10 documents found, page 1 of 1
Implementing metabolic transformation algorithms and their application in agein...
Sá, Bruno; Oliveira, Alexandre Rafael Machado; Rocha, MiguelThis work presents the Python-based implementation and validation of the Metabolic Transformation Algorithm (MTA) and its robust counterpart (rMTA), originally developed in MATLAB. MTA/rMTA facilitates the identification of therapeutic metabolic interventions by simulating gene knockouts and evaluating their potential to redirect metabolic fluxes toward healthier phenotypes. The transition to Python capitalizes...
TROPPO: tissue-specific reconstruction and phenotype prediction using omics data
Oliveira, Alexandre Rafael Machado; Ferreira, Jorge; Vieira, Vítor; Sá, Bruno; Rocha, MiguelThe increasing availability of high-throughput technologies in systems biology has advanced predictive tools like genome-scale metabolic models. Despite this progress, integrating omics data to create accurate, context-specific metabolic models for different tissues or cells remains challenging. A significant issue is that many existing tools rely on proprietary software, which limits accessibility. We introduc...
A systems biology approach to model COVID-19 phenotypes and drive drug discovery
Oliveira, Alexandre Rafael MachadoA COVID-19 é uma doença complexa que teve um impacto profundo na saúde pública a nível global. A variabilidade dos perfis clínicos e das respostas específicas dos tecidos beneficia de abordagens da biologia de sistemas para uma melhor compreensão dos mecanismos de infeção envolvidos. A crescente disponibilidade de dados multi-ómicos, em conjunto com ferramentas computacionais, introduziu a possibilidade de estu...
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...
Metabolic modelling reveals key pathways in COVID-19 in an effort to drive drug...
Oliveira, Alexandre Rafael Machado; Rocha, Miguel; Dias, OscarSince the onset of the COVID-19 pandemic, there has been a pressing need for innovative drugs tackling this disease. In this context, this study aimed to develop context-specific metabolic models using transcriptomics data to uncover significant flux changes and drive drug repurposing. Differential flux analyses revealed significant flux alterations, particularly in fatty acid metabolism, with notable changes o...
Exploring Xylella fastidiosas metabolic traits using a GSM model of the phytopa...
Oliveira, Alexandre Rafael Machado; Cunha, Emanuel Rodrigues; Silva, Miguel; Faria, Cristiana Silva; Dias, OscarXylella fastidiosa is a gram-negative phytopathogenic bacterium able to infect over 500 plant species, with devastating consequences for agricultural and forest-based economies. In the last decade, genome-scale metabolic (GSM) models have become important systems biology tools for studying the metabolic behaviour of different organisms. In this work, a GSM model of X. fastidiosa subsp. pauca De Donno is present...
Systematic assessment of template-based genome-scale metabolic models created w...
Oliveira, Alexandre Rafael Machado; Cunha, Emanuel; Cruz, Fernando João Pereira; Capela, João; Sequeira, J. C.; Sampaio, Marta; Ganâncio, CláudiaGenome-scale metabolic models (GEMs) are essential tools for in silico phenotype prediction and strain optimisation. The most straightforward GEMs reconstruction approach uses published models as templates to generate theinitial draft, requiring further curation. Such an approachis used by BiGG Integration Tool (BIT), available for merlin users. This tool uses models from BiGG Models database as templates for t...
Towards a multivariate analysis of genome-scale metabolic models derived from t...
Oliveira, Alexandre Rafael Machado; Cunha, Emanuel Rodrigues; Cruz, Fernando João Pereira da; Ribeiro, João Manuel Capela AraújoGenome-Scale metabolic models (GEMs) are a relevant tool in systems biology for in silico strain optimisation and drug discovery. An easier way to reconstruct a model is to use available GEMs as templates to create the initial draft, which can be curated up until a simulation-ready model is obtained. This approach is implemented in merlin's BiGG Integration Tool, which reconstructs models from existing GEMs pre...
A kinetic model of the central carbon metabolism for acrylic acid production in...
Oliveira, Alexandre Rafael Machado; Rodrigues, Joana Lúcia Lima Correia; Ferreira, Eugénio C.; Rodrigues, L. R.; Dias, OscarAcrylic acid is an economically important chemical compound due to its high market value. Nevertheless, the majority of acrylic acid consumed worldwide its produced from petroleum derivatives by a purely chemical process, which is not only expensive, but it also contributes towards environment deterioration. Hence, justifying the current need for sustainable novel production methods that allow higher profit mar...
A kinetic model of the central carbon metabolism for acrylic acid production in...
Oliveira, Alexandre Rafael MachadoO Ácido Acrílico (AA) é um composto químico que atualmente possui um valor de mercado considerável. Contudo, a maioria do AA comercializado ainda é proveniente da oxidação de derivados do petróleo, como o propileno e o propeno, método que se revela dispendioso e que contribui para o deterioramento do planeta. Assim sendo, existe a necessidade de encontrar novos métodos, mais sustentáveis, para a produção deste ...