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List of works by Miguel Rocha

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

scientific article
Modeling formalisms in Systems Biology

scientific article published on 05 December 2011
Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models

scientific article published on 25 March 2013
Natural computation meta-heuristics for the in silico optimization of microbial strains

scientific article
Transcript level and sequence determinants of protein abundance and noise in Escherichia coli

scientific article published on 07 February 2014
In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories

scientific article
Reconstructing genome-scale metabolic models with merlin

scientific article published on 6 April 2015
Metabolomics combined with chemometric tools (PCA, HCA, PLS-DA and SVM) for screening cassava (Manihot esculenta Crantz) roots during postharvest physiological deterioration.

scientific article published in April 2014
Evolving Time Series Forecasting ARMA Models

AIBench: a rapid application development framework for translational research in biomedicine

scientific article published on 4 January 2010
Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach

scientific article
An R package for the integrated analysis of metabolomics and spectral data

scientific article
Methods for automated genome-scale metabolic model reconstruction

scientific article published on 31 July 2018
@Note: a workbench for biomedical text mining

scientific article published on 22 April 2009
A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information

scientific article published on December 7, 2010
D-Tailor: automated analysis and design of DNA sequences

scientific article
Genome-Wide Semi-Automated Annotation of Transporter Systems

scientific article
An integrated network visualization framework towards metabolic engineering applications

scientific article
The role of ascorbate peroxidase, guaiacol peroxidase, and polysaccharides in cassava (Manihot esculenta Crantz) roots under postharvest physiological deterioration.

scientific article published on 6 November 2015
Evolution of neural networks for classification and regression

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

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

scientific article published in February 2012
Development and application of efficient pathway enumeration algorithms for metabolic engineering applications

scientific article published on 4 December 2014
Discrimination of Brazilian propolis according to the seasoning using chemometrics and machine learning based on UV-Vis scanning data

scientific article published on October 21, 2015
Analysing Algorithms and Data Sources for the Tissue-Specific Reconstruction of Liver Healthy and Cancer Cells

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

scholarly article published October 2008
Quality of Service constrained routing optimization using Evolutionary Computation

article by Miguel Rocha et al published January 2011 in Applied Soft Computing
An integrated computational environment for elementary modes analysis of biochemical networks

scientific article published in January 2012
Predicting promoters in phage genomes using PhagePromoter

scientific article published on 01 December 2019
Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data

scientific article published on March 18, 2016
Challenges in integrating Escherichia coli molecular biology data

scientific article
Semantic annotation of biological concepts interplaying microbial cellular responses

scientific article
Data supporting the role of enzymes and polysaccharides during cassava postharvest physiological deterioration

scientific article
Transcriptional profiling of HOXA9-regulated genes in human glioblastoma cell models

scientific article published on 19 May 2015
Metabolic Profiling and Classification of Propolis Samples from Southern Brazil: An NMR-Based Platform Coupled with Machine Learning.

scientific article published on 22 December 2015
Symbiotic filtering for spam email detection

Toward better understanding of postharvest deterioration: biochemical changes in stored cassava (Manihot esculenta Crantz) roots

scientific article published on 26 October 2015
A Critical Evaluation of Methods for the Reconstruction of Tissue-Specific Models

An integrated framework for strain optimization

A Comparative Impact Study of Attribute Selection Techniques on Naïve Bayes Spam Filters

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
Transcript-based reannotation for microarray probesets

Merlin: Metabolic Models Reconstruction using Genome-Scale Information*

WebSpecmine: A Website for Metabolomics Data Analysis and Mining

scientific article published on 19 October 2019
UV-Vis and CIELAB Based Chemometric Characterization of Manihot esculenta Carotenoid Contents.

scientific article published on 13 December 2017
The long non-coding RNA HOTAIR is transcriptionally activated by HOXA9 and is an independent prognostic marker in patients with malignant glioma.

scientific article published on 28 February 2018
Implementing Metaheuristic Optimization Algorithms with JECoLi

scholarly article published 2009
A Chemometrics Approach for Nuclear Magnetic Resonance Data to Characterize the Partial Metabolome Banana Peels from Southern Brazil.

scientific article published on 13 December 2017
Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis

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

article

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