[HTML][HTML] A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data
Metagenomic sequencing provides a culture-independent avenue to investigate the
complex microbial communities by constructing metagenome-assembled genomes (MAGs) …
complex microbial communities by constructing metagenome-assembled genomes (MAGs) …
Bioinformatic tools for NGS-based metagenomics to improve the clinical diagnosis of emerging, re-emerging and new viruses
M Ibañez-Lligoña, S Colomer-Castell… - Viruses, 2023 - mdpi.com
Epidemics and pandemics have occurred since the beginning of time, resulting in millions of
deaths. Many such disease outbreaks are caused by viruses. Some viruses, particularly …
deaths. Many such disease outbreaks are caused by viruses. Some viruses, particularly …
vRhyme enables binning of viral genomes from metagenomes
K Kieft, A Adams, R Salamzade, L Kalan… - Nucleic Acids …, 2022 - academic.oup.com
Genome binning has been essential for characterization of bacteria, archaea, and even
eukaryotes from metagenomes. Yet, few approaches exist for viruses. We developed …
eukaryotes from metagenomes. Yet, few approaches exist for viruses. We developed …
Phables: from fragmented assemblies to high-quality bacteriophage genomes
Motivation Microbial communities have a profound impact on both human health and
various environments. Viruses infecting bacteria, known as bacteriophages or phages, play …
various environments. Viruses infecting bacteria, known as bacteriophages or phages, play …
Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses
Symbiont specificity, both at the phylotype and strain level, can have profound
consequences for host ecology and evolution. However, except for insights from a few …
consequences for host ecology and evolution. However, except for insights from a few …
Metagenomic binning with assembly graph embeddings
Motivation Despite recent advancements in sequencing technologies and assembly
methods, obtaining high-quality microbial genomes from metagenomic samples is still not a …
methods, obtaining high-quality microbial genomes from metagenomic samples is still not a …
Unsupervised segmentation of hyperspectral remote sensing images with superpixels
In this paper, we propose an unsupervised method for hyperspectral remote sensing image
segmentation. The method exploits the mean-shift clustering algorithm that takes as input a …
segmentation. The method exploits the mean-shift clustering algorithm that takes as input a …
Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies
Background In the metagenomic assembly of a microbial community, abundant species are
often thought to assemble well given their deeper sequencing coverage. This conjuncture is …
often thought to assemble well given their deeper sequencing coverage. This conjuncture is …
Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity
The plasticity of bacterial and archaeal genomes makes examining their ecological and
evolutionary dynamics both exciting and challenging. The same mechanisms that enable …
evolutionary dynamics both exciting and challenging. The same mechanisms that enable …
Recovery of high quality metagenome-assembled genomes from full-scale activated sludge microbial communities in a tropical climate using longitudinal …
The analysis of metagenome data based on the recovery of draft genomes (so called
metagenome-assembled genomes, or MAG) has assumed an increasingly central role in …
metagenome-assembled genomes, or MAG) has assumed an increasingly central role in …