Current progress and open challenges for applying deep learning across the biosciences
Deep Learning (DL) has recently enabled unprecedented advances in one of the grand
challenges in computational biology: the half-century-old problem of protein structure …
challenges in computational biology: the half-century-old problem of protein structure …
Machine learning and deep learning applications in microbiome research
R Hernández Medina, S Kutuzova… - ISME …, 2022 - academic.oup.com
The many microbial communities around us form interactive and dynamic ecosystems called
microbiomes. Though concealed from the naked eye, microbiomes govern and influence …
microbiomes. Though concealed from the naked eye, microbiomes govern and influence …
Identification of mobile genetic elements with geNomad
Identifying and characterizing mobile genetic elements in sequencing data is essential for
understanding their diversity, ecology, biotechnological applications and impact on public …
understanding their diversity, ecology, biotechnological applications and impact on public …
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
Metagenomic assembly enables new organism discovery from microbial communities, but it
can only capture few abundant organisms from most metagenomes. Here we present …
can only capture few abundant organisms from most metagenomes. Here we present …
CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
Advances in sequencing technologies and bioinformatics tools have dramatically increased
the recovery rate of microbial genomes from metagenomic data. Assessing the quality of …
the recovery rate of microbial genomes from metagenomic data. Assessing the quality of …
Oxford Nanopore R10. 4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or …
Abstract Long-read Oxford Nanopore sequencing has democratized microbial genome
sequencing and enables the recovery of highly contiguous microbial genomes from isolates …
sequencing and enables the recovery of highly contiguous microbial genomes from isolates …
A genome and gene catalog of glacier microbiomes
Glaciers represent a unique inventory of microbial genetic diversity and a record of
evolution. The Tibetan Plateau contains the largest area of low-latitude glaciers and is …
evolution. The Tibetan Plateau contains the largest area of low-latitude glaciers and is …
A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments
Metagenomic binning is the step in building metagenome-assembled genomes (MAGs)
when sequences predicted to originate from the same genome are automatically grouped …
when sequences predicted to originate from the same genome are automatically grouped …
Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan
J Johansen, K Atarashi, Y Arai, N Hirose… - Nature …, 2023 - nature.com
Distinct gut microbiome ecology may be implicated in the prevention of aging-related
diseases as it influences systemic immune function and resistance to infections. Yet, the viral …
diseases as it influences systemic immune function and resistance to infections. Yet, the viral …
Discovery of drug–omics associations in type 2 diabetes with generative deep-learning models
The application of multiple omics technologies in biomedical cohorts has the potential to
reveal patient-level disease characteristics and individualized response to treatment …
reveal patient-level disease characteristics and individualized response to treatment …