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Metabolome

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Understanding mixed environmental exposures using metabolomics via a hierarchical community network model in a cohort of California women in 1960's.

Reproductive toxicology (Elmsford, N.Y.)
Even though the majority of population studies in environmental health focus on a single factor, environmental exposure in the real world is a mixture of many chemicals. The concept of "exposome" leads to an intellectual framework of measuring many e...

Classification of alkaloids according to the starting substances of their biosynthetic pathways using graph convolutional neural networks.

BMC bioinformatics
BACKGROUND: Alkaloids, a class of organic compounds that contain nitrogen bases, are mainly synthesized as secondary metabolites in plants and fungi, and they have a wide range of bioactivities. Although there are thousands of compounds in this class...

Discovery of food identity markers by metabolomics and machine learning technology.

Scientific reports
Verification of food authenticity establishes consumer trust in food ingredients and components of processed food. Next to genetic or protein markers, chemicals are unique identifiers of food components. Non-targeted metabolomics is ideally suited to...

Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples.

Biology direct
BACKGROUND: The availability of hundreds of city microbiome profiles allows the development of increasingly accurate predictors of the origin of a sample based on its microbiota composition. Typical microbiome studies involve the analysis of bacteria...

FOBI: an ontology to represent food intake data and associate it with metabolomic data.

Database : the journal of biological databases and curation
Nutrition research can be conducted by using two complementary approaches: (i) traditional self-reporting methods or (ii) via metabolomics techniques to analyze food intake biomarkers in biofluids. However, the complexity and heterogeneity of these t...

An unsupervised learning approach to identify novel signatures of health and disease from multimodal data.

Genome medicine
BACKGROUND: Modern medicine is rapidly moving towards a data-driven paradigm based on comprehensive multimodal health assessments. Integrated analysis of data from different modalities has the potential of uncovering novel biomarkers and disease sign...

Untargeted Metabolomics for Metabolic Diagnostic Screening with Automated Data Interpretation Using a Knowledge-Based Algorithm.

International journal of molecular sciences
Untargeted metabolomics may become a standard approach to address diagnostic requests, but, at present, data interpretation is very labor-intensive. To facilitate its implementation in metabolic diagnostic screening, we developed a method for automat...

Effect of congenital adrenal hyperplasia treated by glucocorticoids on plasma metabolome: a machine-learning-based analysis.

Scientific reports
BACKGROUND: Congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency leads to impaired cortisol biosynthesis. Treatment includes glucocorticoid supplementation. We studied the specific metabolomics signatures in CAH patients using two di...

How to Apply Supervised Machine Learning Tools to MS Imaging Files: Case Study with Cancer Spheroids Undergoing Treatment with the Monoclonal Antibody Cetuximab.

Journal of the American Society for Mass Spectrometry
As the field of mass spectrometry imaging continues to grow, so too do its needs for optimal methods of data analysis. One general need in image analysis is the ability to classify the underlying regions within an image, as healthy or diseased, for e...