AIMC Topic: Gastrointestinal Microbiome
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Deep in the Bowel: Highly Interpretable Neural Encoder-Decoder Networks Predict Gut Metabolites from Gut Microbiome.
BMC genomics
Jul 20, 2020
BACKGROUND: Technological advances in next-generation sequencing (NGS) and chromatographic assays [e.g., liquid chromatography mass spectrometry (LC-MS)] have made it possible to identify thousands of microbe and metabolite species, and to measure th...
Gut microbiome, big data and machine learning to promote precision medicine for cancer.
Nature reviews. Gastroenterology & hepatology
Jul 9, 2020
The gut microbiome has been implicated in cancer in several ways, as specific microbial signatures are known to promote cancer development and influence safety, tolerability and efficacy of therapies. The 'omics' technologies used for microbiome anal...
PopPhy-CNN: A Phylogenetic Tree Embedded Architecture for Convolutional Neural Networks to Predict Host Phenotype From Metagenomic Data.
IEEE journal of biomedical and health informatics
May 11, 2020
Accurate prediction of the host phenotype from a metagenomic sample and identification of the associated microbial markers are important in understanding potential host-microbiome interactions related to disease initiation and progression. We introdu...
Big data in IBD: big progress for clinical practice.
Gut
Feb 28, 2020
IBD is a complex multifactorial inflammatory disease of the gut driven by extrinsic and intrinsic factors, including host genetics, the immune system, environmental factors and the gut microbiome. Technological advancements such as next-generation se...
Depression phenotype identified by using single nucleotide exact amplicon sequence variants of the human gut microbiome.
Molecular psychiatry
Jan 27, 2020
Single nucleotide exact amplicon sequence variants (ASV) of the human gut microbiome were used to evaluate if individuals with a depression phenotype (DEPR) could be identified from healthy reference subjects (NODEP). Microbial DNA in stool samples o...
Heterologous Machine Learning for the Identification of Antimicrobial Activity in Human-Targeted Drugs.
Molecules (Basel, Switzerland)
Mar 31, 2019
The emergence of microbes resistant to common antibiotics represent a current treat to human health. It has been recently recognized that non-antibiotic labeled drugs may promote antibiotic-resistance mechanisms in the human microbiome by presenting ...
Exploring the interactions between serum free fatty acids and fecal microbiota in obesity through a machine learning algorithm.
Food research international (Ottawa, Ont.)
Dec 5, 2018
Serum free fatty acids (FFA) are generally elevated in obesity. The gut microbiota is involved in the host energy metabolism through the regulation of body fat storage, and a link between diet, FFA and the intestinal microbiota seems to exist. Our ai...
Using Unlabeled Data to Discover Bivariate Causality with Deep Restricted Boltzmann Machines.
IEEE/ACM transactions on computational biology and bioinformatics
Nov 5, 2018
An important question in microbiology is whether treatment causes changes in gut flora, and whether it also affects metabolism. The reconstruction of causal relations purely from non-temporal observational data is challenging. We address the problem ...
Detection of Colorectal Carcinoma Based on Microbiota Analysis Using Generalized Regression Neural Networks and Nonlinear Feature Selection.
IEEE/ACM transactions on computational biology and bioinformatics
Sep 13, 2018
To obtain a screening tool for colorectal cancer (CRC) based on gut microbiota, we seek here to identify an optimal classifier for CRC detection as well as a novel nonlinear feature selection method for determining the most discriminative microbial s...
Synbiotic meal decreases uremic toxins in hemodialysis individuals: A placebo-controlled trial.
Food research international (Ottawa, Ont.)
Aug 9, 2018
Generation of uremic toxins p-cresylsulfate (p-CS), indoxyl sulfate (IS) and indole 3-acetic acid (IAA) in hemodialysis (HD) individuals may be associated with the gut flora and recognized markers of disease progression. This study investigated the e...
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