publicações selecionadas
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artigo académico
- Reconstruction of cell-specific models capturing the influence of metabolism on DNA methylation in cancer. Computers in Biology and Medicine. 2024
- The Characterization and Cytotoxic Evaluation of Chondrosia reniformis Collagen Isolated from Different Body Parts (Ectosome and Choanosome) Envisaging the Development of Biomaterials. Marine Drugs. 2024
- BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2024
- The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber 2023
- Transitions Between Preexposure Prophylaxis Eligibility States and HIV Infection in the Lisbon Cohort of HIV-Negative Men Who Have Sex With Men: A Multistate Model Analysis. American Journal of Epidemiology. 2021
- IEC7871 Quercus suber model: The first multi-tissue diel cycle genome-scale metabolic model of a woody tree. BioRxiv. 2021
- 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
- Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease. Leukemia. 2020
- 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
- A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. Cell Systems. 2017
- A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer. JCO Clinical Cancer Informatics. 2017
- Non-targeted Metabolomic Profiling of Maize Landraces (Zea mays L.) Combined with Chemometric Tools. International Journal of Biochemistry Research and Review. 2017
- Optimizing Segment Routing using Evolutionary Computation. Procedia Computer Science. 2017
- Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data. Lancet Oncology. 2017
- A framework for improving routing configurations using multi-objective optimization mechanisms. Journal of Communications Software and Systems. 2016
- D-Tailor: Automated analysis and design of DNA sequences. Bioinformatics. 2014
- Transcript level and sequence determinants of protein abundance and noise in Escherichia coli. Nucleic Acids Research. 2014
- Bridging the layers: Towards integration of signal transduction, regulation and metabolism into mathematical models. Molecular Biosystems. 2013
- Re-annotation of the genome sequence of Helicobacter pylori 26695.. Journal of Integrative Bioinformatics. 2013
- In silico strain optimization by adding reactions to metabolic models.. Journal of Integrative Bioinformatics. 2012
- A study of the short and long-term regulation of E. coli metabolic pathways.. Journal of Integrative Bioinformatics. 2011
- Automatic Provisioning of QoS Aware OSPF Configurations. Journal of Networks. 2007
- Evolutionary Neural Network Learning Algorithms for Changing Environments. WSEAS Transactions on Systems. 2004
- A unified framework for data modeling on Medical Information Systems. Medical Informatics Europe '99. 1999
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artigo de conferência
- A multi-omics approach for understanding grape metabolism throughout development 2024
- iplants: a repository of plant metabolic data 2024
- Development of Deep Learning approaches to predict relationships between chemical structures and sweetness. IEEE International Joint Conference on Neural Networks (IJCNN). 2022
- Predicting the number of biochemical transformations needed to synthesize a compound. IEEE International Joint Conference on Neural Networks (IJCNN). 2022
- Variational autoencoders and evolutionary algorithms for targeted novel enzyme design 2022
- BioTMPy: A Deep Learning-Based Tool to Classify Biomedical Literature 2021
- A Comparison of Different Compound Representations for Drug Sensitivity Prediction 2021
- Combinatorial Optimization of Succinate Production in Escherichia coli 2021
- Computational Methods for the Identification of Genetic Variants in Complex Diseases 2021
- Computational Tools for the Analysis of 2D-Nuclear Magnetic Resonance Data 2021
- Recurrent Deep Neural Networks for Enzyme Functional Annotation 2021
- Optimizing NFV deployment in Segment Routing,Otimização de implementações NFV em Segment Routing 2021
- R2L: Routing with Reinforcement Learning. IEEE International Joint Conference on Neural Networks (IJCNN). 2021
- Reconciliation of Regulatory Data: The Regulatory Networks of Escherichia coli and Bacillus subtilis. AI Communications. 2020
- A Python Automated Platform for the Classification of Proteins Using Machine Learning 2020
- ProPythia, an automated platform for the classification of peptides/proteins using machine learning 2020
- Hybrid IP/SDN Routing for Inter-Data Center Communications 2020
- merlin v4: an updated platform for reconstructing genome-scale metabolic models 2020
- Towards the Reconstruction of Integrated Genome-Scale Models of Metabolism and Gene Expression. AI Communications. 2019
- Artificial Intelligence in Biological Activity Prediction. AI Communications. 2019
- Troppo - A Python Framework for the Reconstruction of Context-Specific Metabolic Models. AI Communications. 2019
- Triptych: Multi-objective Optimisation of Service Deployment Costs, Application Delay and Bandwidth Usage. IFIP Advances in Information and Communication Technology. 2019
- Deep Neural Networks for Network Routing. IEEE International Joint Conference on Neural Networks (IJCNN). 2019
- Hybrid IP/SDN Routing for Inter-Data Center Communications. IEEE International Conference on Cloud Networking. 2019
- The metabolic model of the Quercus suber (cork oak tree) leaf 2019
- Automating the extraction of essential genes from literature. Computational Methods in Applied Sciences. 2018
- A review on metabolomics data analysis for cancer applications. AI Communications. 2018
- In silico predictions for fucoxanthin production by the diatom phaeodactylum tricornutum. AI Communications. 2018
- Metabolite integration pipeline for the improvement of human metabolic models. AI Communications. 2018
- Segment routing single link failure congestion optimization 2018
- A critical evaluation of automatic atom mapping algorithms and tools. AI Communications. 2017
- Characterization of the chemical composition of banana peels from southern brazil across the seasons using nuclear magnetic resonance and chemometrics. AI Communications. 2017
- Classification tools for carotenoid content estimation in manihot esculenta via metabolomics and machine learning 2017
- Development of text mining tools for information retrieval from patents. AI Communications. 2017
- Evolutionary computation at work for the optimization of link state routing protocols 2017
- Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction 2017
- Influence of solar radiation on the production of secondary metabolites in three rice (Oryza sativa) cultivars. AI Communications. 2017
- Mixed-integer programming model for profiling disease biomarkers from gene expression studies. Computational Methods in Applied Sciences. 2017
- 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. AI Communications. 2017
- Carotenoid analysis of cassava genotypes roots (Manihot Esculenta Crantz) cultivated in southern Brazil using chemometric tools. AI Communications. 2016
- Development of a machine learning framework for biomedical text mining. AI Communications. 2016
- Development of an integrated framework for minimal cut set enumeration in constraint-based models. AI Communications. 2016
- Reconstruction of metabolic models for liver cancer cells. AI Communications. 2016
- A critical evaluation of methods for the reconstruction of tissue-specific models. Computational Methods in Applied Sciences. 2015
- A text mining approach for the extraction of kinetic information from literature. AI Communications. 2015
- An integrated computational platform for metabolomics data analysis. AI Communications. 2015
- Metagenomic Analysis of the Saliva Microbiome with Merlin. AI Communications. 2015
- Microarray gene expression data integration: An application to brain tumor grade determination. AI Communications. 2015
- Reconstructing transcriptional Regulatory Networks using data integration and Text Mining. IEEE International Conference on Bioinformatics and Biomedicine - BIBM. 2015
- Transcript-based reannotation for microarray probesets 2015
- UV-visible scanning spectrophotometry and chemometric analysis as tools to build descriptive and classification models for propolis from Southern Brazil. AI Communications. 2015
- UV-visible spectrophotometry-based metabolomic analysis of Cedrela Fissilis Velozzo (Meliaceae) calluses - a screening tool for culture medium composition and cell metabolic profiles. AI Communications. 2015
- Discrimination of Brazilian Cassava Genotypes (Manihot Esculenta Crantz) According to Their Physicochemical Traits and Functional Properties Through Bioinformatics Tools 2014
- Evaluating pathway enumeration algorithms in metabolic engineering case studies. AI Communications. 2014
- Prediction of protein subunits using KEGG BRITE 2014
- Reg4OptFlux: An OptFlux plug-in that comprises meta-heuristics approaches for Metabolic engineering using integrated models. World Congress on Nature and Biologically Inspired Computing. 2014
- Algorithms to infer metabolic flux ratios from fluxomics data 2013
- An integrated framework for strain optimization 2013
- Evolutionary computation for predicting optimal reaction knockouts and enzyme modulation strategies 2013
- Large scale metabolic characterization using flux balance analysis and data mining 2013
- Network Visualization Tools to Enhance Metabolic Engineering Platforms 2013
- A machine learning and chemometrics assisted interpretation of spectroscopic data - A NMR-based metabolomics platform for the assessment of Brazilian propolis. Computational Methods in Applied Sciences. 2012
- An algorithm to assemble gene-protein-reaction associations for genome-scale metabolic model reconstruction. Computational Methods in Applied Sciences. 2012
- Assembling genome-wide transporter system annotations 2012
- Computational tools for strain optimization by adding reactions 2012
- Computational tools for strain optimization by tuning the optimal level of gene expression 2012
- Evolutionary symbiotic feature selection for email spam detection 2012
- A study on the robustness of strain optimization algorithms 2011
- Highlighting metabolic strategies using network analysis over strain optimization results. Computational Methods in Applied Sciences. 2011
- Multiobjective evolutionary algorithms for intradomain routing optimization 2011
- A collaborative approach for spam detection 2010
- A software tool for network topology analysis under a Metabolic Engineering perspective 2010
- Enhancing Elementary Flux Modes analysis using filtering techniques in an integrated environment 2010
- Genome-scale metabolic models reconstruction of less characterized organisms with Merlin 2010
- Merlin: Metabolic models reconstruction using genome-scale information. IFAC proceedings volumes. 2010
- Metaheuristics for strain optimization using transcriptional information enriched metabolic models. Computational Methods in Applied Sciences. 2010
- Model transformation of metabolic networks using a Petri net based framework. CEUR Workshop Proceedings. 2010
- Pluggable parallelization of evolutionary algorithms applied to the optimization of biological processes 2010
- Tools for traffic engineering on IP networks 2010
- Combining syntactic and ontological knowledge to extract biologically relevant relations from scientific papers 2009
- Implementing metaheuristic optimization algorithms with JECoLi. International Conference on Intelligent Systems Design and Applications. 2009
- Optferm-a computational platform for the optimization of fermentation processes 2009
- Symbiotic Data Mining for personalized spam filtering 2009
- An evolutionary algorithm for unicast/multicast traffic engineering 2008
- A comparative impact study of attribute selection techniques on naïve bayes spam filters 2008
- A framework for the development of biomedical text mining software tools. IEEE International Conference on Bioinformatics and Bioengineering. 2008
- A framework for the integrated analysis of metabolic and regulatory networks. IEEE International Conference on Bioinformatics and Bioengineering. 2008
- A tool for the automatic and manual annotation of biomedical documents 2008
- An evolutionary algorithm for unicast/ multicast traffic engineering 2008
- Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains. IEEE International Conference on Bioinformatics and Bioengineering. 2008
- Forecasting internet traffic by neural networks under univariate and multivariate strategies 2008
- Modelling fed-batch fermentation processes: An approach based on artificial neural networks 2008
- Network analysis of an integrated metabolic/regulatory model of Escherichia coli 2008
- The @Note biomedical text mining workbench 2008
- getALife - An Artificial Life environment for the evaluation of agent-based systems and evolutionary algorithms for reinforcement learning 2008
- A platform for the selection of genes in DNA microarraydata using evolutionary algorithms 2007
- An Ontology-Based Approach To Systems Biology Literature Retrieval and Processing 2007
- Class-based OSPF traffic engineering inspired on evolutionary computation. Computational Methods in Applied Sciences. 2007
- Evolutionary computation for quality of service internet routing optimization. Computational Methods in Applied Sciences. 2007
- Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms 2007
- Topology aware internet traffic forecasting using neural networks. Computational Methods in Applied Sciences. 2007
- A comparison of algorithms for the optimization of fermentation processes 2006
- Efficient OSPF weight allocation for intra-domain QoS optimization. Computational Methods in Applied Sciences. 2006
- Internet traffic forecasting using neural networks. IEEE International Joint Conference on Neural Networks (IJCNN). 2006
- QoS constrained internet routing with evolutionary algorithms 2006
- A New Representation in Evolutionary Algorithms for the Optimization of Bioprocesses 2005
- Evolutionary Design of Neural Networks for Classification and Regression 2005
- Simultaneous evolution of neural network topologies and weights for classification and regression. Computational Methods in Applied Sciences. 2005
- An architecture for co-evolving agents in the ROBOCUP Simulation League 2004
- Ensembles of artificial neural networks with heterogeneous topologies 2004
- Evolutionary algorithms for optimal control in fed-batch fermentation processes 2004
- Adaptive Learning in Changing Environments 2003
- An interdisciplinary E-learning system for the K-6 2003
- Evolutionary neural network learning 2003
- Particle swarms for feedforward neural network training. IEEE International Joint Conference on Neural Networks (IJCNN). 2002
- Real-Time Forecasting by Bio-Inspired Models 2002
- A Meta-Genetic Algorithm for Time Series Forecasting 2001
- Sitting guest at a wedding party : experiments on genetic and evolutionary constrained optimization 2001
- Lamarckian training of feedforward neural networks 2001
- Evolving Time Series Forecasting Neural Network Models 2001
- Genetic and evolutionary algorithms for time series forecasting. Computational Methods in Applied Sciences. 2001
- Lamarkian Training of Feedforward Neural Networks 2001
- Sitting guests at a wedding party: Experiments on genetic and evolutionary constrained optimization 2001
- The relationship between learning and evolution in static and dynamic environments 2000
- Viewing scheduling problems through Genetic and Evolutionary Algorithms. Computational Methods in Applied Sciences. 2000
- An evolutionary and connectionist approach for time series forecasting 1999
- Adaptive Strategies and the Design of Evolutionary Applications 1999
- Adaptive Strategies and the Design of Evolutionary Applications 1999
- An Architecture for Co-Evolving Agents in the ROBOCUP Simulation League 1999
- Preventing premature convergence to local optima in genetic algorithms via random offspring generation. Computational Methods in Applied Sciences. 1999
- A neural network based time series forecasting system 1995
- Neural network based time series forecasting system 1995
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artigo de revista
- Recent advances in data- and knowledge-driven approaches to explore primary microbial metabolism. Current Opinion in Chemical Biology. 2023
- A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer. PLoS Computational Biology. 2023
- Evaluating molecular representations in machine learning models for drug response prediction and interpretability. Journal of Integrative Bioinformatics. 2022
- merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models. Nucleic Acids Research. 2022
- A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale. PLoS Computational Biology. 2022
- A comparison of multi-objective optimization algorithms for weight setting problems in traffic engineering. Natural Computing. 2022
- Exploring synergies between plant metabolic modelling and machine learning. Computational and Structural Biotechnology Journal. 2022
- Reconstruction of tissue-specific genome-scale metabolic models for human cancer stem cells. Computers in Biology and Medicine. 2022
- Systems Biology in ELIXIR: modelling in the spotlight. F1000research. 2022
- UPIMAPI, reCOGnizer and KEGGCharter: bioinformatics tools for functional annotation and visualization of (meta)-omics datasets. Computational and Structural Biotechnology Journal. 2022
- ViralFP: a web application of viral fusion proteins. Frontiers in Medical Technology. 2021
- A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale. BMC Bioinformatics. 2021
- NMRFinder: a novel method for 1D 1H-NMR metabolite annotation. Metabolomics. 2021
- Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses. Molecular Systems Biology. 2021
- Model-guided development of an evolutionarily stable yeast chassis. Molecular Systems Biology. 2021
- ProPythia: A Python package for protein classification based on machine and deep learning. Neurocomputing. 2021
- A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation. Biochemical SocIETy Transactions. 2020
- Traffic Engineering With Three-Segments Routing. IEEE Transactions on Network and Service Management. 2020
- Deep learning for drug response prediction in cancer. Briefings in Bioinformatics. 2020
- Botanical source investigation and evaluation of the effect of seasonality on Brazilian propolis from Apis mellifera L.. Scientia Agrícola. 2020
- CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models. Bioinformatics. 2019
- PhageSuite - phage processing tools. Bioinformatics. 2019
- WebSpecmine: A Website for Metabolomics Data Analysis and Mining. Metabolites. 2019
- SamPler - a novel method for selecting parameters for gene functional annotation routines. BMC Bioinformatics. 2019
- Show us your beaks and we tell you what you eat: Different ecology in sympatric Antarctic benthic octopods under a climate change context. Marine Environmental Research. 2019
- Genomic imbalances defining novel intellectual disability associated loci. Orphanet Journal of Rare Diseases. 2019
- Comparison of pathway analysis and constraint-based methods for cell factory design. BMC Bioinformatics. 2019
- Comparison of pathway analysis and constraint-based methods for cell factory design. BMC Bioinformatics. 2019
- Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications. 2019
- A Model Integration Pipeline for the Improvement of Human Genome-Scale Metabolic Reconstructions. Journal of Integrative Bioinformatics. 2019
- Machine Learning-Enhanced T Cell Neoepitope Discovery for Immunotherapy Design. Cancer Informatics. 2019
- A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering. Antibiotics. 2018
- The long non-coding RNA HOTAIR is transcriptionally activated by HOXA9 and is an independent prognostic marker in patients with malignant glioma. Oncotarget. 2018
- Development of an information retrieval tool for biomedical patents. Computer Methods and Programs in Biomedicine. 2018
- Methods for automated genome-scale metabolic model reconstruction. Biochemical SocIETy Transactions. 2018
- Utilitarian Placement of Composite Services. IEEE Transactions on Network and Service Management. 2018
- Development of a Framework for Metabolic Pathway Analysis-Driven Strain Optimization Methods. Interdisciplinary Sciences-Computational Life Sciences. 2017
- Data-driven reverse engineering of signaling pathways using ensembles of dynamic models. PLoS Computational Biology. 2017
- A Chemometrics Approach for Nuclear Magnetic Resonance Data to Characterize the Partial Metabolome Banana Peels from Southern Brazil. Journal of Integrative Bioinformatics. 2017
- A DREAM challenge to build prediction models for short-term discontinuation of docetaxel in metastatic castration-resistant prostate cancer. JCO Clinical Cancer Informatics. 2017
- Analysing Algorithms and Data Sources for the Tissue-Specific Reconstruction of Liver Healthy and Cancer Cells. Interdisciplinary Sciences-Computational Life Sciences. 2017
- Genome-Wide Semi-Automated Annotation of Transporter Systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2017
- Genome-Wide Semi-Automated Annotation of Transporter Systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2017
- 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
- Non-targeted metabolomic profiling of maize landraces (Zea mays l.) combined with chemometric tools. International Journal of Biochemistry Research and Review. 2017
- Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data. Lancet Oncology. 2017
- UV-Vis and CIELAB Based Chemometric Characterization of Manihot esculenta Carotenoid Contents. Journal of Integrative Bioinformatics. 2017
- A framework for improving routing configurations using multi-objective optimization mechanisms. Journal of Communications Software and Systems. 2016
- Computing and applying atomic regulons to understand gene expression and regulation. Antibiotics. 2016
- Data supporting the role of enzymes and polysaccharides during cassava postharvest physiological deterioration. Data in Brief. 2016
- In silico constraint-based strain optimization methods: The quest for optimal cell factories. Microbiology and Molecular Biology Reviews. 2016
- In vitro exposure of Ulva lactuca Linnaeus (Chlorophyta) to gasoline - Biochemical and morphological alterations. Chemosphere. 2016
- Metabolic Profiling and Classification of Propolis Samples from Southern Brazil: An NMR-Based Platform Coupled with Machine Learning. Journal of Natural Products. 2016
- Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data. Antibiotics. 2016
- The role of ascorbate peroxidase, guaiacol peroxidase, and polysaccharides in cassava (Manihot esculenta Crantz) roots under postharvest physiological deterioration. Food Chemistry. 2016
- Toward better understanding of postharvest deterioration: biochemical changes in stored cassava (Manihot esculenta Crantz) roots:. Food Science and Nutrition. 2016
- Transcriptional profiling of HOXA9-regulated genes in human glioblastoma cell models. Genomics Data. 2015
- Reconstructing genome-scale metabolic models with merlin. Nucleic Acids Research. 2015
- A transcriptomic signature mediated by HOXA9 promotes human glioblastoma initiation, aggressiveness and resistance to temozolomide. Oncotarget. 2015
- An R package for the integrated analysis of metabolomics and spectral data. Computer Methods and Programs in Biomedicine. 2015
- Development and application of efficient pathway enumeration algorithms for metabolic engineering applications. Computer Methods and Programs in Biomedicine. 2015
- Discrimination of Brazilian propolis according to the seasoning using chemometrics and machine learning based on UV-Vis scanning data. Journal of Integrative Bioinformatics. 2015
- Extracting kinetic information from literature with KineticRE. Journal of Integrative Bioinformatics. 2015
- Integrating data from heterogeneous DNA microarray platforms. Journal of Integrative Bioinformatics. 2015
- UV-visible scanning spectrophotometry and chemometric analysis as tools for carotenoids analysis in cassava genotypes (Manihot esculenta Crantz). Journal of Integrative Bioinformatics. 2015
- An integrated network visualization framework towards metabolic engineering applications. BMC Bioinformatics. 2014
- CBFA: Phenotype prediction integrating metabolic models with constraints derived from experimental data. BMC Systems Biology. 2014
- Genome-scale bacterial transcriptional regulatory networks: Reconstruction and integrated analysis with metabolic models. Briefings in Bioinformatics. 2014
- 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
- Optimization of fed-batch fermentation processes with bio-inspired algorithms. Expert Systems with Applications. 2014
- Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach. Bioinformatics. 2014
- Email spam detection: A symbiotic feature selection approach fostered by evolutionary computation. International Journal of Information Technology & Decision Making. 2013
- Parallel evolutionary computation in bioinformatics applications. Computer Methods and Programs in Biomedicine. 2013
- Re-annotation of the genome sequence of Helicobacter pylori 26695. Journal of Integrative Bioinformatics. 2013
- TNA4OptFlux - A software tool for the analysis of strain optimization strategies. BMC Research Notes. 2013
- An integrated computational environment for elementary modes analysis of biochemical networks. International Journal of Data Mining and Bioinformatics. 2012
- In silico strain optimization by adding reactions to metabolic models. Journal of Integrative Bioinformatics. 2012
- Multi-scale Internet traffic forecasting using neural networks and time series methods. Electronics. 2012
- Optimization approaches for the in silico discovery of optimal targets for gene over/underexpression. Journal of Computational Biology. 2012
- Symbiotic filtering for spam email detection. Expert Systems with Applications. 2011
- A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information. Biosystems. 2011
- A study of the short and long-term regulation of E. coli metabolic pathways. Journal of Integrative Bioinformatics. 2011
- Challenges in integrating Escherichia coli molecular biology data. Briefings in Bioinformatics. 2011
- Modeling formalisms in Systems Biology. Amb Express. 2011
- Quality of Service constrained routing optimization using Evolutionary Computation. Applied Soft Computing. 2011
- Semantic annotation of biological concepts interplaying microbial cellular responses. BMC Bioinformatics. 2011
- AIBench: A rapid application development framework for translational research in biomedicine. Computer Methods and Programs in Biomedicine. 2010
- BioDR: Semantic indexing networks for biomedical document retrieval. Expert Systems with Applications. 2010
- OptFlux: An open-source software platform for in silico metabolic engineering. BMC Systems Biology. 2010
- @Note: A workbench for Biomedical Text Mining. Journal of Biomedical Informatics. 2009
- Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinformatics. 2008
- Automatic provisioning of QoS aware OSPF configurations. Journal of Networks. 2007
- Evolution of Neural Networks for Classification and Regression. Neurocomputing. 2007
- Evolutionary neural network learning algorithms for changing environments. WSEAS Transactions on Systems. 2004
- Evolving time series forecasting ARMA models. Journal of Heuristics. 2004
- A Lamarckian Approach for Neural Network Training.. Neural Processing Letters. 2002
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capítulo de livro
- Banana (Musa spp.) as a Source of Bioactive Compounds for Health Promotion 2020
- ProPythia: A Python Automated Platform for the Classification of Proteins Using Machine Learning. AI Communications. 2020
- Predicting Promoters in Phage Genomes Using Machine Learning Models. AI Communications. 2019
- DNA microarrays: Fundamentals, data integration and applications 2019
- From Neglected and Underutilized Crops to Powerful Sources of Vitamin A: Three Case Studies of Mozambican Cultivated Tacca leontopetaloides, Cowpea, and Cassava 2019
- Genome-Scale Metabolic Models 2019
- In vitro fucoxanthin production by the Phaeodactylum tricornutum diatom. Studies in Natural Products Chemistry. 2019
- MOSCA: An Automated Pipeline for Integrated Metagenomics and Metatranscriptomics Data Analysis. AI Communications. 2019
- Remarkable Body Architecture of Marine Sponges as Biomimetic Structure for Application in Tissue Engineering. Springer Series in Biomaterials Science and Engineering. 2019
- Analyzing and designing cell factories with OptFlux. Methods in Molecular Biology. 2018
- Reconstructing High-Quality Large-Scale Metabolic Models with merlin. Methods in Molecular Biology. 2018
- Metabolômica e quimiometria como ferramentas para análises quimio(bio) diversas 2017
- Optimizing Load Balancing Routing Mechanisms with Evolutionary Computation. Ambient Intelligence and Smart Environments. 2016
- Interpreting the Regulatory Interplay in E. coli Metabolic Pathways 2011
- A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems. Computational Methods in Applied Sciences. 2009
- A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models. Computational Methods in Applied Sciences. 2009
- Biomedical Text Mining Applied to Document Retrieval and Semantic Indexing. Computational Methods in Applied Sciences. 2009
- Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis 2009
- Evolutionary Approaches for Strain Optimization Using Dynamic Models under a Metabolic Engineering Perspective. Computational Methods in Applied Sciences. 2009
- Modelling of Biotechnological Processes – An Approach Based on Artificial Neural Networks. Studies in Computational Intelligence. 2009
- A Study of educational robotics in elementary schools 2008
- Differential evolution for the offline and online optimization of fed-batch fermentation processes. Studies in Computational Intelligence. 2008
- Evaluating Evolutionary Algorithms and Differential Evolution for the Online Optimization of Fermentation Processes. Computational Methods in Applied Sciences. 2007
- Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains. Computational Methods in Applied Sciences. 2007
- Time Series Forecasting by Evolutionary Neural Networks 2006
- Evolutionary Algorithms for Static and Dynamic Optimization of Fed-batch Fermentation Processes 2005
- Evolutionary Algorithms for Static and Dynamic Optimization of Fed-batch Fermentation Processes 2005
- Evolutionary Algorithms for Optimal Control in Fed-Batch Fermentation Processes. Computational Methods in Applied Sciences. 2004
- Evolutionary neural network learning. Computational Methods in Applied Sciences. 2003
- A Genetic and Evolutionary Programming Environment with Spatially Structured Populations and Built-In Parallelism. Computational Methods in Applied Sciences. 2001
- A Study of Order Based Genetic and Evolutionary Algorithms in Combinatorial Optimization Problems. Computational Methods in Applied Sciences. 2000
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documento
- Development of comprehensive methodologies for bacteriophage-host studies 2023
- A user-friendly bioinformatics pipeline for metaproteogenomics data analysis 2023
- Prediction of plastic-degrading enzymes in omics data from marine environments 2023
- A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer 2022
- Improving analysis of meta-omics data with the MOSCA framework 2022
- BioTMPy: a Deep Learning-based tool to classify biomedical literature 2021
- BioTMPy: a Deep Learning-based tool to classify biomedicalliterature 2021
- Development of computational tools for the analysis of 2D-nuclear magnetic resonance data 2021
- Molecular determinants of the SARS-CoV-2 fusion peptide activity 2021
- merlin v4. 0: an updated platform for the reconstruction of high-quality genome-scale metabolic models 2021
- UPIMAPI, reCOGnizer and KEGGCharter: three tools for functional annotation 2021
- ViralFP: A webserver of viral fusion proteins 2021
- merlin v4: an updated platform for reconstructing genome-scale metabolic models 2020
- A reconciled version of the cork oak tree genome-scale metabolic model 2020
- A reconciled version of the cork oak tree genome-scale metabolic model 2020
- ProPythia, an automated platform for the classification of peptides/proteins using machine learning 2020
- Method for n-butanol production using heterologous expression of anaerobic pathways 2019
- HABIT – a webserver for interactive T cell neoepitope discovery 2019
- The metabolic model of the Quercus suber (cork oak tree) leaf 2019
- Selected extended papers of the 12th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB). Journal of Integrative Bioinformatics. 2019
- Metabolomics-based approaches on wine authentication: a review with case studies 2018
- Marine invertebrates are a source of bioadhesives with biomimetic interest 2018
- Reconstruction of consensus tissue-specific metabolic models 2018
- Advanced Practical Applications of Computational Biology & Bioinformatics: PACBB15. Current Bioinformatics. 2018
- Specmine: an R package for metabolomics and spectral data analysis and mining 2017
- OptimModels: a framework for strain optimization using kinetic models 2017
- Development of text mining tools for information retrieval and extraction from patents 2017
- 11th International Conference on Practical Applications of Computational Biology & Bioinformatics - Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 616) 2017
- Selected Extended Papers of the 11th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB). Journal of Integrative Bioinformatics. 2017
- MIYeastK: The Metabolic Integrated Yeast Knowledgebase 2016
- Editorial (Thematic Issue: Selected Papers from the Annual PACBB Conference 2014: Special Issue). Current Bioinformatics. 2016
- A metabolic integrated yeast knowledgebase (MIYEASTK) 2016
- An R package for integrated analysis of metabolomics and spectral data 2016
- Development of a machine learning framework for biomedical text mining 2016
- Development of pathway analysis based algorithms for strain optimization 2016
- 10th International Conference on Practical Applications of Computational Biology & Bioinformatics - Part of the Advances in Intelligent Systems and Computing book series (AISC) 2016
- Prediction of drug targets in human pathogens 2015
- Comparing knockout strategies from in silico rational strain design tools 2015
- Reconstruction of regulatory network models and reconciliation with gene expression data 2015
- @Note2 open-source computational tools for biomedical text mining 2015
- Analysis of 140 published GSMs and identification of the most common representation problems 2015
- Evaluation of methods for the reconstruction of specific models from omics data 2015
- Reconciling gene expression data with regulatory network models 2015
- Visualizing omics data in the OptFlux workbench 2015
- Metabolic models reconstruction using genome scale information (merlin): assessment and validation 2015
- A text mining approach for the extraction of kinetic information from literature 2015
- 9th International Conference on Practical Applications of Computational Biology and Bioinformatics - Part of the Advances in Intelligent Systems and Computing book series (AISC) 2015
- MEtabolic models Reconstruction using genome scaLe INformation (merlin) - assessment and validation 2015
- Merlin Latest Developments for Pathways Analysis 2015
- HOXA9 promotes glioblastoma initiation, aggressiveness and resistance to therapy 2014
- Flexible and user friendly tools for the incorporation of fluxomics data into metabolic models 2014
- Reconciling gene expression data with regulatory network models – a stimulon-based approach for integrated metabolic and regulatory modeling of Bacillus subtilis 2014
- On the effects of phenotype prediction methods over strain design algorithms. A multi-objective approach 2014
- Prediction of protein subunits using KEGG BRITE 2014
- Visualization plugin for Optflux: tools for the creation of metabolic layouts and analysis of flux distributions 2014
- OptFlux3: an improved platform for in silico design of cellular factories 2013
- Long Non-Coding RNA HOTAIR is Transcriptionally Activated by HOXA9 and Is Associated with Poor Prognosis in Glioblastoma. 2013
- 7th International Conference on Practical Applications of Computational Biology and Bioinformatics 2013
- Long Non-Coding RNA HOTAIR is Transcriptionally Activated by HOXA9 and Is Associated with Poor Prognosis in Glioblastoma 2013
- A 1H-NMR-based metabolomic analysis of propolis from Santa Catarina state 2012
- HOXA9 target genes in Glioblastoma: characterization and clinical relevance 2012
- Development of dynamic multi-layered bioprocess models 2012
- Regulation of WNT6 expression by HOXA9 in glioblastoma and prognostic implications 2012
- 13C-based metabolic flux analysis 2012
- A generic multi-criterion approach for mutant strain optimization 2012
- Assembling genome-wide transporter system annotations 2012
- HOXA9 transcriptome analysis in Glioblastoma: The bioinformatics beyond the bench 2012
- Highlighting metabolic strategies using network analysis over strain optimization results 2012
- In silico metabolic engineering tool for simulation and optimization of microbial strains accounting integrated metabolic/regulatory information 2012
- In silico optimization of the production of amino-acids in Escherichia coli 2012
- OPTFERM - a computational platform for the optimization of fermentation processes 2012
- Advances in Intelligent and Soft Computing - Proc. of the PACBB 2012 2012
- Bioinformatics open days 2012: detailed program 2012
- Comparing results obtained from the Pathway Activity Profiling (PAPi) algorithm with 13C-based metabolic flux analysis 2011
- Metabolic engineering approaches for strain optimization using evolutionary computation techniques 2011
- Genome-scale metabolic models reconstruction of less characterized organisms with Merlin 2010
- Optflux: an open-source software platform for in silico metabolic engineering 2010
- Computational tools for data integration and regulatory network inference in systems biology 2010
- Digging out evidences on escherichia coli stringent response from scientific literature 2009
- A study on the effects of using gene-reaction rules on in silico strain optimization 2009
- Metabolic reconstruction of less characterized microorganisms : a new methodology for reaction identification from genome sequencing data 2009
- Bridging systems and synthetic biology for the development of improved microbial cell factories 2009
- Multi-criterion approaches for the in silico optimization of mutant microorganisms 2009
- OptFlux: a software for metabolic engineering 2009
- Uncovering mechanisms underlying the Escherichia coli stringent response: application of text mining approaches to identify meaningful relations in text documents 2009
- Metabolic reconstruction of less characterized microorganisms: a new methodology for reaction identification from genome sequencing data. 2009
- Bringing text miners and biologists closer together 2009
- Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface 2009
- Systems Biology for the development of microbial cell factories 2009
- OptGene: a framework for in silico metabolic engineering 2008
- Evolutionary multiobjective algorithms for in silico metabolic engineering 2008
- An integrated analysis of the metabolic and regulatory networks of escherichia coli K12 2008
- Network analysis of an integrated metabolic/regulatory model of Escherichia coli 2008
- The @Note biomedical text mining workbench 2008
- Constraint-based approach for in silico Escherichia coli combined regulatory/metabolic modelling 2007
- Literature mining applied to systems biology information retrieval 2007
- An improved evolutionary algorithm-based framework for identifying in silico metabolic engineering targets 2006
- Evolutionary algorithms for offline and online optimization of fed-batch fermentation processes 2005
- A diel multi-tissue genome-scale metabolic model ofVitis vinifera
- HABIT - a web server for interactive T cell neoepitope discovery
- M-PARTY - Mining Protein dAtasets foR Targeted EnzYmes
- SPINET: Syndemic Protein Interaction NETworks
-
livro
- Preface 2023
- Preface 2022
- Preface 2021
- Preface 2020
- Preface 2019
- Automated network resilience optimization using computational intelligence methods 2016
- Comparison of Single and Multi-objective Evolutionary Algorithms for Robust Link-state Routing 2016
- 9th International Conference on Practical Applications of Computational Biology and Bioinformatics 2015
- A framework for robust traffic engineering using evolutionary computation 2013
- Robust optimization of intradomain routing using Evolutionary Algorithms 2013
- A software platform for evolutionary computation with pluggable parallelism and quality assurance 2011
- Traffic engineering approaches using multicriteria optimization techniques 2011
- Spam email filtering using network-level properties 2010
- A Study of educational robotics in elementary schools 2008
- Multiconstrained optimization of networks with multicast and unicast traffic 2008
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poster de conferência
- Practical Applications of Computational Biology and Bioinformatics, 12th International Conference. AI Communications. 2018