publicações selecionadas
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artigo académico
- Unraveling the Potential of Chondrosia reniformis Collagen for Tissue Engineering Scaffolds, with Particular Insights into Chondrogenic Differentiation. Biomacromolecules. 2026
- 3D-Printed Cell-Instructive Scaffolds Based on Chondrosia reniformis Collagen and Sr-Doped Calcium Phosphates for Bone Tissue Engineering. ACS Biomaterials Science and Engineering. 2025
- Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction. BMC Bioinformatics. 2025
- Deepmol: an automated machine and deep learning framework for computational chemistry. Journal of Cheminformatics. 2024
- A diel multi-tissue genome-scale metabolic model of Vitis vinifera. PLoS Computational Biology. 2024
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MOSCA 2.0: A bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis and visualization. Molecular Ecology Resources. 2024 - 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
- M-PARTY: Mining Enzymes in Omics Data 2024
- A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer. PLoS Computational Biology. 2023
- The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber. 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
- Biomaterials and Bioactive Natural Products from Marine Invertebrates: From Basic Research to Innovative Applications. Marine Drugs. 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
- UPIMAPI, reCOGnizer and KEGGCharter: bioinformatics tools for functional annotation and visualization of (meta)-omics datasets. Computational and Structural Biotechnology Journal. 2022
- 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
- Diverse and Productive Source of Biopolymer Inspiration: Marine Collagens. Biomacromolecules. 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. AI Communications. 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
- 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
- The Effect of Depth on the Morphology, Bacterial Clearance, and Respiration of the Mediterranean Sponge Chondrosia reniformis (Nardo, 1847). Marine Drugs. 2020
- Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease. Leukemia. 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
- 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
- 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
- Comparative Analysis of the Adhesive Proteins of the Adult Stalked Goose Barnacle Pollicipes pollicipes (Cirripedia: Pedunculata). Marine Biotechnology. 2018
- A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering. African Journal of Biotechnology. 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
- 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
- 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
- Non-targeted Metabolomic Profiling of Maize Landraces (Zea mays L.) Combined with Chemometric Tools. International Journal of Biochemistry Research and Review. 2017
- A Chemometrics Approach for Nuclear Magnetic Resonance Data to Characterize the Partial Metabolome Banana Peels from Southern Brazil. Journal of Integrative Bioinformatics. 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
- 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
- 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. African Journal of Biotechnology. 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. African Journal of Biotechnology. 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
- D-Tailor: Automated analysis and design of DNA sequences. Bioinformatics. 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
- 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
- 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. Expert Systems. 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
- 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. AI Communications. 2007
- Evolving time series forecasting ARMA models. Journal of Heuristics. 2004
- A Lamarckian Approach for Neural Network Training.. Neural Processing Letters. 2002
- 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. IFAC-PapersOnLine. 2024
- Metabolic modelling reveals key pathways in COVID-19 in an effort to drive drug purposing. IFAC-PapersOnLine. 2024
- iplants: a repository of plant metabolic data 2024
- Combining Evolutionary Algorithms with Reaction Rules Towards Focused Molecular Design 2023
- Development of Deep Learning approaches to predict relationships between chemical structures and sweetness 2022
- A Comparison of Different Compound Representations for Drug Sensitivity Prediction 2021
- BioTMPy: A Deep Learning-Based Tool to Classify Biomedical Literature 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. Iberian Conference on Information Systems and Technologies (CISTI). 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. Advances in Intelligent Systems and Computing. 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. Advances in Intelligent Systems and Computing. 2019
- Artificial Intelligence in Biological Activity Prediction. Advances in Intelligent Systems and Computing. 2019
- Troppo - A Python Framework for the Reconstruction of Context-Specific Metabolic Models. Advances in Intelligent Systems and Computing. 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
- MOSCA: An automated pipeline for integrated metagenomics and metatranscriptomics data analysis. Advances in Intelligent Systems and Computing. 2019
- Automating the extraction of essential genes from literature. International Journal on Software Tools for Technology Transfer. 2018
- A review on metabolomics data analysis for cancer applications. Advances in Intelligent Systems and Computing. 2018
- In silico predictions for fucoxanthin production by the diatom phaeodactylum tricornutum. Advances in Intelligent Systems and Computing. 2018
- Metabolite integration pipeline for the improvement of human metabolic models. Advances in Intelligent Systems and Computing. 2018
- Segment routing single link failure congestion optimization 2018
- Segment routing single link failure congestion optimization 2018
- A critical evaluation of automatic atom mapping algorithms and tools. Advances in Intelligent Systems and Computing. 2017
- 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
- Classification tools for carotenoid content estimation in manihot esculenta via metabolomics and machine learning. Advances in Intelligent Systems and Computing. 2017
- Development of text mining tools for information retrieval from patents. Advances in Intelligent Systems and Computing. 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. Advances in Intelligent Systems and Computing. 2017
- Mixed-integer programming model for profiling disease biomarkers from gene expression studies. International Journal on Software Tools for Technology Transfer. 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. Advances in Intelligent Systems and Computing. 2017
- Carotenoid analysis of cassava genotypes roots (Manihot Esculenta Crantz) cultivated in southern Brazil using chemometric tools. Advances in Intelligent Systems and Computing. 2016
- Development of a machine learning framework for biomedical text mining. Advances in Intelligent Systems and Computing. 2016
- Development of an integrated framework for minimal cut set enumeration in constraint-based models. Advances in Intelligent Systems and Computing. 2016
- Reconstruction of metabolic models for liver cancer cells. Advances in Intelligent Systems and Computing. 2016
- A critical evaluation of methods for the reconstruction of tissue-specific models. International Journal on Software Tools for Technology Transfer. 2015
- A text mining approach for the extraction of kinetic information from literature. Advances in Intelligent Systems and Computing. 2015
- An integrated computational platform for metabolomics data analysis. Advances in Intelligent Systems and Computing. 2015
- Metagenomic Analysis of the Saliva Microbiome with Merlin. Advances in Intelligent Systems and Computing. 2015
- Microarray gene expression data integration: An application to brain tumor grade determination. Advances in Intelligent Systems and Computing. 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. Advances in Intelligent Systems and Computing. 2015
- 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
- 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. Advances in Intelligent Systems and Computing. 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. International Journal on Software Tools for Technology Transfer. 2012
- An algorithm to assemble gene-protein-reaction associations for genome-scale metabolic model reconstruction. International Journal on Software Tools for Technology Transfer. 2012
- Assembling genome-wide transporter system annotations 2012
- Computational tools for strain optimization by adding reactions. Advances in Intelligent Systems and Computing. 2012
- Computational tools for strain optimization by tuning the optimal level of gene expression. Advances in Intelligent Systems and Computing. 2012
- Evolutionary symbiotic feature selection for email spam detection 2012
- A study on the robustness of strain optimization algorithms. Advances in Intelligent Systems and Computing. 2011
- Highlighting metabolic strategies using network analysis over strain optimization results. International Journal on Software Tools for Technology Transfer. 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
- Merlin: Metabolic models reconstruction using genome-scale information. IFAC proceedings volumes. 2010
- Metaheuristics for strain optimization using transcriptional information enriched metabolic models. International Journal on Software Tools for Technology Transfer. 2010
- Model transformation of metabolic networks using a Petri net based framework 2010
- Pluggable parallelization of evolutionary algorithms applied to the optimization of biological processes 2010
- A study on the effects of using gene-reaction rules on in silico strain optimization 2009
- Bringing text miners and biologists closer together 2009
- Digging out evidences on escherichia coli stringent response from scientific literature 2009
- Implementing metaheuristic optimization algorithms with JECoLi. International Conference on Intelligent Systems Design and Applications. 2009
- Multi-criterion approaches for the in silico optimization of mutant microorganisms 2009
- OptFlux: a software for metabolic engineering 2009
- Optferm-a computational platform for the optimization of fermentation processes 2009
- Symbiotic Data Mining for personalized spam filtering 2009
- Uncovering mechanisms underlying the Escherichia coli stringent response: application of text mining approaches to identify meaningful relations in text documents 2009
- 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
- Evolutionary multiobjective algorithms for in silico metabolic engineering 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. Advances in Intelligent Systems and Computing. 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 2007
- Evolutionary computation for quality of service internet routing optimization 2007
- Optimization of bacterial strains with variable-sized evolutionary algorithms 2007
- Topology aware internet traffic forecasting using neural networks 2007
- A comparison of algorithms for the optimization of fermentation processes 2006
- Efficient OSPF weight allocation for intra-domain QoS optimization. International Journal on Software Tools for Technology Transfer. 2006
- Internet traffic forecasting using neural networks 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
- Evolutionary algorithms for offline and online optimization of fed-batch fermentation processes 2005
- Simultaneous evolution of neural network topologies and weights for classification and regression 2005
- 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 2002
- Genetic and evolutionary algorithms for time series forecasting 2001
- Lamarkian Training of Feedforward Neural Networks 2001
- Sitting guests at a wedding party: Experiments on genetic and evolutionary constrained optimization 2001
- Viewing scheduling problems through Genetic and Evolutionary Algorithms. International Journal on Software Tools for Technology Transfer. 2000
- 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. International Journal on Software Tools for Technology Transfer. 1999
- Neural network based time series forecasting system 1995
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capítulo de livro
- Marine Sponge-Derived Biomaterials and Their Biomedical Applications 2025
- Marine Sponges and Derived Biopolymers for Regenerative Medicine 2024
- 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. Advances in Intelligent Systems and Computing. 2020
- Predicting Promoters in Phage Genomes Using Machine Learning Models. Advances in Intelligent Systems and Computing. 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
- 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
- Optimizing Load Balancing Routing Mechanisms with Evolutionary Computation. Ambient Intelligence and Smart Environments. 2016
- Interpreting the Regulatory Interplay in E. coli Metabolic Pathways. Advances in Intelligent Systems and Computing. 2011
- A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems. International Journal on Software Tools for Technology Transfer. 2009
- A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models. International Journal on Software Tools for Technology Transfer. 2009
- Biomedical Text Mining Applied to Document Retrieval and Semantic Indexing. International Journal on Software Tools for Technology Transfer. 2009
- Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis. Advances in Intelligent Systems and Computing. 2009
- Evolutionary Approaches for Strain Optimization Using Dynamic Models under a Metabolic Engineering Perspective. International Journal on Software Tools for Technology Transfer. 2009
- Modelling of Biotechnological Processes – An Approach Based on Artificial Neural Networks. Studies in Computational Intelligence. 2009
- 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. International Journal on Software Tools for Technology Transfer. 2007
- Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains. International Journal on Software Tools for Technology Transfer. 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 Optimal Control in Fed-Batch Fermentation Processes. International Journal on Software Tools for Technology Transfer. 2004
- A Genetic and Evolutionary Programming Environment with Spatially Structured Populations and Built-In Parallelism 2001
- A Study of Order Based Genetic and Evolutionary Algorithms in Combinatorial Optimization Problems. International Journal on Software Tools for Technology Transfer. 2000
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documento
- Towards Enhanced Computational Prediction of Anti-CRISPR Proteins 2025
- Chondrosia reniformis as source of compounds and inspiration for developing tissue engineering scaffolds 2025
- TROPPO: tissue-specific reconstruction and phenotype prediction using omics data. Bioinformatics Advances. 2025
- Enhancing Phage Virulence Prediction: New Methodologies and Comparative Assessment 2025
- Implementing metabolic transformation algorithms and their application in ageing-related research 2025
- Cellular and biochemical alterations induced by diesel oil in the brown alga Sargassum cymosum var. stenophyllum cultured in vitro. Chemosphere. 2025
- Investigating the stiffening phenomenon in Chondrosia reniformis using high-throughput transcriptomic and proteomic analyses 2025
- Computationally-designed miniproteins showing neutralization activity against SARS-CoV-2 2024
- Individual-Based Modeling elucidates about the role of nanomaterials on methane production 2024
- Individual-based modelling elucidates about the role of nanomaterials on methane production 2024
- Systems Biology in ELIXIR: modelling in the spotlight. F1000research. 2024
- Recent advances in data- and knowledge-driven approaches to explore primary microbial metabolism. Current Opinion in Chemical Biology. 2023
- 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
- Metaproteogenomics analysis of an anaerobic bioreactor with the MOSCA pipeline 2023
- Uncovering the role of conductive nanomaterials on anaerobic digestion 2023
- User-friendly and reproducible Metaproteogenomics: studying communities on all levels of life 2023
- 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
- 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
- Development of deep learning approaches to predict relationships between chemical structures and sweetness. IEEE International Joint Conference on Neural Networks (IJCNN). 2022
- 3D printed scaffolds based on marine sponge collagen and Sr-doped fish bones for bone tissue engineering 2021
- Collagen extraction, isolation and characterization from marine sponges 2021
- ViralFP: a web application of viral fusion proteins. Frontiers in Medical Technology. 2021
- BioTMPy: a Deep Learning-based tool to classify biomedical literature 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
- IEC7871 Quercus suber model: The first multi-tissue diel cycle genome-scale metabolic model of a woody tree. International Journal of Medical Microbiology. 2021
- UPIMAPI, reCOGnizer and KEGGCharter: three tools for functional annotation 2021
- ViralFP: A webserver of viral fusion proteins 2021
- Banana (Musa spp.) as a source of bioactive compounds for health promotion 2020
- 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
- Characterization of collagen from the marine invertebrate Actinia fragacea (Cnidaria) and assessment of biotechnological potential 2019
- Production of Collagen From Maricultured Sponge Chondrosia reniformis 2019
- Method for n-butanol production using heterologous expression of anaerobic pathways 2019
- Biomedical potential of the sea anemone Actinia fragacea (Cnidaria) 2019
- Development of Novel Biomedical Applications Based on Chondrosia Reniformis Collagen Aggregation Phenomenon 2019
- Show us your beaks and we tell you what you eat: Different ecology in sympatric Antarctic benthic octopods under a climate change context. 2019
- Study of structural and functional proteins in the sea anemone Actinia fragacea (Cnidaria) and their potential biomedical interest 2019
- Understanding and mimicking Chondrosia reniformis collagen aggregation phenomenon 2019
- Contributing of “omics” for the understanding of Chondrosia reniformis collagen aggregation phenomenom 2019
- HABIT – a webserver for interactive T cell neoepitope discovery 2019
- Selected extended papers of the 12th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB). Journal of Integrative Bioinformatics. 2019
- The metabolic model of the Quercus suber (cork oak tree) leaf 2019
- The metabolic model of the Quercus suber (cork oak tree) leaf 2019
- Metabolomics-based approaches on wine authentication: a review with case studies 2018
- Chondrosia reniformis adaptability phenomenon as a source of inspiration for the development of biotechnological applications: biomimetic aggregation of collagen 2018
- Marine invertebrates are a source of bioadhesives with biomimetic interest 2018
- Bioadhesion in the marine crustacean Pollicipes pollicipes 2018
- Chondrosia reniformis dynamic collagenous tissues and aggregating factor(s) as a source of inspiration for the development of biomedical applications 2018
- Reconstruction of consensus tissue-specific metabolic models 2018
- Advanced Practical Applications of Computational Biology & Bioinformatics: PACBB15. Current Bioinformatics. 2018
- Interaction between marine collagens and Chondrosia reniformis marine sponge extract under the context of dynamic collagenous tissues 2017
- New adhesive proteins from the Deep sea hydrothermal vent mussel Bathymodiolus azoricus 2017
- Specmine: an R package for metabolomics and spectral data analysis and mining 2017
- OptimModels: a framework for strain optimization using kinetic models 2017
- Extraction and purification of collagen and aggregating factor(s) from Chondrosia reniformis for the production of biomimetic hydrogels 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
- A DREAM challenge to build prediction models for short-term discontinuation of docetaxel in metastatic castration-resistant prostate cancer. JCO Clinical Cancer Informatics. 2017
- Metabolômica e quimiometria como ferramentas para análises quimio(bio) diversas 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
- 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 framework for improving routing configurations using multi-objective optimization mechanisms. Journal of Communications Software and Systems. 2016
- A metabolic integrated yeast knowledgebase (MIYEASTK) 2016
- An R package for integrated analysis of metabolomics and spectral data 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
- Characterization of Pollicipes pollicipes cement protein-100K gene 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
- Re-annotation of the genome sequence of Helicobacter pylori 26695. Journal of Integrative Bioinformatics. 2013
- A 1H-NMR-based metabolomic analysis of propolis from Santa Catarina state 2012
- Evolutionary symbiotic feature selection for email spam detection 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
- 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
- Assembling genome-wide transporter system annotations 2012
- Bioinformatics open days 2012: detailed program 2012
- In silico strain optimization by adding reactions to metabolic models. Journal of Integrative Bioinformatics. 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
- Computational tools for data integration and regulatory network inference in systems biology 2010
- Enhancing Elementary Flux Modes analysis using filtering techniques in an integrated environment. Advances in Intelligent Systems and Computing. 2010
- Genome-scale metabolic models reconstruction of less characterized organisms with Merlin 2010
- Model transformation of metabolic networks using a Petri net based framework. CEUR Workshop Proceedings. 2010
- Tools for traffic engineering on IP networks 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
- Combining syntactic and ontological knowledge to extract biologically relevant relations from scientific papers 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
- OptFerm - a computational platform for the optimization of fermentation processes 2009
- Systems Biology for the development of microbial cell factories 2009
- A tool for the automatic and manual annotation of biomedical documents 2008
- OptGene: a framework 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
- An evolutionary algorithm for unicast/multicast traffic engineering 2008
- Forecasting Internet traffic by Neural Networks under univariate and multivariate strategies 2008
- A Study of educational robotics in elementary schools 2008
- The @Note biomedical text mining workbench 2008
- An ontology-based approach to systems biology literature retrieval and processing 2007
- Topology aware Internet traffic forecasting using neural networks. International Journal on Software Tools for Technology Transfer. 2007
- Class-based OSPF traffic engineering inspired on evolutionary computation. International Journal on Software Tools for Technology Transfer. 2007
- Automatic provisioning of QoS aware OSPF configurations. Journal of Networks. 2007
- Evolutionary computation for quality of service internet routing optimization. International Journal on Software Tools for Technology Transfer. 2007
- Optimization of bacterial strains with variable-sized evolutionary algorithms 2007
- 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
- Internet traffic forecasting using neural networks. IEEE International Joint Conference on Neural Networks (IJCNN). 2006
- Qos constrained internet routing with evolutionary algorithms 2006
- A comparison of algorithms for the optimization of fermentation processes 2006
- A new representation in evolutionary algorithms for the optimization of bioprocesses 2005
- Simultaneous evolution of neural network topologies and weights for classification and regression. International Journal on Software Tools for Technology Transfer. 2005
- Evolutionary design of neural networks for classification and regression 2005
- Evolutionary algorithms for offline and online optimization of fed-batch fermentation processes 2005
- Evolutionary algorithms for static and dynamic optimization of fed-batch fermentation processes 2005
- An architecture for co-evolving agents in the ROBOCUP Simulation League 2004
- Evolutionary neural network learning algorithms for changing environments. WSEAS Transactions on Systems. 2004
- Ensembles of artificial neural networks with heterogeneous topologies 2004
- Evolutionary neural network learning. International Journal on Software Tools for Technology Transfer. 2003
- Adaptive learning in changing environments 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
- Genetic and evolutionary algorithms for time series forecasting. International Journal on Software Tools for Technology Transfer. 2001
- Lamarckian training of feedforward neural networks 2001
- Evolving Time Series Forecasting Neural Network Models 2001
- A genetic and evolutionary programming environment with spatially structured populations and built-in parallelism. International Journal on Software Tools for Technology Transfer. 2001
- The relationship between learning and evolution in static and dynamic environments 2000
- An evolutionary and connectionist approach for time series forecasting 1999
- Adaptive strategies and the design of evolutionary applications 1999
- A neural network based time series forecasting system 1995
- 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
- Predicting precursors of plant specialized metabolites using DeepMol automated machine learning
- SPINET: Syndemic Protein Interaction NETworks
- SPINET: Syndemic Protein Interaction NETworks
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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
- Multiconstrained optimization of networks with multicast and unicast traffic 2008
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teses
- 17a-ethinylestradiol analysis of endo- and exometabolome of ulva lactuca (chlorophyta) by 1H-NMR spectroscopy and bioinformatics tools. Advances in Intelligent Systems and Computing. 2018