Reconstruction of cell-specific models capturing the influence of metabolism on DNA methylation in cancer

Computers in Biology and Medicine

2024 | journal-article

A diel multi-tissue genome-scale metabolic model ofVitis vinifera

2024 | preprint

BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models

IEEE/ACM Transactions on Computational Biology and Bioinformatics

2024 | journal-article

Combining Evolutionary Algorithms with Reaction Rules Towards Focused Molecular Design

2023 | conference-paper

A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer

PLOS Computational Biology

2023 | journal-article

Preface

Lecture Notes in Networks and Systems

2023 | book

Evaluating molecular representations in machine learning models for drug response prediction and interpretability

Journal of Integrative Bioinformatics

2022 | journal-article

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

PLOS Computational Biology

2022 | journal-article

merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models

Nucleic Acids Research

2022 | journal-article

A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer

2022 | preprint

A Comparison of Different Compound Representations for Drug Sensitivity Prediction

Lecture Notes in Networks and Systems

2022 | book

A comparison of multi-objective optimization algorithms for weight setting problems in traffic engineering

Natural Computing

2022 | journal-article

BioTMPy: A Deep Learning-Based Tool to Classify Biomedical Literature

Lecture Notes in Networks and Systems

2022 | book

Combinatorial Optimization of Succinate Production in Escherichia coli

Lecture Notes in Networks and Systems

2022 | book

Computational Methods for the Identification of Genetic Variants in Complex Diseases

Lecture Notes in Networks and Systems

2022 | conference-paper

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

Lecture Notes in Networks and Systems

2022 | book

Preface

Lecture Notes in Networks and Systems

2022 | book

ProPythia: A Python package for protein classification based on machine and deep learning

Neurocomputing

2022 | journal-article

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

Computers in Biology and Medicine

2022 | journal-article

Recurrent Deep Neural Networks for Enzyme Functional Annotation

Lecture Notes in Networks and Systems

2022 | book

MEWpy: a computational strain optimization workbench in Python

Bioinformatics

2021 | journal-article

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

Molecular Systems Biology

2021 | journal-article

Deep learning for drug response prediction in cancer

Briefings in Bioinformatics

2021 | journal-article

Model-guided development of an evolutionarily stable yeast chassis

Molecular Systems Biology

2021 | journal-article

NMRFinder: a novel method for 1D ¹H-NMR metabolite annotation

Metabolomics

2021 | journal-article

Optimizing NFV deployment in Segment Routing,Otimização de implementações NFV em Segment Routing

Iberian Conference on Information Systems and Technologies, CISTI

2021 | conference-paper

Preface

Advances in Intelligent Systems and Computing

2021 | book

ProPythia: A Python Automated Platform for the Classification of Proteins Using Machine Learning

Advances in Intelligent Systems and Computing

2021 | book

R2L: Routing with Reinforcement Learning

Proceedings of the International Joint Conference on Neural Networks

2021 | conference-paper

Reconciliation of Regulatory Data: The Regulatory Networks of Escherichia coli and Bacillus subtilis

Advances in Intelligent Systems and Computing

2021 | conference-paper

The first multi-tissue diel genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber

bioRxiv

2021 | other

ViralFP: A webserver of viral fusion proteins

arXiv

2021 | other

A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation

Biochemical Society Transactions

2020 | journal-article

Artificial Intelligence in Biological Activity Prediction

Advances in Intelligent Systems and Computing

2020 | book

Botanical source investigation and evaluation of the effect of seasonality on Brazilian propolis from Apis mellifera L.

Scientia Agricola

2020 | journal-article

Metabolomic fingerprinting as a powerful diagnostic tool to assess the effects of abiotic stress in plants and seeds

CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources

2020 | journal-article

Predicting Promoters in Phage Genomes Using Machine Learning Models

Advances in Intelligent Systems and Computing

2020 | book

Preface

Advances in Intelligent Systems and Computing

2020 | book

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

Advances in Intelligent Systems and Computing

2020 | book

Traffic Engineering with Three-Segments Routing

IEEE Transactions on Network and Service Management

2020 | journal-article

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

2020 | book-chapter

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

Bioinformatics

2019 | journal-article

Predicting promoters in phage genomes using PhagePromoter

Bioinformatics

2019 | journal-article

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

BMC Bioinformatics

2019 | journal-article

WebSpecmine: A Website for Metabolomics Data Analysis and Mining

Metabolites

2019 | journal-article

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

Journal of Integrative Bioinformatics

2019 | journal-article

Selected Extended Papers of the 12th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB)

Journal of Integrative Bioinformatics

2019 | journal-article

HABIT – a webserver for interactive T cell neoepitope discovery

2019 | other

17α-ethinylestradiol analysis of endo- and exometabolome of ulva lactuca (chlorophyta) by ¹H-NMR spectroscopy and bioinformatics tools

Advances in Intelligent Systems and Computing

2019 | conference-paper

A review on metabolomics data analysis for cancer applications

Advances in Intelligent Systems and Computing

2019 | book

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Nature Communications

2019 | journal-article

DNA microarrays: Fundamentals, data integration and applications

Encyclopedia of Biomedical Engineering

2019 | book-chapter

Deep Neural Networks for Network Routing

Proceedings of the International Joint Conference on Neural Networks

2019 | conference-paper

Hybrid IP/SDN Routing for Inter-Data Center Communications

Proceeding of the 2019 IEEE 8th International Conference on Cloud Networking, CloudNet 2019

2019 | conference-paper

In silico predictions for fucoxanthin production by the diatom phaeodactylum tricornutum

Advances in Intelligent Systems and Computing

2019 | book

In vitro fucoxanthin production by the Phaeodactylum tricornutum diatom

Studies in Natural Products Chemistry

2019 | book-chapter

MOSCA: An automated pipeline for integrated metagenomics and metatranscriptomics data analysis

Advances in Intelligent Systems and Computing

2019 | book

Machine Learning-Enhanced T Cell Neoepitope Discovery for Immunotherapy Design

Cancer Informatics

2019 | journal-article

Metabolite integration pipeline for the improvement of human metabolic models

Advances in Intelligent Systems and Computing

2019 | book

Preface

Advances in Intelligent Systems and Computing

2019 | book

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

BMC bioinformatics

2019 | journal-article

Triptych: Multi-objective optimisation of service deployment costs, application delay and bandwidth usage

2019 IFIP Networking Conference, IFIP Networking 2019

2019 | conference-paper

Reconstruction of consensus tissue-specific metabolic models

2018 | other

Advanced practical applications of computational biology & bioinformatics: PACBB’15

Current Bioinformatics

2018 | journal-article

Analyzing and designing cell factories with OptFlux

Methods in Molecular Biology

2018 | book-chapter

Automating the extraction of essential genes from literature

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2018 | conference-paper

Development of an information retrieval tool for biomedical patents

Computer Methods and Programs in Biomedicine

2018 | journal-article

Methods for automated genome-scale metabolic model reconstruction

Biochemical Society Transactions

2018 | journal-article

Reconstructing high-quality large-scale metabolic models with merlin

Methods in Molecular Biology

2018 | book-chapter

Segment routing single link failure congestion optimization

ICETE 2018 - Proceedings of the 15th International Joint Conference on e-Business and Telecommunications

2018 | conference-paper

The long non-coding RNA HOTAIR is transcriptionally activated by HOXA9 and is an independent prognostic marker in patients with malignant glioma

Oncotarget

2018 | journal-article

Utilitarian Placement of Composite Services

IEEE Transactions on Network and Service Management

2018 | journal-article

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

Interdisciplinary Sciences: Computational Life Sciences

2017 | journal-article

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

PLOS Computational Biology

2017 | journal-article

A Chemometrics Approach for Nuclear Magnetic Resonance Data to Characterize the Partial Metabolome Banana Peels from Southern Brazil

Journal of integrative bioinformatics

2017 | journal-article

A critical evaluation of automatic atom mapping algorithms and tools

Advances in Intelligent Systems and Computing

2017 | book

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

Interdisciplinary Sciences: Computational Life Sciences

2017 | journal-article

Characterization of the chemical composition of banana peels from southern brazil across the seasons using nuclear magnetic resonance and chemometrics

Advances in Intelligent Systems and Computing

2017 | conference-paper

Classification tools for carotenoid content estimation in manihot esculenta via metabolomics and machine learning

Advances in Intelligent Systems and Computing

2017 | book

Development of text mining tools for information retrieval from patents

Advances in Intelligent Systems and Computing

2017 | book

Evolutionary computation at work for the optimization of link state routing protocols

GECCO 2017 - Proceedings of the Genetic and Evolutionary Computation Conference Companion

2017 | conference-paper

Genome-Wide Semi-Automated Annotation of Transporter Systems

IEEE/ACM Transactions on Computational Biology and Bioinformatics

2017 | journal-article

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

GECCO 2017 - Proceedings of the Genetic and Evolutionary Computation Conference Companion

2017 | conference-paper

Influence of solar radiation on the production of secondary metabolites in three rice (Oryza sativa) cultivars

Advances in Intelligent Systems and Computing

2017 | book

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

Marine Pollution Bulletin

2017 | journal-article

Mixed-integer programming model for profiling disease biomarkers from gene expression studies

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2017 | conference-paper

Optimizing Segment Routing using Evolutionary Computation

Procedia Computer Science

2017 | conference-paper

Preface

Advances in Intelligent Systems and Computing

2017 | book

Selected Extended Papers of the 11th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB)

Journal of integrative bioinformatics

2017 | journal-article

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

Journal of integrative bioinformatics

2017 | journal-article

UV-vis spectrophotometry and chemometrics as tools for recognition of the biochemical profiles of organic banana peels (Musa sp.) according to the seasonality in southern Brazil

Advances in Intelligent Systems and Computing

2017 | book

A framework for improving routing configurations using multi-objective optimization mechanisms

Journal of Communications Software and Systems

2016 | journal-article

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

Computer Methods and Programs in Biomedicine

2016 | journal-article

Automated network resilience optimization using computational intelligence methods

Studies in Computational Intelligence

2016 | book

Computing and applying atomic regulons to understand gene expression and regulation

Frontiers in Microbiology

2016 | journal-article

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

Data in Brief

2016 | journal-article

Development of a machine learning framework for biomedical text mining

Advances in Intelligent Systems and Computing

2016 | book

Development of an integrated framework for minimal cut set enumeration in constraint-based models

Advances in Intelligent Systems and Computing

2016 | conference-paper

In silico constraint-based strain optimization methods: The quest for optimal cell factories

Microbiology and Molecular Biology Reviews

2016 | journal-article

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

Chemosphere

2016 | journal-article

Metabolic Profiling and Classification of Propolis Samples from Southern Brazil: An NMR-Based Platform Coupled with Machine Learning

Journal of Natural Products

2016 | journal-article

Preface

Advances in Intelligent Systems and Computing

2016 | book

Reconstruction of metabolic models for liver cancer cells

Advances in Intelligent Systems and Computing

2016 | book

Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data

Frontiers in Microbiology

2016 | journal-article

Selected papers from the annual PACBB conference 2014: Special issue

Current Bioinformatics

2016 | journal-article

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

Food Chemistry

2016 | journal-article

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

Food Science and Nutrition

2016 | journal-article

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

Advances in Intelligent Systems and Computing

2015 | book

A critical evaluation of methods for the reconstruction of tissue-specific models

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2015 | conference-paper

A text mining approach for the extraction of kinetic information from literature

Advances in Intelligent Systems and Computing

2015 | book

A transcriptomic signature mediated by HOXA9 promotes human glioblastoma initiation, aggressiveness and resistance to temozolomide

Oncotarget

2015 | journal-article

An integrated computational platform for metabolomics data analysis

Advances in Intelligent Systems and Computing

2015 | book

Carotenoid analysis of cassava genotypes roots (Manihot Esculenta Crantz) cultivated in southern Brazil using chemometric tools

Advances in Intelligent Systems and Computing

2015 | conference-paper

Comparison of single and multi-objective evolutionary algorithms for robust link-state routing

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2015 | conference-paper

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

Computer Methods and Programs in Biomedicine

2015 | journal-article

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

Journal of integrative bioinformatics

2015 | journal-article

Extracting kinetic information from literature with KineticRE

Journal of integrative bioinformatics

2015 | journal-article

Integrating data from heterogeneous DNA microarray platforms

Journal of integrative bioinformatics

2015 | journal-article

Microarray gene expression data integration: An application to brain tumor grade determination

Advances in Intelligent Systems and Computing

2015 | book

Preface

Advances in Intelligent Systems and Computing

2015 | book

Reconstructing genome-scale metabolic models with merlin

Nucleic Acids Research

2015 | journal-article

Reconstructing transcriptional Regulatory Networks using data integration and Text Mining

Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

2015 | conference-paper

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

Bioinformatics

2015 | journal-article

Transcript-based reannotation for microarray probesets

Proceedings of the ACM Symposium on Applied Computing

2015 | conference-paper

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

Genomics Data

2015 | journal-article

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

Journal of integrative bioinformatics

2015 | journal-article

UV-visible scanning spectrophotometry and chemometric analysis as tools to build descriptive and classification models for propolis from Southern Brazil

Advances in Intelligent Systems and Computing

2015 | book

UV-visible spectrophotometry-based metabolomic analysis of Cedrela Fissilis Velozzo (Meliaceae) calluses - a screening tool for culture medium composition and cell metabolic profiles

Advances in Intelligent Systems and Computing

2015 | book

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

Advances in Intelligent Systems and Computing

2014 | conference-paper

An integrated network visualization framework towards metabolic engineering applications

BMC Bioinformatics

2014 | journal-article

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

BMC Systems Biology

2014 | journal-article

D-Tailor: Automated analysis and design of DNA sequences

Bioinformatics

2014 | journal-article

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

Advances in Intelligent Systems and Computing

2014 | conference-paper

Evaluating pathway enumeration algorithms in metabolic engineering case studies

Advances in Intelligent Systems and Computing

2014 | book

Genome-scale bacterial transcriptional regulatory networks: Reconstruction and integrated analysis with metabolic models

Briefings in Bioinformatics

2014 | journal-article

Genome-scale bacterial transcriptional regulatory networks: Reconstruction and integrated analysis with metabolic models

Briefings in Bioinformatics

2014 | journal-article

Metabolomics combined with chemometric tools (PCA, HCA, PLS-DA and SVM) for screening cassava (Manihot esculenta Crantz) roots during postharvest physiological deterioration

Food Chemistry

2014 | journal-article

Metagenomic analysis of the saliva microbiome with merlin

Advances in Intelligent Systems and Computing

2014 | conference-paper

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

Expert Systems with Applications

2014 | journal-article

Preface

Advances in Intelligent Systems and Computing

2014 | book

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

2014 6th World Congress on Nature and Biologically Inspired Computing, NaBIC 2014

2014 | conference-paper

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

Nucleic Acids Research

2014 | journal-article

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

Advances in Intelligent Systems and Computing

2013 | book

A framework for robust traffic engineering using evolutionary computation

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2013 | conference-paper

Algorithms to infer metabolic flux ratios from fluxomics data

Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013

2013 | conference-paper

An integrated framework for strain optimization

2013 IEEE Congress on Evolutionary Computation, CEC 2013

2013 | conference-paper

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

Molecular BioSystems

2013 | journal-article

Email spam detection: A symbiotic feature selection approach fostered by evolutionary computation

International Journal of Information Technology and Decision Making

2013 | journal-article

Evolutionary computation for predicting optimal reaction knockouts and enzyme modulation strategies

2013 IEEE Congress on Evolutionary Computation, CEC 2013

2013 | conference-paper

Large scale metabolic characterization using flux balance analysis and data mining

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2013 | conference-paper

Network Visualization Tools to Enhance Metabolic Engineering Platforms

Advances in Intelligent Systems and Computing

2013 | book

Parallel evolutionary computation in bioinformatics applications

Computer Methods and Programs in Biomedicine

2013 | journal-article

Preface

Advances in Intelligent Systems and Computing

2013 | book

Re-annotation of the genome sequence of Helicobacter pylori 26695.

Journal of integrative bioinformatics

2013 | journal-article

Robust optimization of intradomain routing using Evolutionary Algorithms

Advances in Intelligent Systems and Computing

2013 | book

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

BMC Research Notes

2013 | journal-article

A machine learning and chemometrics assisted interpretation of spectroscopic data - A NMR-based metabolomics platform for the assessment of Brazilian propolis

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2012 | conference-paper

Advances in Intelligent and Soft Computing: Preface

Advances in Intelligent and Soft Computing

2012 | book

An algorithm to assemble gene-protein-reaction associations for genome-scale metabolic model reconstruction

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2012 | book

An integrated computational environment for elementary modes analysis of biochemical networks

International Journal of Data Mining and Bioinformatics

2012 | journal-article

Computational tools for strain optimization by adding reactions

Advances in Intelligent and Soft Computing

2012 | book

Computational tools for strain optimization by tuning the optimal level of gene expression

Advances in Intelligent and Soft Computing

2012 | conference-paper

Evolutionary symbiotic feature selection for email spam detection

ICINCO 2012 - Proceedings of the 9th International Conference on Informatics in Control, Automation and Robotics

2012 | conference-paper

In silico strain optimization by adding reactions to metabolic models.

Journal of integrative bioinformatics

2012 | journal-article

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

Expert Systems

2012 | journal-article

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

Journal of Computational Biology

2012 | conference-paper

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

BioSystems

2011 | journal-article

A software platform for evolutionary computation with pluggable parallelism and quality assurance

IFIP Advances in Information and Communication Technology

2011 | conference-paper

A study of the short and long-term regulation of E. coli metabolic pathways.

Journal of integrative bioinformatics

2011 | journal-article

A study on the robustness of strain optimization algorithms

Advances in Intelligent and Soft Computing

2011 | conference-paper

Challenges in integrating Escherichia coli molecular biology data

Briefings in Bioinformatics

2011 | journal-article

Highlighting metabolic strategies using network analysis over strain optimization results

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2011 | conference-paper

Interpreting the regulatory interplay in E. Coli metabolic pathways

Advances in Intelligent and Soft Computing

2011 | book

Modeling formalisms in systems biology

AMB Express

2011 | journal-article

Multiobjective evolutionary algorithms for intradomain routing optimization

2011 IEEE Congress of Evolutionary Computation, CEC 2011

2011 | conference-paper

Quality of Service constrained routing optimization using Evolutionary Computation

Applied Soft Computing Journal

2011 | journal-article

Semantic annotation of biological concepts interplaying microbial cellular responses

BMC Bioinformatics

2011 | journal-article

Symbiotic filtering for spam email detection

Expert Systems with Applications

2011 | journal-article

Traffic engineering approaches using multicriteria optimization techniques

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2011 | conference-paper

A collaborative approach for spam detection

Proceedings - 2nd International Conference on Evolving Internet, Internet 2010, 1st International Conference on Access Networks, Services and Technologies, Access 2010

2010 | conference-paper

A software tool for network topology analysis under a Metabolic Engineering perspective

2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010

2010 | conference-paper

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

Computer Methods and Programs in Biomedicine

2010 | journal-article

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

Advances in Bioinformatics

2010 | book-chapter

BioDR: Semantic indexing networks for biomedical document retrieval

Expert Systems with Applications

2010 | journal-article

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

Advances in Bioinformatics

2010 | book-chapter

Merlin: Metabolic models reconstruction using genome-scale information

IFAC Proceedings Volumes (IFAC-PapersOnline)

2010 | conference-paper

Metaheuristics for strain optimization using transcriptional information enriched metabolic models

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2010 | conference-paper

Model transformation of metabolic networks using a Petri net based framework

CEUR Workshop Proceedings

2010 | conference-paper

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

BMC Systems Biology

2010 | journal-article

Parallelisation Service in the AspectGrid Framework

Ibergrid: 4th Iberian Grid Infrastructure Conference Proceedings

2010 | book

Pluggable parallelization of evolutionary algorithms applied to the optimization of biological processes

Proceedings of the 18th Euromicro Conference on Parallel, Distributed and Network-Based Processing, PDP 2010

2010 | conference-paper

Spam email filtering using network-level properties

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2010 | conference-paper

@Note: A workbench for Biomedical Text Mining

Journal of Biomedical Informatics

2009 | journal-article

A critical review on modelling formalisms and simulation tools in computational biosystems

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2009 | conference-paper

A software tool for the simulation and optimization of dynamic metabolic models

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2009 | book

Biomedical text mining applied to document retrieval and semantic indexing

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2009 | book

Data integration issues in the reconstruction of the genome-scale metabolic model of Zymomonas mobillis

Advances in Soft Computing

2009 | book

Evolutionary approaches for strain optimization using dynamic models under a metabolic engineering perspective

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2009 | conference-paper

Implementing metaheuristic optimization algorithms with JECoLi

ISDA 2009 - 9th International Conference on Intelligent Systems Design and Applications

2009 | conference-paper

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2009 | book

Modelling fed-batch fermentation processes: An approach based on artificial neural networks

Advances in Soft Computing

2009 | conference-paper

Modelling of biotechnological processes -An approach based on artificial neural networks

Studies in Computational Intelligence

2009 | book

Optferm-a computational platform for the optimization of fermentation processes

ESM 2009 - 2009 European Simulation and Modelling Conference: Modelling and Simulation 2009

2009 | conference-paper

Symbiotic Data Mining for personalized spam filtering

Proceedings - 2009 IEEE/WIC/ACM International Conference on Web Intelligence, WI 2009

2009 | conference-paper

A comparative impact study of attribute selection techniques on naïve bayes spam filters

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2008 | conference-paper

A framework for the development of biomedical text mining software tools

8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008

2008 | conference-paper

A framework for the integrated analysis of metabolic and regulatory networks

8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008

2008 | conference-paper

A tool for the automatic and manual annotation of biomedical documents

3rd International Symposium on Semantic Mining in Biomedicine, SMBM 2008 - Proceedings

2008 | conference-paper

An evolutionary algorithm for unicast/ multicast traffic engineering

ICINCO 2008 - Proceedings of the 5th International Conference on Informatics in Control, Automation and Robotics

2008 | conference-paper

Differential evolution for the offline and online optimization of fed-batch fermentation processes

Studies in Computational Intelligence

2008 | book

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

8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008

2008 | conference-paper

Forecasting internet traffic by neural networks under univariate and multivariate strategies

Artificial Neural Networks and Intelligent Information Processing - Proc. 4th Int. Workshop on Artificial Neural Networks and Intelligent Information Processing, ANNIIP 2008; ICINCO 2008

2008 | conference-paper

Multiconstrained optimization of networks with multicast and unicast traffic

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2008 | conference-paper

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

BMC Bioinformatics

2008 | journal-article

getALife - An Artificial Life environment for the evaluation of agent-based systems and evolutionary algorithms for reinforcement learning

Studies in Computational Intelligence

2008 | book

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

Proceedings of GECCO 2007: Genetic and Evolutionary Computation Conference

2007 | conference-paper

Automatic provisioning of QoS aware OSPF configurations

Journal of Networks

2007 | journal-article

Class-based OSPF traffic engineering inspired on evolutionary computation

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2007 | conference-paper

Evaluating evolutionary algorithms and differential evolution for the online optimization of fermentation processes

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2007 | conference-paper

Evaluating simulated annealing algorithms in the optimization of bacterial strains

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2007 | conference-paper

Evolution of neural networks for classification and regression

Neurocomputing

2007 | journal-article

Evolutionary computation for quality of service internet routing optimization

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2007 | conference-paper

Optimization of bacterial strains with variable-sized evolutionary algorithms

2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology, CIBCB 2007

2007 | journal-article

Topology aware internet traffic forecasting using neural networks

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2007 | conference-paper

A comparison of algorithms for the optimization of fermentation processes

2006 IEEE Congress on Evolutionary Computation, CEC 2006

2006 | conference-paper

Efficient OSPF weight allocation for intra-domain QoS optimization

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2006 | conference-paper

Internet traffic forecasting using neural networks

IEEE International Conference on Neural Networks - Conference Proceedings

2006 | journal-article

QoS constrained internet routing with evolutionary algorithms

2006 IEEE Congress on Evolutionary Computation, CEC 2006

2006 | conference-paper

A new representation in Evolutionary Algorithms for the optimization of bioprocesses

2005 IEEE Congress on Evolutionary Computation, IEEE CEC 2005. Proceedings

2005 | conference-paper

Evolutionary algorithms for static and dynamic optimization of fed-batch fermentation processes

Adaptive and Natural Computing Algorithms

2005 | book-chapter

Evolutionary design of neural networks for classification and regression

Adaptive and Natural Computing Algorithms

2005 | book-chapter

Simultaneous evolution of neural network topologies and weights for classification and regression

Lecture Notes in Computer Science

2005 | conference-paper

Time series forecasting by evolutionary neural networks

Artificial Neural Networks in Real-Life Applications

2005 | book-chapter

Evolutionary algorithms for optimal control in fed-batch fermentation processes

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2004 | book

Evolving time series forecasting ARMA models

Journal of Heuristics

2004 | journal-article

An interdisciplinary E-learning system for the K-6

Proceedings of the IASTED International Conference on Computers and Advanced Technology in Education

2003 | conference-paper

Evolutionary neural network learning

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2003 | book

A lamarckian approach for neural network training

Neural Processing Letters

2002 | journal-article

Particle swarms for feedforward neural network training

Proceedings of the International Joint Conference on Neural Networks

2002 | conference-paper

A genetic and evolutionary programming environment with spatially structured populations and Built-In Parallelism

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2001 | conference-paper

Genetic and evolutionary algorithms for time series forecasting

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2001 | book

Sitting guests at a wedding party: Experiments on genetic and evolutionary constrained optimization

Proceedings of the IEEE Conference on Evolutionary Computation, ICEC

2001 | conference-paper

A study of order based genetic and evolutionary algorithms in combinatorial optimization problems

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2000 | conference-paper

Viewing scheduling problems through Genetic and Evolutionary Algorithms

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2000 | conference-paper

A unified framework for data modeling on medical information systems

Studies in Health Technology and Informatics

1999 | conference-paper

Adaptive strategies and the design of evolutionary applications

Gecco-99: Proceedings of the Genetic and Evolutionary Computation Conference

1999 | book

An evolutionary and genetic view of the job-shop scheduling problem

Simulation in Industry'99: 11th European Simulation Symposium 1999

1999 | book

Preventing premature convergence to local optima in genetic algorithms via random offspring generation

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

1999 | conference-paper

Neural network based time series forecasting system

IEEE International Conference on Neural Networks - Conference Proceedings

1995 | conference-paper

MOBioPro-Nature-based computation in the modeling and optimization of biotechnological processes

Fundação para a Ciência e a Tecnologia, I.P.

2005-07 to 2008-06 | 59899

AspectGrid: Pluggable Grid Aspects for Scientific Applications

Fundação para a Ciência e a Tecnologia, I.P.

2007-07 to 2010-12 | 81880

Bridging Systems and Synthetic Biology for the development of Improved Microbial Cell Factories

Fundação para a Ciência e a Tecnologia, I.P.

2009-04 to 2012-09 | 84035

HeliSysBio - Molecular Systems Biology Helicobacter pylori

Fundação para a Ciência e a Tecnologia, I.P.

2010-04 to 2013-09 | 104235

GAsPar: General-purpose Aspect-Oriented framework for heterogeneous multicore Parallel systems

Fundação para a Ciência e a Tecnologia, I.P.

2010-06 to 2013-12 | 108937

ToMEGIM: Computational Tools for Metabolic Engineering using Genome-scale Integrated Models

Fundação para a Ciência e a Tecnologia, I.P.

2011-03 to 2014-07 | 115176

SPAM Telescope Miner: worldwide unsolicited email detection using data mining techniques

Universidade de Coimbra

2008-01 to 2010-12 | 64541

The Transcriptome of the Oncogenic HOXA9 Homeoprotein in Human Glioblastoma: Characterization and Functional Significance

Fundação para a Ciência e a Tecnologia, I.P.

2011-04 to 2014-09 | 113795

In silico reconstruction of Streptococcus pneumoniae cellular networks and their impact on virulence

Fundação para a Ciência e a Tecnologia, I.P.

2011-01 to 2014-06 | 113824

ToMEGIM: Computational Tools for Metabolic Engineering using Genome-scale Integrated Models

Fundação para a Ciência e a Tecnologia

2011-03 to 2014-07 | PTDC/EIA-EIA/115176/2009

MOBioPro-Nature-based computation in the modeling and optimization of biotechnological processes

Fundação para a Ciência e a Tecnologia

2005-07 to 2008-06 | POSC/ EIA/59899/2004

AspectGrid: Pluggable Grid Aspects for Scientific Applications

Fundação para a Ciência e a Tecnologia

2007-07 to 2010-12 | GRID/GRI/81880/2006

SPAM Telescope Miner: worldwide unsolicited email detection using data mining techniques

Fundação para a Ciência e a Tecnologia

2008-01 to 2010-12 | PTDC/EIA/64541/2006

Bridging Systems and Synthetic Biology for the development of Improved Microbial Cell Factories

Fundação para a Ciência e a Tecnologia

2009-04 to 2012-09 | MIT-Pt/BS-BB/0082/2008

HeliSysBio - Molecular Systems Biology Helicobacter pylori

Fundação para a Ciência e a Tecnologia

2010-04 to 2013-09 | PTDC/EBB-EBI/104235/2008

GAsPar: General-purpose Aspect-Oriented framework for heterogeneous multicore Parallel systems

Fundação para a Ciência e a Tecnologia

2010-06 to 2013-12 | PTDC/EIA-EIA/108937/2008

In silico reconstruction of Streptococcus pneumoniae cellular networks and their impact on virulence

Fundação para a Ciência e a Tecnologia

2011-01 to 2014-06 | PTDC/EBB-EBI/113824/2009

The Transcriptome of the Oncogenic HOXA9 Homeoprotein in Human Glioblastoma: Characterization and Functional Significance

Fundação para a Ciência e a Tecnologia

2011-04 to 2014-09 | PTDC/SAU-GMG/113795/2009

DeepBio – Deep and machine learning for industrial biotechnology

Agência Nacional de Inovação SA

2019-07 to 2022-06 | NORTE-01-0247-FEDER-039831

SHIKIFACTORY100 – Modular cell factories for the production of 100 compounds from the shikimate pathway

EU Framework Programme for Research and Innovation Nanotechnologies Advanced Materials Advanced Manufacturing and Processing and Biotechnology

2019-01 to 2023-02 | 814408

ViralFP - Using computational and experimental methods to provide a global characterization of viral fusion peptides

Fundação para a Ciência e a Tecnologia

2018-10 to 2021-09 | NORTE-01-0145-FEDER-028200

BioData.pt - Portuguese Biological Data Network

Fundação para a Ciência e a Tecnologia

2017-06 to 2020-06 | POCI-01-0145-FEDER-022231

DD-Decaf - Bioinformatics Services for Data-Driven Design of Cell Factories and Communities

European Commission

2016-03 to 2020-02 | H2020-LEIT-BIO-2015-1 686070-1

SISBI – Sistema Inteligente de Suporte à Decisão em Biotecnologia Industrial

Agência Nacional de Inovação SA

2016-01 to 2018-12 | NORTE-01-0247-FEDER-003381

DYNAMICS - Analysis and optimization of industrial microorganisms under dynamic process conditions

European Commission

2015-04 to 2018-03 | ERA-IB-2/0002/2014

An integrated computational platform for knowledge extraction from metabolomics data applied to the analysis of natural products

Conselho Nacional de Desenvolvimento Científico e Tecnológico

2014-03 to 2018-02 | PVE

PropMine: Desenvolvimento de ferramentas de descrição e classificação da própolis brasileira via metabolómica e mineração de dados

Fundação para a Ciência e a Tecnologia

2014-03 to 2017-02 | PropMine

PEM – Platform for Metabolic Engineering

Agência Nacional de Inovação SA

2012-07 to 2015-06 | 23060

SYSINBIO- Systems Biology as a Driver for Industrial Biotechnology

European Commission

2008-12 to 2012-11 | 212766

Machine Learning Applications in Systems Biology Research

Fundação Luso-Americana

2007- to 2009- | FLAD-FCT

Intelligent Agents Simulation for the RoboCup

Fundação para a Ciência e a Tecnologia

2003- to 2006- | POSI/ROBO/ 43904/2002