of efficient pathway enumeration algorithms for metabolic engineering applications

scientific article published on 4 December 2014

Development of a Framework for Metabolic Pathway Analysis-Driven Strain Optimization Methods

scientific article

Development of an Integrated Framework for Minimal Cut Set Enumeration in Constraint-Based Models

article

Dietary Sugars Analysis: Quantification of Fructooligossacharides during Fermentation by HPLC-RI Method

scientific article published on 31 July 2014

Differential Evolution for the Offline and Online Optimization of Fed-Batch Fermentation Processes

Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate

scientific article published on 30 September 2019

Enhancing Elementary Flux Modes Analysis Using Filtering Techniques in an Integrated Environment

Erratum to: Quantitative physiology and elemental composition of Kluyveromyces lactis CBS 2359 during growth on glucose at different specific growth rates

scientific article published on 12 October 2017

Estimation of biomass composition from genomic and transcriptomic information

scientific article

Estimation of multiple biomass growth rates and biomass concentration in a class of bioprocesses

scientific article published on 18 June 2003

Evaluating Pathway Enumeration Algorithms in Metabolic Engineering Case Studies

Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains

scholarly article published October 2008

Evaluating the integration of proteomic data for the prediction of intracellular fluxes after knockout experiments

Evolutionary Algorithms for Static and Dynamic Optimization of Fed-batch Fermentation Processes

Evolutionary Approaches for Strain Optimization Using Dynamic Models under a Metabolic Engineering Perspective

article

Evolutionary computation for predicting optimal reaction knockouts and enzyme modulation strategies

Evolutionary programming as a platform for in silico metabolic engineering

scientific article

Exploring the gap between dynamic and constraint-based models of metabolism.

scientific article published on 28 January 2012

Extracting kinetic information from literature with KineticRE.

scientific article published on 3 November 2015

Galacto-oligosaccharides production during lactose hydrolysis by free Aspergillus oryzae β-galactosidase and immobilized on magnetic polysiloxane-polyvinyl alcohol

article

Genome scale metabolic network reconstruction of the pathogen Enterococcus faecalis

Genome-Wide Semi-Automated Annotation of Transporter Systems

scientific article

Genome-wide metabolic (re-) annotation of Kluyveromyces lactis

scientific article

Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis

scientific article

Genome-wide sequencing and metabolic annotation of Pythium irregulare CBS 494.86: understanding Eicosapentaenoic acid production

scientific article published on 28 June 2019

Highlighting Metabolic Strategies Using Network Analysis over Strain Optimization Results

Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations.

scientific article published on 10 March 2010

Identification and microbial production of the raspberry phenol salidroside that is active against Huntington's disease

scientific article published on 05 November 2018

Identification of metabolic engineering targets through analysis of optimal and sub-optimal routes

scientific article (publication date: 2013)

Identification of minimal metabolic pathway models consistent with phenotypic data

article

Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction

Impact of the cultivation strategy on resveratrol production from glucose in engineered Corynebacterium glutamicum.

scientific article published on 12 November 2017

Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiae.

scientific article published on 13 May 2016

In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories

scientific article

Inclusion of maintenance energy improves the intracellular flux predictions of CHO

scientific article published on 11 June 2021

Influence of the RelA Activity on E. coli Metabolism by Metabolite Profiling of Glucose-Limited Chemostat Cultures.

scientific article published on 12 October 2012

Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes

scientific article

Interpreting the Regulatory Interplay in E. coli Metabolic Pathways

scholarly article by Anália Lourenço et al published 2011 in Advances in Intelligent and Soft Computing

Large Scale Dynamic Model Reconstruction for the Central Carbon Metabolism of Escherichia coli

scholarly article by Rafael S. Costa et al published 2009 in Lecture Notes in Computer Science

Merlin: Metabolic Models Reconstruction using Genome-Scale Information*

Metabolic engineering strategies for butanol production in Escherichia coli

scientific article published on 06 May 2020

Metabolic footprint analysis of recombinant Escherichia coli strains during fed-batch fermentations.

scientific article

Metabolic footprinting of Escherichia coli grown in fed-batch fermentation during recombinant protein production

Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes

article

Metabolic responses to recombinant bioprocesses in Escherichia coli

scientific article published on 26 September 2012

Model-guided development of an evolutionarily stable yeast chassis

scientific article published on 01 July 2021

Modeling formalisms in Systems Biology

scientific article published on 05 December 2011

Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli

scientific article

Modelling Fed-Batch Fermentation Processes: An Approach Based on Artificial Neural Networks

scholarly article

Modelling of Biotechnological Processes – An Approach Based on Artificial Neural Networks

scholarly article by Eduardo Valente et al published 2009 in Studies in Computational Intelligence

Monitoring of fed-batch E. coli fermentations with software sensors

scientific article published on 26 August 2008

Natural computation meta-heuristics for the in silico optimization of microbial strains

scientific article

New improved method for fructooligosaccharides production by Aureobasidium pullulans

article

On-line simultaneous monitoring of glucose and acetate with FIA during high cell density fermentation of recombinant E. coli

scholarly article by Isabel Rocha & E.C Ferreira published July 2002 in Analytica Chimica Acta

OptFlux: an open-source software platform for in silico metabolic engineering

scientific article

Optimization and Culture Conditions to Improve Helicobacter Pylori Growth in HAM's F-12 Medium by Response Surface Methodology

article

Optimization approaches for the in silico discovery of optimal targets for gene over/underexpression

scientific article published in February 2012

Optimization of fed-batch fermentation processes with bio-inspired algorithms

scholarly article by Miguel Rocha et al published April 2014 in Expert Systems with Applications

Production of mannosylglycerate in Saccharomyces cerevisiae by metabolic engineering and bioprocess optimization

scientific article published on 16 November 2018

Quantitative physiology and elemental composition of Kluyveromyces lactis CBS 2359 during growth on glucose at different specific growth rates

scientific article

Random sampling of elementary flux modes in large-scale metabolic networks

scientific article

Reconstructing genome-scale metabolic models with merlin

scientific article published on 6 April 2015

Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data

scientific article

Rhodococcus opacus B4: a promising bacterium for production of biofuels and biobased chemicals.

scientific article

Salmonella typhimurium and Escherichia coli dissimilarity: Closely related bacteria with distinct metabolic profiles.

scientific article published on 22 June 2015

Selection of Elementary Modes for Bioprocess Control

Semantic annotation of biological concepts interplaying microbial cellular responses

scientific article

State and specific growth estimation in heterologous protein production by Pichia pastoris

article

Stoichiometric Representation of Gene-Protein-Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

scientific article

Stringent response of Escherichia coli: revisiting the bibliome using literature mining.

scientific article published on 30 December 2011

Systems biology perspectives on minimal and simpler cells

scientific article

TNA4OptFlux--a software tool for the analysis of strain optimization strategies

scientific article

Turnover Dependent Phenotypic Simulation: A Quantitative Constraint-Based Simulation Method That Accommodates All Main Strain Design Strategies

scientific article published on 15 April 2019

UV spectrophotometry method for the monitoring of galacto-oligosaccharides production

article

Virtual laboratories in (bio)chemical engineering education

What is the relationship between intracellular and extracellular metabolites? The theory of “metabolic overflow” put into test

scholarly article by Silas Villas-Boas published in July 2014

Yeast Metabolomics: Sample Preparation for a GC/MS-Based Analysis

Yeast metabolic chassis designs for diverse biotechnological products

scientific article published on 19 July 2016

iOD907, the first genome-scale metabolic model for the milk yeast Kluyveromyces lactis.

scientific article published on 22 May 2014

Paulina is supported by:

About Paulina

Help