In experimental evolution, laboratory-controlled conditions select for the adaptation of
species, which can be monitored in real time. Despite the current popularity of such …

Metagenomic sequencing is a powerful tool for examining the diversity and complexity of
microbial communities. Most widely used tools for taxonomic profiling of metagenomic …

The Sanger sequencing method produces relatively long DNA sequences of unmatched
quality and has been considered for long time as the gold standard for sequencing DNA …

Whole genome sequencing (WGS) provides the highest resolution for genome-based
species identification and can provide insight into the antimicrobial resistance and virulence …

Biofilms are a major form of microbial life in which cells form dense surface associated
communities that can persist for many generations. The long-life of biofilm communities …

Background The three-dimensional (3D) architecture of the genome has a highly ordered
and hierarchical nature, which influences the regulation of essential nuclear processes at …

Background Bacterial strains under the same species can exhibit different biological
properties, making strain-level composition analysis an important step in understanding the …

While specific mutations allow organisms to adapt to stressful environments, most changes
in an organism's DNA negatively impact fitness. The mutation rate is therefore strictly …

Identifying bacterial strains in metagenome and microbiome samples using computational
analyses of short-read sequences remains a difficult problem. Here, we present an analysis …

Detecting genetic variants in metagenomic data is a priority for understanding the evolution,
ecology, and functional characteristics of microbial communities. Many tools that perform this …