8 documents found, page 1 of 1
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...
TranSyT, an innovative framework for identifying transport systems
Lagoa, Davide Rafael Santos; Faria, José P.; Liu, Filipe; Cunha, Emanuel Rodrigues; Henry, Christopher S.; Dias, OscarThe importance and rate of development of genome-scale metabolic models have been growing for the last years, increasing the demand for software solutions that automate several steps of this process. However, since TRIAGEs release, software development for automatic integration of transport reactions into models has stalled. Here we present the Transport Systems Tracker (TranSyT), the next iteration of TRIAGE. ...
Revising lipid chemical structures in genome-wide metabolic models with BOIMMG
Ribeiro, João Manuel Capela Araújo; Liu, Filipe; Dias, OscarAn important step in the reconstruction of Genome-Scale Metabolic (GSM) models is the integration of biochemical data. Such information is often incomplete or generic, lacking in completely defined chemical structures for several molecules, including lipids. The inumerous combinations of fatty acids in the side chains of lipids, hinder their storage in databases and integration into GSM models. Generic represen...
MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.Reconstructing metabolic reaction networks enables the development of testable hypotheses of an organisms metabolism under different conditions1. State-of-the-art genome-scale metabolic models (GEMs) can include thousands of metabolites and reactions that are assigned to subcellular locations. Geneproteinreaction (GPR) rules and annotations using database information can add meta-information to GEMs. GEMs with ...
Towards a genome-wide transport systems encoding genes tracker
Lagoa, D.; Liu, Filipe; Ferreira, Eugénio C.; Faria, J.; Henry, C.; Dias, Oscar[Excerpt] Introduction: TRIAGE, is a tool currently embedded in merlin , which performs the identification of transport systems and automatically generates transport reactions for every metabolite transported by those carriers. Reactions generated by TRIAGE can be directly integrated in GSM models, as all metabolites involved have KEGG and/or ChEBI identifiers. Up to our knowledge, this is the only tool capable...
Development and application of efficient pathway enumeration algorithms for met...
Liu, Filipe; Vilaça, Paulo; Rocha, I.; Rocha, MiguelMetabolic Engineering (ME) aims to design microbial cell factories towards the production of valuable compounds. In this endeavor, one important task relates to the search for the most suitable heterologous pathway(s) to add to the selected host. Different algorithms have been developed in the past towards this goal, following distinct approaches spanning constraint-based modelling, graph-based methods and know...
Prediction of protein subunits using KEGG BRITE
Dias, Oscar; Liu, Filipe; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, I.The increased importance of genome-scale metabolic models (GSMMs) within systems biology and metabolic engineering, led to the development of several computational frameworks dedicated to their reconstruction. One of the toughest challenges, when reconstructing a model is associated to the identification of gene-protein-reaction (GPR) associations, a step usually performed by manually searching literature. In t...
Evaluating pathway enumeration algorithms in metabolic engineering case studies
Liu, Filipe; Vilaça, Paulo; Rocha, I.; Rocha, MiguelThe design of cell factories for the production of compounds involves the search for suitable heterologous pathways. Different strategies have been proposed to infer such pathways, but most are optimization approaches with specific objective functions, not suited to enumerate multiple pathways. In this work, we analyze two pathway enumeration algorithms based on graph representations: the Solution Structure Gen...