113 documents found, page 1 of 12
Ionic liquid-based nanoemulsion as a promising strategy to enhance the bioacces...
Sousa, Vítor; Lüdtke, Fernanda Luisa; Hijo, Ariel A. C. Toledo; Loureiro, Luís; Dias, Oscar; Vicente, A. A.; Pinheiro, A. C.; Geada, PedroDunaliella salina is a unicellular halophile green microalga that presents the capacity to accumulate high amounts of β-carotene, a bioactive compound widely recognized by its health benefits. To fulfil its biological functions, however, β-carotene needs to be bioaccessible, which is challenging as its bioaccessibility is typically low. A promising strategy to overcome β-carotene's low bioaccessibility is its e...
DeepTransyt, annotation of transporter proteins using deep learning
Cardoso, Gonçalo; Liu, Filipe; Henry, Christopher S.; Dias, OscarGenome-Scale Metabolic (GSM) models are essential tools for studying and engineering cellular metabolism, with transporter annotation representing a critical step in their reconstruction. However, traditional annotation methods, such as homology-based approaches like BLAST, are very dependent on the existence of available data, struggling when it comes to novel examples. To address these challenges, DeepTransyt...
Comparative assessment of protein large language models for enzyme commission n...
Capela, João; Zimmermann-Kogadeeva, Maria; Dijk, Aalt D. J. van; de Ridder, Dick; Dias, Oscar; Rocha, MiguelBackground: Protein large language models (LLM) have been used to extract representations of enzyme sequences to predict their function, which is encoded by enzyme commission (EC) numbers. However, a comprehensive comparison of different LLMs for this task is still lacking, leaving questions about their relative performance. Moreover, protein sequence alignments (e.g. BLASTp or DIAMOND) are often combined with ...
PhageDPO: A machine-learning based computational framework for identifying phag...
Vieira, Maria Fernanda; Duarte, José; Domingues, Rita; Oliveira, Hugo Alexandre Mendes; Dias, OscarBacteriophages (phages) are the most predominant and genetically diverse biological entities on Earth. Phages are viruses that infect bacteria and encode numerous proteins with potential biotechnological application. However, most phage-encoded proteins remain functionally uncharacterized. Depolymerases (DPOs) in particular, enzymes that degrade external polysaccharide structures, have garnered increasing inter...
diel_models: a python package for systematic integration of daynight cycles int...
Martins, Luciana; Capela, João; Cunha, Emanuel Rodrigues; Sampaio, Marta; Dias, OscarIn recent years, genome-scale metabolic models have become indispensable tools for studying complex metabolic processes occurring within living organisms. Understanding plants metabolic behaviour under diel cycles (24-h daynight cycles) is essential to explain their adaptive strategies to different light conditions. However, integrating these cycles in plant GEMs is complex, laborious, time-consuming, and not s...
Reconstruction and exploitation of a dedicated Genome-Scale Metabolic Model of ...
Viana, Romeu; Couceiro, Diogo; Newton, William; Coutinho, Luís; Dias, Oscar; Coelho, Carolina; Teixeira, Miguel CachoC. neoformans is notorious for causing severe pulmonary and central nervous system infections, particularly in immunocompromised patients. High mortality rates, associated with its tropism and adaptation to the brain microenvironment and its drug resistance profile, makes this pathogen a public health threat and a World Health Organization (WHO) priority.In this study, we reconstructed GSMM iRV890 for C. neofor...
Unveiling new features of the human pathogen Cryptococcus neoformans through th...
Viana, Romeu; Couceiro, Diogo; Newton, William; Coutinho, Luís; Dias, Oscar; Coelho, Carolina; Teixeira, Miguel CachoCryptococcus neoformans is notorious for causing severe pulmonary and central nervous system infections, particularly in immunocompromised patients. High mortality rates, associated with its tropism and adaptation to the brain microenvironment and its drug resistance profile, make this pathogen a public health threat and a World Health Organization (WHO) priority. This study presents the first reconstructed gen...
Saccharomyces cerevisiae as a host for chondroitin production
Couto, Márcia R.; Rodrigues, Joana Lúcia Lima Correia; Dias, Oscar; Rodrigues, Lígia M.Chondroitin is a glycosaminoglycan that has gained widespread use in nutraceuticals and pharmaceuticals, mainly for treating osteoarthritis. Traditionally, it has been extracted from animal cartilage but recently, biotechnological processes have emerged as a commercial alternative to avoid the risk of viral or prion contamination and offer a vegan-friendly source. Typically, these methods involve producing the ...
BioISO: an objective-oriented application for assisting the curation of genome-...
Cruz, Fernando João Pereira; Capela, João; Ferreira, Eugénio C.; Rocha, Miguel; Dias, OscarAs the reconstruction of Genome-Scale Metabolic Models (GEMs) becomes standard practice in systems biology, the number of organisms having at least one metabolic model is peaking at an unprecedented scale. The automation of laborious tasks, such as gap-finding and gap-filling, allowed the development of GEMs for poorly described organisms. However, the quality of these models can be compromised by the automatio...
FROG analysis ensures the reproducibility of genome scale metabolic models
Raman, Karthik; Kratochvil, Miroslav; Olivier, Brett G.; Konig, Matthias; Sengupta, Pratyay; Baskaran, Dinesh Kumar Kuppa; Nguyen, Tung V NGenome scale metabolic models (GEMs) and other constraint-based models (CBMs) play a pivotal role in understanding biological phenotypes and advancing research in areas like metabolic engineering, human disease modelling, drug discovery, and personalized medicine. Despite their growing application, a significant challenge remains in ensuring the reproducibility of GEMs, primarily due to inconsistent reporting a...