BACKGROUND: Phage therapy, reemerging as a promising approach to counter antimicrobial-resistant infections, relies on a comprehensive understanding of the specificity of individual phages. Yet the significant diversity within phage populations prese...
Nanopore sequencers can enrich or deplete the targeted DNA molecules in a library by reversing the voltage across individual nanopores. However, it requires substantial computational resources to achieve rapid operations in parallel at read-time sequ...
Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many microbial genomes have been sequenced by short read sequenc...
, a gram-negative bacterium, is a common pathogen causing nosocomial infection. The drug-resistance rate of is increasing year by year, posing a severe threat to public health worldwide. has been listed as one of the pathogens causing the global c...
The effectiveness of deep learning methods can be largely attributed to the automated extraction of relevant features from raw data. In the field of functional genomics, this generally concerns the automatic selection of relevant nucleotide motifs fr...
CyanoPATH is a database that curates and analyzes the common genomic functional repertoire for cyanobacteria harmful algal blooms (CyanoHABs) in eutrophic waters. Based on the literature of empirical studies and genome/protein databases, it summarize...
Virulence factors (VFs) enable pathogens to infect their hosts. A wealth of individual, disease-focused studies has identified a wide variety of VFs, and the growing mass of bacterial genome sequence data provides an opportunity for computational met...
CRISPR-Cas are adaptive immune systems that degrade foreign genetic elements in archaea and bacteria. In carrying out their immune functions, CRISPR-Cas systems heavily rely on RNA components. These CRISPR (cr) RNAs are repeat-spacer units that are p...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
Escherichia coli is a species of bacteria that can be present in a wide variety of mammalian hosts and potentially soil environments. E. coli has an open genome and can show considerable diversity in gene content between isolates. It is a reasonable ...
Database : the journal of biological databases and curation
Jan 1, 2020
Small open reading frames (ORFs) have been systematically disregarded by automatic genome annotation. The difficulty in finding patterns in tiny sequences is the main reason that makes small ORFs to be overlooked by computational procedures. However,...