Clinical metagenomic next-generation sequencing for pathogen detection

W Gu, S Miller, CY Chiu - Annual Review of Pathology …, 2019 - annualreviews.org
Nearly all infectious agents contain DNA or RNA genomes, making sequencing an attractive
approach for pathogen detection. The cost of high-throughput or next-generation …

Advancing personalized medicine through the application of whole exome sequencing and big data analytics

P Suwinski, CK Ong, MHT Ling, YM Poh… - Frontiers in …, 2019 - frontiersin.org
There is a growing attention toward personalized medicine. This is led by a fundamental
shift from the 'one size fits all'paradigm for treatment of patients with conditions or …

New approaches for metagenome assembly with short reads

M Ayling, MD Clark, RM Leggett - Briefings in bioinformatics, 2020 - academic.oup.com
In recent years, the use of longer range read data combined with advances in assembly
algorithms has stimulated big improvements in the contiguity and quality of genome …

A metagenomics and case-control study to identify viruses associated with bovine respiratory disease

TFF Ng, NO Kondov, X Deng… - Journal of …, 2015 - Am Soc Microbiol
Bovine respiratory disease (BRD) is a common health problem for both dairy and beef cattle,
resulting in significant economic loses. In order to identify viruses associated with BRD, we …

Recovering complete and draft population genomes from metagenome datasets

N Sangwan, F Xia, JA Gilbert - Microbiome, 2016 - Springer
Assembly of metagenomic sequence data into microbial genomes is of fundamental value to
improving our understanding of microbial ecology and metabolism by elucidating the …

Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses

T Shan, S Yang, H Wang, H Wang, J Zhang, G Gong… - Microbiome, 2022 - Springer
Background Wild birds may harbor and transmit viruses that are potentially pathogenic to
humans, domestic animals, and other wildlife. Results Using the viral metagenomic …

Choice of assembly software has a critical impact on virome characterisation

TDS Sutton, AG Clooney, FJ Ryan, RP Ross, C Hill - Microbiome, 2019 - Springer
Background The viral component of microbial communities plays a vital role in driving
bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite …

Metagenome-assembled genomes uncover a global brackish microbiome

LW Hugerth, J Larsson, J Alneberg, MV Lindh… - Genome biology, 2015 - Springer
Background Microbes are main drivers of biogeochemical cycles in oceans and lakes.
Although the genome is a foundation for understanding the metabolism, ecology and …

Marine hydrocarbon-degrading bacteria breakdown poly (ethylene terephthalate)(PET)

R Denaro, F Aulenta, F Crisafi, F Di Pippo… - Science of The Total …, 2020 - Elsevier
Pollution of aquatic ecosystems by plastic wastes poses severe environmental and health
problems and has prompted scientific investigations on the fate and factors contributing to …

Overview of virus metagenomic classification methods and their biological applications

S Nooij, D Schmitz, H Vennema, A Kroneman… - Frontiers in …, 2018 - frontiersin.org
Metagenomics poses opportunities for clinical and public health virology applications by
offering a way to assess complete taxonomic composition of a clinical sample in an …