BACKGROUND: Microorganisms in activated sludge (AS) play key roles in the wastewater treatment processes. However, their ecological behaviors and differences from microorganisms in other environments have mainly been studied using the 16S rRNA gene t...
BACKGROUND: Microbes are greatly associated with human health and disease, especially in densely populated cities. It is essential to understand the microbial ecosystem in an urban environment for cities to monitor the transmission of infectious dise...
BACKGROUND: Recent advances in high-volume sequencing technology and mining of genomes from metagenomic samples call for rapid and reliable genome quality evaluation. The current release of the PATRIC database contains over 220,000 genomes, and curre...
BACKGROUND: The availability of hundreds of city microbiome profiles allows the development of increasingly accurate predictors of the origin of a sample based on its microbiota composition. Typical microbiome studies involve the analysis of bacteria...
BACKGROUND: Research has found that human associated microbial communities play a role in homeostasis and the disruption of these communities may be important in an array of medical conditions. However outside of the human body many of these communit...
The characterization of antimicrobial resistance genes from high-throughput sequencing data has become foundational in public health research and regulation. This requires mapping sequence reads to databases of known antimicrobial resistance genes to...
BACKGROUND: Metagenomics is the application of modern genomic techniques to investigate the members of a microbial community directly in their natural environments and is widely used in many studies to survey the communities of microbial organisms th...
BACKGROUND: Metagenomic data of whole genome sequences (WGS) from samples across several cities around the globe may unravel city specific signatures of microbes. Illumina MiSeq sequencing data was provided from 12 cities in 7 different countries as ...
BACKGROUND: Microbiome profiles in the human body and environment niches have become publicly available due to recent advances in high-throughput sequencing technologies. Indeed, recent studies have already identified different microbiome profiles in...
Omics data usually have ultra-high dimension (p) and small sample size (n). Standard support vector machines (SVMs), which minimize the L norm for the primal variables, only lead to sparse solutions for the dual variables. L based SVMs, directly mini...
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