AIMC Topic: Metagenomics
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Improving viral annotation with artificial intelligence.
mBio
Sep 4, 2024
Viruses of bacteria, "phages," are fundamental, poorly understood components of microbial community structure and function. Additionally, their dependence on hosts for replication positions phages as unique sensors of ecosystem features and environme...
Inflammatory bowel disease genomics, transcriptomics, proteomics and metagenomics meet artificial intelligence.
United European gastroenterology journal
Aug 31, 2024
Various extrinsic and intrinsic factors such as drug exposures, antibiotic treatments, smoking, lifestyle, genetics, immune responses, and the gut microbiome characterize ulcerative colitis and Crohn's disease, collectively called inflammatory bowel ...
A powerful machine learning approach to identify interactions of differentially abundant gut microbial subsets in patients with metastatic and non-metastatic pancreatic cancer.
Gut microbes
Jul 7, 2024
Pancreatic cancer has a dismal prognosis, as it is often diagnosed at stage IV of the disease and is characterized by metastatic spread. Gut microbiota and its metabolites have been suggested to influence the metastatic spread by modulating the host ...
Tracing the origin and authenticity of Spanish PDO honey using metagenomics and machine learning.
International journal of food microbiology
Jun 8, 2024
The Protected Designation of Origin (PDO) indication for foods intends to guarantee the conditions of production and the geographical origin of regional products within the European Union. Honey products are widely consumed due to their health-promot...
Exploring the roles of ribosomal peptides in prokaryote-phage interactions through deep learning-enabled metagenome mining.
Microbiome
May 24, 2024
BACKGROUND: Microbial secondary metabolites play a crucial role in the intricate interactions within the natural environment. Among these metabolites, ribosomally synthesized and post-translationally modified peptides (RiPPs) are becoming a promising...
Deciphering the microbial landscape of lower respiratory tract infections: insights from metagenomics and machine learning.
Frontiers in cellular and infection microbiology
May 23, 2024
BACKGROUND: Lower respiratory tract infections represent prevalent ailments. Nonetheless, current comprehension of the microbial ecosystems within the lower respiratory tract remains incomplete and necessitates further comprehensive assessment. Lever...
Genomic language model predicts protein co-regulation and function.
Nature communications
Apr 3, 2024
Deciphering the relationship between a gene and its genomic context is fundamental to understanding and engineering biological systems. Machine learning has shown promise in learning latent relationships underlying the sequence-structure-function par...
Waste to resource: Mining antimicrobial peptides in sludge from metagenomes using machine learning.
Environment international
Mar 11, 2024
The emergence of antibiotic-resistant bacteria poses a huge threat to the treatment of infections. Antimicrobial peptides are a class of short peptides that widely exist in organisms and are considered as potential substitutes for traditional antibio...
An unsupervised deep learning framework for predicting human essential genes from population and functional genomic data.
BMC bioinformatics
Sep 18, 2023
BACKGROUND: The ability to accurately predict essential genes intolerant to loss-of-function (LOF) mutations can dramatically improve the identification of disease-associated genes. Recently, there have been numerous computational methods developed t...
ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning.
PLoS computational biology
May 1, 2023
The number of published metagenome assemblies is rapidly growing due to advances in sequencing technologies. However, sequencing errors, variable coverage, repetitive genomic regions, and other factors can produce misassemblies, which are challenging...
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