AIMC Topic: Gastrointestinal Microbiome
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Identification of antimicrobial peptides from the human gut microbiome using deep learning.
Nature biotechnology
Mar 3, 2022
The human gut microbiome encodes a large variety of antimicrobial peptides (AMPs), but the short lengths of AMPs pose a challenge for computational prediction. Here we combined multiple natural language processing neural network models, including LST...
Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer.
Scientific reports
Jan 10, 2022
Gut microbiome is gaining interest because of its links with several diseases, including colorectal cancer (CRC), as well as the possibility of being used to obtain non-intrusive predictive disease biomarkers. Here we performed a meta-analysis of 104...
Accurate diagnosis of atopic dermatitis by combining transcriptome and microbiota data with supervised machine learning.
Scientific reports
Jan 7, 2022
Atopic dermatitis (AD) is a common skin disease in childhood whose diagnosis requires expertise in dermatology. Recent studies have indicated that host genes-microbial interactions in the gut contribute to human diseases including AD. We sought to de...
Identifying Microbe-Disease Association Based on a Novel Back-Propagation Neural Network Model.
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2021
Over the years, numerous evidences have demonstrated that microbes living in the human body are closely related to human life activities and human diseases. However, traditional biological experiments are time-consuming and expensive, so it has becom...
Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network.
PLoS computational biology
Sep 22, 2021
Recurrent neural networks with memory and attention mechanisms are widely used in natural language processing because they can capture short and long term sequential information for diverse tasks. We propose an integrated deep learning model for micr...
Kefir modulates gut microbiota and reduces DMH-associated colorectal cancer via regulation of intestinal inflammation in adulthood offsprings programmed by neonatal overfeeding.
Food research international (Ottawa, Ont.)
Sep 8, 2021
Obesity is associated with chronic inflammation, intestinal dysbiosis, and colorectal cancer risk. The anti-cancer effects of kefir are highlighted. Here, lactating Wistar rats were divided into: Normal litter (NL); Kefir normal litter (KNL); Small l...
Delivery mode and perinatal antibiotics influence the predicted metabolic pathways of the gut microbiome.
Scientific reports
Sep 1, 2021
Delivery mode and perinatal antibiotics influence gut microbiome composition in children. Most microbiome studies have used the sequencing of the bacterial 16S marker gene but have not reported the metabolic function of the gut microbiome, which may ...
Microbiome Preprocessing Machine Learning Pipeline.
Frontiers in immunology
Jun 18, 2021
BACKGROUND: 16S sequencing results are often used for Machine Learning (ML) tasks. 16S gene sequences are represented as feature counts, which are associated with taxonomic representation. Raw feature counts may not be the optimal representation for ...
Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.
Genome biology
Mar 30, 2021
The human microbiome is increasingly mined for diagnostic and therapeutic biomarkers using machine learning (ML). However, metagenomics-specific software is scarce, and overoptimistic evaluation and limited cross-study generalization are prevailing i...
Nonlinear machine learning pattern recognition and bacteria-metabolite multilayer network analysis of perturbed gastric microbiome.
Nature communications
Mar 26, 2021
The stomach is inhabited by diverse microbial communities, co-existing in a dynamic balance. Long-term use of drugs such as proton pump inhibitors (PPIs), or bacterial infection such as Helicobacter pylori, cause significant microbial alterations. Ye...
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