Miguel Rocha

Miguel Rocha, Jorge Henrique Martins de Pinho, João Luís Ferreira Sobral, 2010, 2010 18th Euromicro Conference on Parallel, Distributed and Network-based Processing.

Model‐guided development of an evolutionarily stable yeast chassis

P. Kötter, P. Jouhten, K. Patil, 2021, Molecular systems biology.

Reconstruction of tissue-specific genome-scale metabolic models for human cancer stem cells

Miguel Rocha, R. Neves, Tânia Barata, 2021, Comput. Biol. Medicine.

DNA Microarrays: Fundamentals, Data Integration and Applications

Miguel Rocha, Eduardo Valente, Miguel Rocha, 2019, Encyclopedia of Biomedical Engineering.

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

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2009 .

Reconstructing High-Quality Large-Scale Metabolic Models with merlin.

Miguel Rocha, Isabel Rocha, Oscar Dias, 2018, Methods in molecular biology.

Computational Tools for the Analysis of 2D-Nuclear Magnetic Resonance Data

Miguel Rocha, Marcelo Maraschin, Bruno Pereira, 2021, PACBB.

A Review on Metabolomics Data Analysis for Cancer Applications

Miguel Rocha, Sara Cardoso, Delora Baptista, 2018, PACBB.

UV-Visible Spectrophotometry-Based Metabolomic Analysis of Cedrela Fissilis Velozzo (Meliaceae) Calluses - A Screening Tool for Culture Medium Composition and Cell Metabolic Profiles

Miguel Rocha, Marcelo Maraschin, Fernanda Kokowicz Pilatti, 2015, PACBB.

WebSpecmine: A Website for Metabolomics Data Analysis and Mining

Miguel Rocha, Telma Afonso, Sara Cardoso, 2019, Metabolites.

Towards the Reconstruction of Integrated Genome-Scale Models of Metabolism and Gene Expression

Miguel Rocha, Oscar Días, Diogo Lima, 2019, PACBB.

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

Miguel Rocha, Isabel Rocha, Paulo Maia, 2019, BMC Bioinformatics.

Analyzing and Designing Cell Factories with OptFlux.

Miguel Rocha, Isabel Rocha, Paulo Maia, 2018, Methods in molecular biology.

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

Miguel Rocha, Paulo Maia, Isabel Rocha, 2017, GECCO.

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

Miguel Rocha, Paulo Maia, Isabel Rocha, 2014, BMC Systems Biology.

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

Miguel Rocha, Paulo Vilaça, Rui Mendes, 2014, 2014 Sixth World Congress on Nature and Biologically Inspired Computing (NaBIC 2014).

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

I. Rocha, J. P. Pinto, Miguel Rocha, 2013, BMC Research Notes.

Optimization Approaches for the In Silico Discovery of Optimal Targets for Gene Over/Underexpression

Rui Pereira, Miguel Rocha, Isabel Rocha, 2012, J. Comput. Biol..

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

Miguel Rocha, Isabel Rocha, Emanuel J. V. Gonçalves, 2012, PACBB.

OptGene: a framework for in silico metabolic engineering

E. Ferreira, I. Rocha, Paulo Maia, 2008 .

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

Miguel Rocha, João Cardoso, Paulo Vilaça, 2012, PRIB.

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

Miguel Rocha, João Cardoso, Isabel Rocha, 2013, BMC Research Notes.

Highlighting Metabolic Strategies Using Network Analysis over Strain Optimization Results

Miguel Rocha, Isabel Rocha, José P. Pinto, 2011, PRIB.

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

Miguel Rocha, Florentino Fernández Riverola, Daniel Glez-Peña, 2010, Comput. Methods Programs Biomed..

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

Miguel Rocha, Eugénio C. Ferreira, Jens Nielsen, 2008, BMC Bioinformatics.

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

Miguel Rocha, Marcelo Maraschin, Christopher Costa, 2015, PACBB.

SamPler – a novel method for selecting parameters for gene functional annotation routines

Eugénio C. Ferreira, Isabel Rocha, Fernando Cruz, 2019, BMC Bioinformatics.

13C-based metabolic flux analysis

Miguel Rocha, Sónia Carneiro, Rafael Carreira, 2012 .

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

Miguel Rocha, Marcelo Maraschin, Bianca Coelho, 2014, PACBB.

A Critical Evaluation of Automatic Atom Mapping Algorithms and Tools

Miguel Rocha, Paulo Vilaça, Nuno Osório, 2017, PACBB.

Semantic annotation of biological concepts interplaying microbial cellular responses

Rui Pereira, Miguel Rocha, Eugénio C. Ferreira, 2011, BMC Bioinformatics.

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

Miguel Rocha, Eugénio C. Ferreira, Paulo Maia, 2008, 2008 8th IEEE International Conference on BioInformatics and BioEngineering.

WebSpecmine: a website for metabolomics data analysis and mining.

Miguel Rocha, Sara Cardoso, Marcelo Maraschin, 2018, Proceedings of 3rd International Electronic Conference on Metabolomics.

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models

Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga, 2017, PLoS Comput. Biol..

Banana ( Musa spp .) as a Source of Bioactive Compounds for Health Promotion

Miguel Rocha, M. Maraschin, C. V. Borges, 2020 .

An ontology-based approach to systems biology literature retrieval and processing

Miguel Rocha, Eugénio C. Ferreira, José João Almeida, 2007 .

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

Miguel Rocha, Paulo Maia, Emanuel J. V. Gonçalves, 2011, EANN/AIAI.

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

David Henriques, Miguel Rocha, Julio Saez-Rodriguez, 2015, Bioinform..

Algorithms to infer metabolic flux ratios from fluxomics data

Miguel Rocha, Rafael Carreira, Silas Granato Villas-Bôas, 2013, 2013 IEEE International Conference on Bioinformatics and Biomedicine.

Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living, 10th International Work-Conference on Artificial Neural Networks, IWANN 2009 Workshops, Salamanca, Spain, June 10-12, 2009. Proceedings, Part II

Juan M. Corchado, Emilio Corchado, Miguel Rocha, 2009, IWANN.

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

Miguel Rocha, Sara Correia, Miguel Rocha, 2015, EPIA.

MEWpy: a computational strain optimization workbench in Python

Miguel Rocha, Vitor Pereira, Fernando Cruz, 2021, Bioinform..

Re-annotation of the genome sequence of Helicobacter pylori 26695

Miguel Rocha, Isabel Rocha, Tiago Resende, 2013, J. Integr. Bioinform..

Re-annotation of the genome sequence of Helicobacter pylori 26695

I. Rocha, Miguel Rocha, D. Correia, 2013, Journal of integrative bioinformatics.

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

Miguel Rocha, Rúben Rodrigues, Vítor Vieira, 2018, J. Integr. Bioinform..

Metabolite Integration Pipeline for the Improvement of Human Metabolic Models

Miguel Rocha, Rúben Rodrigues, Jorge Ferreira, 2018, PACBB.

An integrated framework for strain optimization

Miguel Rocha, Paulo Maia, Isabel Rocha, 2013, 2013 IEEE Congress on Evolutionary Computation.

An integrated computational environment for elementary modes analysis of biochemical networks

Miguel Rocha, Paulo Maia, Isabel Rocha, 2012, Int. J. Data Min. Bioinform..

In silico strain optimization by adding reactions to metabolic models

Miguel Rocha, Sara Correia, Miguel Rocha, 2012, J. Integr. Bioinform..

OptFlux: a software for metabolic engineering

Jens Nielsen, Paulo Maia, Isabel Rocha, 2009 .

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

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2009, IWANN.

Network Visualization Tools to Enhance Metabolic Engineering Platforms

Miguel Rocha, Paulo Vilaça, Alberto Noronha, 2013, PACBB.

Computational Tools for Strain Optimization by Adding Reactions

Miguel Rocha, Sara Correia, Miguel Rocha, 2012, PACBB.

In silico strain optimization by adding reactions to metabolic models

Miguel Rocha, S. Correia, 2012, Journal of integrative bioinformatics.

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

Miguel Rocha, Paulo Maia, Isabel Rocha, 2010, IWPACBB.

Merlin: Metabolic Models Reconstruction using Genome-Scale Information*

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2010 .

HABIT – a Webserver for interactive T cell neoepitope discovery

Miguel Rocha, Vítor Vieira, Joana S. Martins, 2019, bioRxiv.

A framework for the development of Biomedical Text Mining software tools

Eugénio C. Ferreira, Miguel Rocha, Anália Lourenço, 2008, 2008 8th IEEE International Conference on BioInformatics and BioEngineering.

Genome-Wide Semi-Automated Annotation of Transporter Systems

Miguel Rocha, Eugénio C. Ferreira, João Cardoso, 2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

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

I. Rocha, Paulo Maia, Miguel Rocha, 2017, Interdisciplinary Sciences: Computational Life Sciences.

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

Miguel Rocha, Paulo Maia, Isabel Rocha, 2016, PACBB.

Large Scale Metabolic Characterization Using Flux Balance Analysis and Data Mining

Miguel Rocha, Miguel Rocha, 2013, ICANNGA.

A Study of the Short and Long-term Regulation of E. coli Metabolic Pathways

E. Ferreira, I. Rocha, J. P. Pinto, 2011, J. Integr. Bioinform..

Interpreting the Regulatory Interplay in E. coli Metabolic Pathways

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2011, PACBB.

A framework for the integrated analysis of metabolic and regulatory networks

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2008, 2008 8th IEEE International Conference on BioInformatics and BioEngineering.

Analysis of the Effect of Reversibility Constraints on the Predictions of Genome-Scale Metabolic Models

Miguel Rocha, Rick L. Stevens, Christopher S. Henry, 2010, IWPACBB.

Model Transformation of Metabolic Networks using a Petri Net Based Framework

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2010, ACSD/Petri Nets Workshops.

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

I. Rocha, Paulo Maia, Miguel Rocha, 2019, BMC Bioinformatics.

Discrimination of Brazilian propolis according to the seasoning using chemometrics and machine learning based on UV-Vis scanning data

Miguel Rocha, Marcelo Maraschin, Christopher Costa, 2015, J. Integr. Bioinform..

Discrimination of Brazilian propolis according to the seasoning using chemometrics and machine learning based on UV-Vis scanning data

Miguel Rocha, M. Maraschin, R. Moresco, 2015, Journal of integrative bioinformatics.

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

Miguel Rocha, Marcelo Maraschin, Christopher Costa, 2016, Comput. Methods Programs Biomed..

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

Miguel Rocha, Marcelo Maraschin, Rafael Carreira, 2012, PRIB.

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

Miguel Rocha, João Carlos Sequeira, Maria Madalena Alves, 2018, PACBB.

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

Miguel Rocha, Eduardo Valente, Miguel Rocha, 2015, PACBB.

Troppo - A Python Framework for the Reconstruction of Context-Specific Metabolic Models

Miguel Rocha, Jorge Gomes, Jorge Ferreira, 2019, PACBB.

Challenges in integrating Escherichia coli molecular biology data

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2011, Briefings Bioinform..

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

Miguel Rocha, Isabel Rocha, José P. Pinto, 2010, BCB '10.

COMPUTATIONAL TOOLS FOR DATA INTEGRATION AND REGULATORY NETWORK INFERENCE IN SYSTEMS BIOLOGY

Miguel Rocha, Isabel Rocha, José P. Pinto, 2010 .

Uncovering mechanisms underlying the Escherichia coli stringent response : application of text mining approaches to identify meaningful relations in text documents

E. Ferreira, I. Rocha, Miguel Rocha, 2009 .

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

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2009, IWANN.

ViralFP: A webserver of viral fusion proteins

Miguel Rocha, D. Lousa, Pedro Moreira, 2021, 2103.14754.

17α-Ethinylestradiol Analysis of Endo- and Exometabolome of Ulva lactuca (Chlorophyta) by 1H-NMR Spectroscopy and Bioinformatics Tools

Miguel Rocha, Sara Cardoso, Marcelo Maraschin, 2018, PACBB.

Artificial Intelligence in Biological Activity Prediction

Miguel Rocha, Tiago Resende, João Correia, 2019, PACBB.

Machine Learning-Enhanced T Cell Neoepitope Discovery for Immunotherapy Design

Joana S. Martins, Miguel Rocha, Carlos Magalhães, 2019, Cancer informatics.

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

Miguel Rocha, Isabel Rocha, Eduardo Valente, 2008, IWPACBB.

Implementing Metaheuristic Optimization Algorithms with JECoLi

Miguel Rocha, Paulo Maia, Pedro Evangelista, 2009, 2009 Ninth International Conference on Intelligent Systems Design and Applications.

Development of an information retrieval tool for biomedical patents

Miguel Rocha, H. Costa, Rúben Rodrigues, 2018, Comput. Methods Programs Biomed..

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

Miguel Rocha, Vítor Vieira, Miguel Rocha, 2019, Bioinform..

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

Miguel Rocha, Isabel Rocha, Paulo Vilaça, 2015, Comput. Methods Programs Biomed..

Evaluating Pathway Enumeration Algorithms in Metabolic Engineering Case Studies

Miguel Rocha, Isabel Rocha, Paulo Vilaça, 2014, PACBB.

Analyzing and Designing Cell Factories with OptFlux.

I. Rocha, Paulo Maia, Paulo Vilaça, 2018, Methods in molecular biology.

Combining syntactic and ontological knowledge to extract biologically relevant relations from scientific papers

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2009 .

A tool for the automatic and manual annotation of biomedical documents

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2008, SMBM 2008.

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

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2014, Expert Syst. Appl..

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

Eva Regina de Oliveira, Miguel Rocha, M. Maraschin, 2017, Marine pollution bulletin.

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

Miguel Rocha, M. Maraschin, V. Uarrota, 2016, Food chemistry.

Evolutionary computation for predicting optimal reaction knockouts and enzyme modulation strategies

Miguel Rocha, Isabel Rocha, Pedro Evangelista, 2013, 2013 IEEE Congress on Evolutionary Computation.

Metaheuristics for Strain Optimization Using Transcriptional Information Enriched Metabolic Models

Miguel Rocha, Paulo Maia, Isabel Rocha, 2010, EvoBIO.

Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains

Miguel Rocha, Eugénio C. Ferreira, Paulo Maia, 2007, EPIA Workshops.

Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2007, 2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology.

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

Miguel Rocha, Marcelo Maraschin, Telma Afonso, 2017, PACBB.

BioDR: Semantic indexing networks for biomedical document retrieval

Eugénio C. Ferreira, Luis Mateus Rocha, Miguel Rocha, 2010, Expert Syst. Appl..