AIMC Topic: Metabolic Networks and Pathways

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METSP: a maximum-entropy classifier based text mining tool for transporter-substrate identification with semistructured text.

BioMed research international
The substrates of a transporter are not only useful for inferring function of the transporter, but also important to discover compound-compound interaction and to reconstruct metabolic pathway. Though plenty of data has been accumulated with the deve...

The role of regulation in the origin and synthetic modelling of minimal cognition.

Bio Systems
In this paper we address the question of minimal cognition by investigating the origin of some crucial cognitive properties from the very basic organisation of biological systems. More specifically, we propose a theoretical model of how a system can ...

Machine Learning Models and Pathway Genome Data Base for Trypanosoma cruzi Drug Discovery.

PLoS neglected tropical diseases
BACKGROUND: Chagas disease is a neglected tropical disease (NTD) caused by the eukaryotic parasite Trypanosoma cruzi. The current clinical and preclinical pipeline for T. cruzi is extremely sparse and lacks drug target diversity.

Systems analysis of gene ontology and biological pathways involved in post-myocardial infarction responses.

BMC genomics
BACKGROUND: Pathway analysis has been widely used to gain insight into essential mechanisms of the response to myocardial infarction (MI). Currently, there exist multiple pathway databases that organize molecular datasets and manually curate pathway ...

Measuring semantic similarities by combining gene ontology annotations and gene co-function networks.

BMC bioinformatics
BACKGROUND: Gene Ontology (GO) has been used widely to study functional relationships between genes. The current semantic similarity measures rely only on GO annotations and GO structure. This limits the power of GO-based similarity because of the li...

Discovering the metabolic pathway of liver disease by breath mass spectrometry combined with machine learning.

Journal of pharmaceutical and biomedical analysis
On account of the low concentration and complex background, most methods for detecting VOCs in exhaled breath samples required preconcentration prior to instrumental analysis. In the current study, a simple and rapid method is developed for analyzing...

MS2MP: A Deep Learning Framework for Metabolic Pathway Prediction from MS/MS-Based Untargeted Metabolomics.

Analytical chemistry
MS/MS-based untargeted metabolomics generates complex data, but pathway enrichment analysis is constrained by the low annotation rates of metabolic features. Here, we propose MS2MP, a novel deep learning-based framework for KEGG pathway prediction di...

Metabolic pathway alterations in cerebrospinal fluid as diagnostic biomarkers for primary central nervous system lymphoma.

Clinica chimica acta; international journal of clinical chemistry
Primary Central Nervous System Lymphoma (PCNSL) is a rare and aggressive type of hematological malignancy that can pose diagnostic challenges. Early detection is critical for effective treatment and better patient outcomes. The goal of this study was...

Application of a metabolic network-based graph neural network for the identification of toxicant-induced perturbations.

Toxicological sciences : an official journal of the Society of Toxicology
Transcriptomic analyses have been an effective approach to investigate the biological responses and metabolic perturbations by environmental contaminants in rodent models. However, it is well recognized that metabolic networks are highly connected an...