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List of works by Eugénio C. Ferreira

10th International Chemical and Biological Engineering Conference – CHEMPOR 2008 – Integrating Life Sciences & Engineering Special Section

@Note: a workbench for biomedical text mining

scientific article published on 22 April 2009

A Comparative Proteome Analysis of Escherichia coli ΔrelA Mutant Cells.

scientific article published on 27 October 2016

A Comparison between bright field and phase-contrast image analysis techniques in activated sludge morphological characterization.

scientific article published on 26 January 2010

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

Activated sludge characterization through microscopy: a review on quantitative image analysis and chemometric techniques.

scientific article published on 16 September 2013

Activated sludge process monitoring through in situ near-infrared spectral analysis.

scientific article published in January 2008

An Overview of the Evolution of Infrared Spectroscopy Applied to Bacterial Typing.

scientific article published in November 2017

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

Automated image analysis to improve bead ingestion toxicity test counts in the protozoan Tetrahymena pyriformis.

scientific article published in January 2003

Automatic identification of activated sludge disturbances and assessment of operational parameters.

scientific article published on 26 January 2013

BioDR: Semantic indexing networks for biomedical document retrieval

Biomedical Text Mining Applied to Document Retrieval and Semantic Indexing

COVID-19, Chikungunya, Dengue and Zika Diseases: An Analytical Platform Based on MALDI-TOF MS, IR Spectroscopy and RT-qPCR for Accurate Diagnosis and Accelerate Epidemics Control

scientific article published on 30 March 2021

Challenges in integrating Escherichia coli molecular biology data

scientific article

Characterization of activated sludge abnormalities by image analysis and chemometric techniques

scientific article published on 12 June 2011

Correction: Population Dynamics of a Salmonella Lytic Phage and Its Host: Implications of the Host Bacterial Growth Rate in Modelling

scientific article published on 25 August 2015

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

scientific article

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

Determination of diffusion coefficients of glycerol and glucose from starch based thermoplastic compounds on simulated physiological solution.

scientific article published in March 2005

Development of a method using image analysis for the measurement of cellulose-binding domains adsorbed onto cellulose fibers.

scientific article published on 8 November 2007

Development of an image analysis procedure for identifying protozoa and metazoa typical of activated sludge system.

scientific article

Development of image analysis techniques as a tool to detect and quantify morphological changes in anaerobic sludge: I. Application to a granulation process.

scientific article published in July 2004

Development of image analysis techniques as a tool to detect and quantify morphological changes in anaerobic sludge: II. Application to a granule deterioration process triggered by contact with oleic acid.

scientific article published in July 2004

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

Dilution and magnification effects on image analysis applications in activated sludge characterization

scientific article published on 31 August 2010

Discrimination of clinically relevant Candida species by Fourier-transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR)

scholarly article in RSC Advances, vol. 6 no. 94, 2016

Economic analysis and environmental impact assessment of three different fermentation processes for fructooligosaccharides production.

scientific article published on 26 September 2015

Effect of hyperbaric stress on yeast morphology: study by automated image analysis

article

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

scientific article published on 18 June 2003

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

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

article

Exploiting intrinsic fluorescence spectroscopy to discriminate between Acinetobacter calcoaceticus–Acinetobacter baumannii complex species

article

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

scientific article published on 28 January 2012

FT-NIR spectroscopy analysis for monitoring the microbial production of 2-phenylethanol using crude glycerol as carbon source

scientific article published in 2022

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

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

scientific article published on 10 March 2010

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

Identifying different types of bulking in an activated sludge system through quantitative image analysis.

scientific article

Image analysis application for the study of activated sludge floc size during the treatment of synthetic and real fishery wastewaters.

scientific article

Image analysis technique as a tool to identify morphological changes in Trametes versicolor pellets according to exopolysaccharide or laccase production.

scientific article published on 13 December 2013

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

scientific article published on 12 October 2012

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

Kinetic and stoichiometric characterization of a fixed biofilm reactor by pulse respirometry ⬇️

scientific article published on 09 November 2011

Kinetic and stoichiometric parameters estimation in a nitrifying bubble column through "in-situ" pulse respirometry.

scientific article published in May 2008

Knowledge-based fuzzy system for diagnosis and control of an integrated biological wastewater treatment process.

scientific article

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

Life cycle assessment of bacterial cellulose production

scientific article published in 2021

Mapping Salmonella typhimurium pathways using 13C metabolic flux analysis

scientific article published on 04 December 2018

Merlin: Metabolic Models Reconstruction using Genome-Scale Information*

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 responses to recombinant bioprocesses in Escherichia coli ⬇️

scientific article published on September 26, 2012

Modeling formalisms in Systems Biology

scientific article published on 05 December 2011

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

Molecular aspects and comparative genomics of bacteriophage endolysins.

scientific article published on 13 February 2013

Monitoring intracellular polyphosphate accumulation in enhanced biological phosphorus removal systems by quantitative image analysis

scientific article published on January 2014

Monitoring of activated sludge settling ability through image analysis: validation on full-scale wastewater treatment plants.

scientific article published on 23 August 2008

Morphological analysis of Yarrowia lipolytica under stress conditions through image processing

scientific article published on 02 April 2003

Morphology and physiology of anaerobic granular sludge exposed to an organic solvent

scientific article published on 09 January 2009

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

scientific article

Near-infrared spectroscopy for the detection and quantification of bacterial contaminations in pharmaceutical products

scientific article published on 4 July 2015

New PLS analysis approach to wine volatile compounds characterization by near infrared spectroscopy (NIR).

scientific article published on 6 November 2017

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

scientific article

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

Polyhydroxyalkanoate granules quantification in mixed microbial cultures using image analysis: Sudan Black B versus Nile Blue A staining.

scientific article published on 14 January 2015

Population dynamics of a Salmonella lytic phage and its host: implications of the host bacterial growth rate in modelling

scientific article

Prediction of intracellular storage polymers using quantitative image analysis in enhanced biological phosphorus removal systems ⬇️

scientific article published on February 16, 2013

Principal component analysis and quantitative image analysis to predict effects of toxics in anaerobic granular sludge.

scientific article published on 19 October 2008

Quantification of pharmaceutical compounds in wastewater samples by near infrared spectroscopy (NIR)

scientific article published on 24 October 2018

Quantification of the CBD-FITC conjugates surface coating on cellulose fibres.

scientific article published on 9 January 2008

Quantitative image analysis as a diagnostic tool for monitoring structural changes of anaerobic granular sludge during detergent shock loads.

scientific article

Quantitative image analysis as a tool for Yarrowia lipolytica dimorphic growth evaluation in different culture media.

scientific article published on 3 November 2015

Quantitative image analysis for the characterization of microbial aggregates in biological wastewater treatment: a review.

scientific article published on 29 May 2013

Quantitative image analysis of polyhydroxyalkanoates inclusions from microbial mixed cultures under different SBR operation strategies.

scientific article

Quantitative monitoring of an activated sludge reactor using on-line UV-visible and near-infrared spectroscopy

scientific article published on 24 August 2009

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 published on September 15, 2012

Reconstructing High-Quality Large-Scale Metabolic Models with merlin

scientific article published in January 2018

Reconstructing genome-scale metabolic models with merlin

scientific article published on 6 April 2015

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

scientific article published on 22 June 2015

Selection and Characterization of a Multivalent Salmonella Phage and Its Production in a Nonpathogenic Escherichia coli Strain ⬇️

scientific article published on September 3, 2010

Selection of Elementary Modes for Bioprocess Control

Semantic annotation of biological concepts interplaying microbial cellular responses

scientific article

Simultaneous partial nitrification and 2-fluorophenol biodegradation with aerobic granular biomass: Reactor performance and microbial communities.

scientific article

Stalked protozoa identification by image analysis and multivariable statistical techniques.

scientific article published on 8 March 2008

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

article

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

scientific article published on 30 December 2011

The use of antibiotics to improve phage detection and enumeration by the double-layer agar technique

scientific article published on 23 July 2009

Virtual laboratories in (bio)chemical engineering education

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

scientific article published on 22 May 2014

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