Search filters

List of works by Miguel Rocha

10th International Conference on Practical Applications of Computational Biology & Bioinformatics

7th International Conference on Practical Applications of Computational Biology & Bioinformatics

8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014)

9th International Conference on Practical Applications of Computational Biology and Bioinformatics

@Note: a workbench for biomedical text mining

scientific article published on 22 April 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

A Collaborative Approach for Spam Detection

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

A Critical Evaluation of Methods for the Reconstruction of Tissue-Specific Models

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

A Framework for Robust Traffic Engineering Using Evolutionary Computation

article published in 2013

A Machine Learning and Chemometrics Assisted Interpretation of Spectroscopic Data – A NMR-Based Metabolomics Platform for the Assessment of Brazilian Propolis

article

A Model Integration Pipeline for the Improvement of Human Genome-Scale Metabolic Reconstructions

scientific article published on 21 December 2018

A Software Platform for Evolutionary Computation with Pluggable Parallelism and Quality Assurance

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

A Study of Order Based Genetic and Evolutionary Algorithms in Combinatorial Optimization Problems

A Study on the Robustness of Strain Optimization Algorithms

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 December 7, 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 pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale

scientific article published on 24 June 2022

A platform for the selection of genes in DNA microarraydata using evolutionary algorithms

article

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

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

scientific article published on 4 January 2010

Algorithms to infer metabolic flux ratios from fluxomics data

An Algorithm to Assemble Gene-Protein-Reaction Associations for Genome-Scale Metabolic Model Reconstruction

article

An Integrated Computational Platform for Metabolomics Data Analysis

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

scientific article

An integrated computational environment for elementary modes analysis of biochemical networks

scientific article published in January 2012

An integrated framework for strain optimization

An integrated network visualization framework towards metabolic engineering applications

scientific article

Analysing Algorithms and Data Sources for the Tissue-Specific Reconstruction of Liver Healthy and Cancer Cells

scientific article

Analyzing and Designing Cell Factories with OptFlux

scientific article published in January 2018

Automated Network Resilience Optimization Using Computational Intelligence Methods

Automating the Extraction of Essential Genes from Literature

article

Biomedical Text Mining Applied to Document Retrieval and Semantic Indexing

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models

scientific article published on 25 March 2013

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

scientific article

Carotenoid Analysis of Cassava Genotypes Roots (Manihot Esculenta Crantz) Cultivated in Southern Brazil Using Chemometric Tools

article

Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses

scientific article published on 01 January 2021

Challenges in integrating Escherichia coli molecular biology data

scientific article

Classification Tools for Carotenoid Content Estimation in Manihot esculenta via Metabolomics and Machine Learning

scientific article

CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models

scientific article published on 01 December 2019

Comparison of Single and Multi-objective Evolutionary Algorithms for Robust Link-State Routing

Comparison of pathway analysis and constraint-based methods for cell factory design

scientific article published on 20 June 2019

Computational Tools for Strain Optimization by Adding Reactions

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

article

D-Tailor: automated analysis and design of DNA sequences

scientific article

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

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

scientific article

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

scientific article published on 4 December 2014

Development of Text Mining Tools for Information Retrieval from Patents

article

Development of a Machine Learning Framework for Biomedical Text Mining

article

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

article

Development of an information retrieval tool for biomedical patents

scientific article published on 14 March 2018

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

Discrimination of Brazilian Cassava Genotypes (Manihot esculenta Crantz) According to Their Physicochemical Traits and Functional Properties through Bioinformatics Tools

article

EMAIL SPAM DETECTION: A SYMBIOTIC FEATURE SELECTION APPROACH FOSTERED BY EVOLUTIONARY COMPUTATION

article published in 2013

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

Evolution of neural networks for classification and regression

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

Evolving Time Series Forecasting ARMA Models

Genome-Wide Semi-Automated Annotation of Transporter Systems

scientific article

Highlighting Metabolic Strategies Using Network Analysis over Strain Optimization Results

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

Implementing Metaheuristic Optimization Algorithms with JECoLi

scholarly article published 2009

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

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

In vitro exposure of Ulva lactuca Linnaeus (Chlorophyta) to gasoline - Biochemical and morphological alterations

scientific article

MEWpy: a computational strain optimization workbench in Python

scientific article published in 2021

MOSCA: An Automated Pipeline for Integrated Metagenomics and Metatranscriptomics Data Analysis

Merlin: Metabolic Models Reconstruction using Genome-Scale Information*

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

Metabolite Integration Pipeline for the Improvement of Human Metabolic Models

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

Metabolomics of Ulva lactuca Linnaeus (Chlorophyta) exposed to oil fuels: Fourier transform infrared spectroscopy and multivariate analysis as tools for metabolic fingerprint.

scientific article published on 12 November 2016

Metagenomic Analysis of the Saliva Microbiome with Merlin

Methods for automated genome-scale metabolic model reconstruction

scientific article published on 31 July 2018

Microarray Gene Expression Data Integration: An Application to Brain Tumor Grade Determination

article

Mixed-Integer Programming Model for Profiling Disease Biomarkers from Gene Expression Studies

article

Modeling formalisms in Systems Biology

scientific article published on 05 December 2011

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

Multi-scale Internet traffic forecasting using neural networks and time series methods

Multiobjective Evolutionary Algorithms for intradomain routing optimization

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

scientific article

Network Visualization Tools to Enhance Metabolic Engineering Platforms

scholarly article by Alberto Noronha et al published 2013 in Advances in Intelligent Systems and Computing

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

scientific 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

Parallel evolutionary computation in bioinformatics applications

scientific article

Pluggable Parallelization of Evolutionary Algorithms Applied to the Optimization of Biological Processes

Predicting promoters in phage genomes using PhagePromoter

scientific article published on 01 December 2019

Quality of Service constrained routing optimization using Evolutionary Computation

article by Miguel Rocha et al published January 2011 in Applied Soft Computing

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

Reconstructing transcriptional Regulatory Networks using data integration and Text Mining

Reconstruction of Metabolic Models for Liver Cancer Cells

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

scientific article

Reg4OptFlux: an OptFlux plug-in that comprises meta-heuristics approaches for Metabolic engineering using integrated models

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach

scientific article

Robust Optimization of Intradomain Routing Using Evolutionary Algorithms

Semantic annotation of biological concepts interplaying microbial cellular responses

scientific article

Spam Email Filtering Using Network-Level Properties

Symbiotic Data Mining for Personalized Spam Filtering

Symbiotic filtering for spam email detection

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

scientific article

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

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

Time Series Forecasting by Evolutionary Neural Networks

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

scientific article published on 26 October 2015

Traffic Engineering Approaches Using Multicriteria Optimization Techniques

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

scientific article published on 07 February 2014

Transcript-based reannotation for microarray probesets

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

scientific article published on 19 May 2015

UV-Vis and CIELAB Based Chemometric Characterization of Manihot esculenta Carotenoid Contents.

scientific article published on 13 December 2017

UV-Visible Scanning Spectrophotometry and Chemometric Analysis as Tools to Build Descriptive and Classification Models for Propolis from Southern Brazil

article

UV-visible scanning spectrophotometry and chemometric analysis as tools for carotenoids analysis in cassava genotypes (Manihot esculenta Crantz).

scientific article published on 21 October 2015

WebSpecmine: A Website for Metabolomics Data Analysis and Mining

scientific article published on 19 October 2019

getALife - An Artificial Life Environment for the Evaluation of Agent-Based Systems and Evolutionary Algorithms for Reinforcement Learning

scholarly article published in Studies in Computational Intelligence

Paulina is supported by:

About Paulina

Help