Computational tools for the analysis of uncultivated phage genomes

JS Andrade-Martínez, LC Camelo Valera… - Microbiology and …, 2022 - Am Soc Microbiol
Over a century of bacteriophage research has uncovered a plethora of fundamental aspects
of their biology, ecology, and evolution. Furthermore, the introduction of community-level …

Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity

T Zuo, Q Liu, F Zhang, YK Yeoh, Y Wan, H Zhan… - Microbiome, 2021 - Springer
Abstract Background Coronavirus disease 2019 (COVID-19) caused by the enveloped RNA
virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 …

Metatranscriptomics reveals the diversity of the tick virome in Northwest China

Y Kong, G Zhang, L Jiang, P Wang, S Zhang… - Microbiology …, 2022 - Am Soc Microbiol
Blood-sucking ticks are obligate parasites and vectors of a variety of human and animal
viruses. Some tick-borne viruses have been identified as pathogens of infectious diseases in …

MetaPhage: an automated pipeline for analyzing, annotating, and classifying bacteriophages in metagenomics sequencing data

M Pandolfo, A Telatin, G Lazzari, EM Adriaenssens… - Msystems, 2022 - Am Soc Microbiol
Phages are the most abundant biological entities on the planet, and they play an important
role in controlling density, diversity, and network interactions among bacterial communities …

Application and Comparison of Machine Learning and Database-Based Methods in Taxonomic Classification of High-Throughput Sequencing Data

Q Tian, P Zhang, Y Zhai, Y Wang… - Genome Biology and …, 2024 - academic.oup.com
The advent of high-throughput sequencing technologies has not only revolutionized the field
of bioinformatics but has also heightened the demand for efficient taxonomic classification …

Highly divergent and diverse viral community infecting sylvatic mosquitoes from Northeast Brazil

AF da Silva, LC Machado, LMI da Silva… - Journal of …, 2024 - journals.asm.org
Mosquitoes can transmit several pathogenic viruses to humans, but their natural viral
community is also composed of a myriad of other viruses such as insect-specific viruses …

The VirAnnot pipeline: A resource for automated viral diversity estimation and operational taxonomy units assignation for virome sequencing data

M Lefebvre, S Theil, Y Ma… - Phytobiomes Journal, 2019 - Am Phytopath Society
Viral metagenomics relies on high-throughput sequencing and on bioinformatic analyses to
access the genetic content and diversity of entire viral communities. No universally accepted …

[HTML][HTML] High prevalence of Enterovirus E, Bovine Kobuvirus, and Astrovirus revealed by viral metagenomics in fecal samples from cattle in Central Colombia

JE Medina, S Castañeda, L Páez-Triana… - Infection, Genetics and …, 2024 - Elsevier
Livestock plays a crucial role in ensuring food security and driving the global economy.
However, viral infections can have far-reaching consequences beyond economic …

Viral Diversity and Epidemiology in Critically Endangered Yangtze Finless Porpoises (Neophocaena asiaeorientalis asiaeorientalis)

X Zhao, C Dai, S Qian, Q Tang, L Li, Y Hao… - Microbiology …, 2023 - Am Soc Microbiol
The Yangtze finless porpoise (YFP)(Neophocaena asiaeorientalis asiaeorientalis) is a
critically endangered freshwater cetacean, with about 1,249 individuals thought to be left in …

Optimized metavirome analysis of marine DNA virus communities for taxonomic profiling

KE Kim, SW Jung, JS Park, HJ Kim, C Lee, SY Ha… - Ocean Science …, 2022 - Springer
Recent advances in metavirome technology have provided new insights into viral diversity
and function. The bioinformatic process of metavirome study is generally divided into two (or …