publicações selecionadas
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artigo académico
- Ionic liquid-based nanoemulsion as a promising strategy to enhance the bioaccessibility of ß-carotene obtained from Dunaliella salina. Food Hydrocolloids. 2026
- PhageDPO: A machine-learning based computational framework for identifying phage depolymerases. Computers in Biology and Medicine. 2025
- Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction. BMC Bioinformatics. 2025
- Recovery and encapsulation of Dunaliella salina -carotene through a novel sustainable approach: Sequential application of an ionic liquid as naturally-derived solvent and emulsifier. Food Chemistry. 2024
- A diel multi-tissue genome-scale metabolic model of Vitis vinifera. PLoS Computational Biology. 2024
- Saccharomyces cerevisiae as a Host for Chondroitin Production. SynBio. 2024
- Development of highly effective growth strategies aiming at improving the content of carotenoids in Dunaliella salina IFDSAL-JY215. Sustainable Food Technology. 2024
- BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2024
- Development of highly effective growth strategies aiming at improving the content of carotenoids in Dunaliella salina IFDSAL-JY215. Sustainable Food Technology. 2024
- Optimization of chondroitin production in E. coli using genome scale models. Molecular Systems Design & Engineering. 2024
- TranSyT, an innovative framework for identifying transport systems. Bioinformatics. 2023
- Microalgae biomass as an alternative source of biocompounds: New insights and future perspectives of extraction methodologies. Food Research International. 2023
- Metabolic reconstruction of the human pathogen Candida auris. FEMS Yeast Research. 2023
- Systems biology's role in leveraging microalgal biomass potential: Current status and future perspectives. Algae Research. 2023
- The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber. PLoS Computational Biology. 2023
- Systematic assessment of template-based genome-scale metabolic models created with the BiGG Integration Tool. Journal of Integrative Bioinformatics. 2022
- merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models. Nucleic Acids Research. 2022
- Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking 2022
- A Genome-Scale Metabolic Model for the Human Pathogen Candida Parapsilosis and Early Identification of Putative Novel Antifungal Drug Targets. Genes. 2022
- Exploring synergies between plant metabolic modelling and machine learning. Computational and Structural Biotechnology Journal. 2022
- OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes. Life Science Alliance. 2021
- Insights into the genome architecture and evolution of Shiga toxin encoding bacteriophages of Escherichia coli. BMC Genomics. 2021
- A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli. PLoS Computational Biology. 2021
- A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale. BMC Bioinformatics. 2021
- A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale. BMC Bioinformatics. 2021
- Enhancing acetic acid and 5-hydroxymethyl furfural tolerance of C. saccharoperbutylacetonicum through adaptive laboratory evolution. Enzyme and Microbial Technology. 2021
- A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation. Biochemical SocIETy Transactions. 2020
- Genome-Scale Metabolic Model of the Human Pathogen Candida albicans: A Promising Platform for Drug Target Prediction. Journal of Invasive Fungal Infections. 2020
- A Tailspike with Exopolysaccharide Depolymerase Activity from a New Providencia stuartii Phage Makes Multidrug-Resistant Bacteria Susceptible to Serum-Mediated Killing. Applied and Environmental Microbiology. 2020
- PhageSuite - phage processing tools. Bioinformatics. 2019
- Staphylococci phages display vast genomic diversity and evolutionary relationships. BMC Genomics. 2019
- SamPler - a novel method for selecting parameters for gene functional annotation routines. BMC Bioinformatics. 2019
- Genome-wide sequencing and metabolic annotation of Pythium irregulare CBS 494.86: understanding Eicosapentaenoic acid production. BMC Biotechnology. 2019
- iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6. African Journal of Biotechnology. 2019
- Erratum to: Quantitative physiology and elemental composition of Kluyveromyces lactis CBS 2359 during growth on glucose at different specific growth rates. Antonie van Leeuwenhoek. 2017
- Genome-Wide Semi-Automated Annotation of Transporter Systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2017
- Quantitative physiology and elemental composition of Kluyveromyces lactis CBS 2359 during growth on glucose at different specific growth rates. Antonie van Leeuwenhoek. 2017
- Reconstructing genome-scale metabolic models with merlin. Nucleic Acids Research. 2015
- Genome-wide metabolic re-annotation of Ashbya gossypii: New insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis. BMC Genomics. 2014
- iOD907, the first genome-scale metabolic model for the milk yeast Kluyveromyces lactis. African Journal of Biotechnology. 2014
- Genome-wide metabolic (re-) annotation of Kluyveromyces lactis. BMC Genomics. 2012
- Dilution and Magnification Effects on Image Analysis Applications in Activated Sludge Characterization. Microscopy and Microanalysis. 2010
- A Comparison between Bright Field and Phase-Contrast Image Analysis Techniques in Activated Sludge Morphological Characterization. Microscopy and Microanalysis. 2010
- Correlation between sludge settling ability and image analysis information using partial least squares. Analytica Chimica Acta. 2009
- Monitoring of activated sludge settling ability through image analysis: Validation on full-scale wastewater treatment plants. Bioprocess Engineering. 2009
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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
- Towards a genome-scale metabolic model of Dunaliella salina. IFAC-PapersOnLine. 2024
- iplants: a repository of plant metabolic data 2024
- Exploring Xylella fastidiosa's Metabolic Traits Using a GSM Model of the Phytopathogenic Bacterium. Lecture Notes in Networks and Systems. 2022
- Metabolic engineering of Escherichia coli for biotechnological chondroitin production 2021
- Reconciliation of Regulatory Data: The Regulatory Networks of Escherichia coli and Bacillus subtilis. Advances in Intelligent Systems and Computing. 2020
- Towards the Reconstruction of the Genome-Scale Metabolic Model of Lactobacillus acidophilus La-14. Advances in Intelligent Systems and Computing. 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
- Towards a genome-wide transport systems encoding genes tracker 2018
- Modelling interspecies interactions of syntrophic communities 2017
- Towards an improved version of Kluyveromyces lactis genome-scale metabolic model 2016
- Metagenomic Analysis of the Saliva Microbiome with Merlin. Advances in Intelligent Systems and Computing. 2015
- Towards a genome-scale metabolic model of the Streptococcus pneumoniae R6 avirulent strain 2015
- Prediction of protein subunits using KEGG BRITE 2014
- Reconstruction of a genome-scale metabolic model for the filamentous fungus Ashbya gossypii 2013
- iOD962 - the first genome-scale metabolic model of Kluyveromyces lactis 2013
- Assembling genome-wide transporter system annotations 2012
- Reconstructing genome-scale metabolic models with merlin: the Ashbya gossypii case study 2012
- Reconstruction of a genome-scale metabolic model for the riboflavin producer fungus Ashbya gossypii 2012
- Revealing new biotechnological potentialities of the riboflavin producer fungus Ashbya gossypii by means of the construction and analysis of its metabolic network 2011
- Towards genome-wide semi-automated transporter system annotations 2011
- Merlin: Metabolic models reconstruction using genome-scale information. IFAC proceedings volumes. 2010
- Oral communication | Relationship between sludge volume index and biomass structure within activated sludge systems 2008
- Bright field versus phase contrast microscopy in activated sludge image acquisition methodologies 2008
- Dilution effects on aggregates and filaments contents in automated image analysis methodologies 2008
- Evaluation of activated sludge systems by image analysis procedures 2008
- Evaluation of activated sludge systems by image analysis procedures (oral presentation) 2008
- Oral communication | Evaluation of activated sludge systems by image analysis procedures 2008
- Poster communication | Bright Field versus Phase Contrast microscopy in activated sludge image acquisition methodologies 2008
- Relationship between sludge volume index and biomass structure within activated sludge systems 2008
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capítulo de livro
- Towards a Multivariate Analysis of Genome-Scale Metabolic Models Derived from the BiGG Models Database. Lecture Notes in Networks and Systems. 2022
- Predicting Promoters in Phage Genomes Using Machine Learning Models. Advances in Intelligent Systems and Computing. 2019
- Reconstructing High-Quality Large-Scale Metabolic Models with merlin. Methods in Molecular Biology. 2018
- Systems Biology in Fungi 2013
- Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis. Advances in Intelligent Systems and Computing. 2009
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documento
- Towards Enhanced Computational Prediction of Anti-CRISPR Proteins 2025
- Enhancing Phage Virulence Prediction: New Methodologies and Comparative Assessment 2025
- Reconstruction and exploitation of a dedicated Genome-Scale Metabolic Model of the human pathogen C. neoformans 2025
- DeepTransyt, annotation of transporter proteins using deep learning 2025
- Unveiling new features of the human pathogen Cryptococcus neoformans through the reconstruction and exploitation of a dedicated genome-scale metabolic model 2025
- diel_models: a python package for systematic integration of daynight cycles into plant genome-scale metabolic models. Bioinformatics Advances. 2025
- Dunaliella salina ß-carotene encapsulation: Utilization of Ionic Liquid cholinium oleate as extraction solvent and emulsifier 2024
- FROG analysis ensures the reproducibility of genome scale metabolic models 2024
- Nanoemulsion as a promising strategy to enhance the bioaccessibility of beta-carotene obtained from D. salina 2024
- COAST: A bioinformatic tool to identify the closest proteomes 2024
- Exploring methane mitigation strategies in photosynthetic microorganisms through genome-scale metabolic models 2024
- Advances in the diversity of Acinetobacter phage-encoded capsular depolymerases 2023
- Dunaliella salina biomass, a noble source of carotenoids: optimization process of ß-carotene accumulation 2023
- Development of comprehensive methodologies for bacteriophage-host studies 2023
- Machine learning in the service of phage analysis: advancements, applications, and future prospects 2023
- Bioinformatics approaches for engineering L-Tyrosine production in Escherichia coli 2022
- COAST: A bioinformatic tool to identify the closest proteomes 2022
- Drug Target Identification based on the construction of a Genome-scale metabolic model for the human pathogen Candida parapsilosis 2022
- Understanding the complete reservoir of bacteriophage depolymerases against A. baumannii capsules 2022
- Revising lipid chemical structures in genome-wide metabolic models with BOIMMG 2021
- Understanding the genome architecture and evolution of Shiga toxin encoding bacteriophages of Escherichia coli 2021
- Stoichiometric genome-scale models for the chondroitin production in Escherichia coli 2021
- Stoichiometric genome-scale models for the chondroitin production in Escherichia coli. 2021
- merlin v4. 0: an updated platform for the reconstruction of high-quality genome-scale metabolic models 2021
- A computational approach to finding new drug targets for pathogenic Candida species 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
- Quercus suber model - iEC7871 2021
- The Biochemical cOmplex data Integration in Metabolic Models at Genome-scale database and tool 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
- Genome-scale metabolic model of the human pathogen C. albicans: aiming the identification of promising new drug targets 2019
- Towards the integration of regulatory networks with metabolic models 2019
- A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli 2019
- Biological networks constraint-based In Silico Optimization 2019
- ProTReND - online database of transcriptional regulatory networks 2019
- The metabolic model of the Quercus suber (cork oak tree) leaf 2019
- Transport Systems Tracker 2019
- Endolysin binding domain is highly conserved in staphylococcal phage genomes 2018
- Towards a genome-wide transport systems encoding genes tracker 2018
- Eicosapentaenoic acid (EPA) production in silico by Pythium irregulare, as value-added product, using sugarcane vinasse as carbon source 2017
- Modelling interspecies interactions of syntrophic communities 2017
- Towards the identification of pathways for lipids biosynthesis in HCB 2017
- Towards an improved version of Kluyveromyces lactis genome-scale metabolic model 2016
- Systems biology in fungi 2015
- Metabolic models reconstruction using genome scale information (merlin): assessment and validation 2015
- MEtabolic models Reconstruction using genome scaLe INformation (merlin) - assessment and validation 2015
- Merlin Latest Developments for Pathways Analysis 2015
- Towards a Genome-Scale Metabolic Model of the Streptococcus Pneumoniae R6 Avirulent Strain 2015
- Prediction of protein subunits using KEGG BRITE 2014
- Reconstruction of a genome-scale metabolic model for the filamentous fungus Ashbya gossypii 2014
- Reconstruction of the genome-scale metabolic network of Kluyveromyces lactis 2013
- Reconstruction of a genome-scale metabolic model for the filamentous fungus Ashbya gossypii 2013
- Towards a genome-scale metabolic model for the Kluyveromyces lactis yeast 2013
- Towards a genome-scale metabolic model for the Kluyveromyces lactis yeast. 2013
- iOD962 - the first genome-scale metabolic model of Kluyveromyces lactis 2013
- Assembling genome-wide transporter system annotations 2012
- Reconstructing genome-scale metabolic models with merlin : the Ashbya gossypii case study 2012
- Reconstructing genome-scale metabolic models with merlin: the Ashbya gossypii case study 2012
- Reconstruction of a genome-scale metabolic model for the filamentous fungus Ashbya gossypii 2012
- Reconstruction of a genome-scale metabolic model for the riboflavin producer fungus Ashbya gossypii 2012
- Revealing new biotechnological potentialities of the riboflavin producer fungus Ashbya gossypii by means of the construction and analysis of its metabolic network 2011
- Towards genome-wide semi-automated transporter system annotations 2011
- Genome-scale metabolic models reconstruction of less characterized organisms with Merlin 2010
- Reconstructing genome-scale metabolic models with Merlin 2010
- Metabolic reconstruction of less characterized microorganisms : a new methodology for reaction identification from genome sequencing data 2009
- Metabolic reconstruction of less characterized microorganisms: a new methodology for reaction identification from genome sequencing data. 2009
- Relationship between sludge volume index and biomass structure within activated sludge systems 2008
- Bright field versus phase contrast microscopy in activated sludge image acquisition methodologies 2008
- Correlation between sludge settleability and image analysis information using Partial Least Squares 2008
- Dilution effects on aggregates and filaments contents in automated image analysis methodologies 2008
- Evaluation of activated sludge systems by image analysis procedures 2008
- Monitoring activated sludge systems from wastewater treatment plants : automated image analysis procedures and their relation with operating parameters 2007
- Monitoring activated sludge systems from wastewater treatment plants: automated image analysis procedures and their relation with operating parameters 2007
- Poster communication | Monitoring activated sludge systems from wastewater treatment plants: automated image analysis procedures and their relation with operating parameters 2007
- A diel multi-tissue genome-scale metabolic model ofVitis vinifera
- In Silico Design of Saccharomyces cerevisiae Strains for Improved Production of Chondroitin
- PhageDPO: Phage Depolymerase Finder
- Predicting precursors of plant specialized metabolites using DeepMol automated machine learning
- Saccharomyces cerevisiae as a Host for Chondroitin Production
- TranSyT, the Transport Systems Tracker
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teses
- Design and optimization of microbial communities 2024
- GEMification: gamification of genome-scale metabolic models 2024
- M3L: exploring synergies between metabolic modelling and machine learning for studying plants 2024
- Blueprint: documenting the complexity of metabolic regulation by reconstruction of integrated metabolic-regulatory models 2023
- Development and integration of topology-based methods for gap-filling of metabolic networks 2023
- Development of a serious game to stimulate the learning of genome-scale metabolic modeling concepts 2023
- Development of an artificial intelligence breast cancer diagnostic tool 2023
- Development of deep learning models for scRNA data analysis 2023
- Integrating machine learning and mechanistic modeling towards adaptation of plants to climate change 2023
- PhageAnnotate viral genome classifier 2023
- PhageSNP: prediction of the effect of hypermutable phage proteins along Staphylococcus genus 2023
- Bioinformatics approaches for engineering L-tyrosine production in Escherichia coli 2022
- Development and analysis of mathematical models to study metabolic constraints and capacities in different photosynthetic types 2022
- Development and implementation of methodologies for integrating omics data with genomic-scaled metabolic models 2022
- Development of DNA sequence classifiers based on deep learning 2022
- Development of a deep learning-based computational framework for the classification of protein sequences 2022
- Development of a framework for the classification of antibiotics adjuvants 2022
- Ecological modelling to describe the role of light on microbial interactions in Ulva spp. with implications in aquaculture 2022
- Genome-scale metabolic modelling of an extremophile microbial community 2022
- Multi-view learning for multiomics data integration for the study of plants 2022
- Biochemical complex data generation and integration in genome-scale metabolic models 2021
- PhageDPO: phage depolymerase finder 2021
- PhagePro: prophage finding tool 2021
- Unveiling the production of metabolites with flavor enhancement through genome-scale metabolic modelling of a lambic beer microbial community 2021
- A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli 2019
- Comparative analysis and characterization of industrial Streptococcus thermophilus genomes 2019
- Development and implementation of a repository for transcriptional regulatory information 2019
- Genome-scale metabolic modelling of the pathogen Xylella fastidiosa 2019
- Genome-scale reconstruction of the metabolic model of the probiotic bacterium Lactobacillus acidophilus 2019
- Identification and classification of transporter proteins using deep learning models 2019
- Implementation of the object-relational mapping tool Hibernate in merlin’s framework 2019
- In silico characterization of microbial communities interaction in soil samples 2019
- In silico objective-driven optimization of microbial communities 2019
- Modelling interspecies interactions of syntrophic communities of Syntrophobacter fumaroxidans and Methanospirillum hungatei 2019
- Reconstructing of the metabolic network of Lactobacillus rhamnosus 2019
- Development of bioinformatics tools to accelerate the reconstruction of genome-scale models 2018
- Nitrobacter vulgaris: genome-scale model reconstruction and interactions with Nitrosomonas europaea 2018
- PhagePromoter: phage promoters online analysis tool 2018
- Development and implementation of bioinformatics tools for the reconstruction of GiSMos 2017
- Reconstructing the metabolic network of Lactobacillus helveticus on a genome-wide scale 2017
- Reconstruction of the genome-scale metabolic model of Nitrosomonas europaea 2017
- Development of a computational approach for the identification and annotation of transport proteins 2016
- Reconstruction of the Genome-scale Metabolic Network of Kluyveromyces lactis 2013