[HTML][HTML] Current challenges to virus discovery by meta-transcriptomics

JCA Cobbin, J Charon, E Harvey, EC Holmes… - Current opinion in …, 2021 - Elsevier
Meta-transcriptomic next-generation sequencing has transformed virus discovery,
dramatically expanding our knowledge of the known virosphere. Nevertheless, the use of …

[HTML][HTML] Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

M Asplund, KR Kjartansdóttir, S Mollerup… - Clinical Microbiology …, 2019 - Elsevier
Objectives Sample preparation for high-throughput sequencing (HTS) includes treatment
with various laboratory components, potentially carrying viral nucleic acids, the extent of …

Tumour virology in the era of high-throughput genomics

KW Tang, E Larsson - … of the Royal Society B: Biological …, 2017 - royalsocietypublishing.org
With the advent of massively parallel sequencing, oncogenic viruses in tumours can now be
detected in an unbiased and comprehensive manner. Additionally, new viruses or strains …

A virome-wide clonal integration analysis platform for discovering cancer viral etiology

X Chen, J Kost, A Sulovari, N Wong, WS Liang… - Genome …, 2019 - genome.cshlp.org
Oncoviral infection is responsible for 12%–15% of cancer in humans. Convergent evidence
from epidemiology, pathology, and oncology suggests that new viral etiologies for cancers …

Metagenomic identification of viral sequences in laboratory reagents

AF Porter, J Cobbin, CX Li, JS Eden, EC Holmes - Viruses, 2021 - mdpi.com
Metagenomic next-generation sequencing has transformed the discovery and diagnosis of
infectious disease, with the power to characterise the complete 'infectome'(bacteria, viruses …

DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples

M Alawi, L Burkhardt, D Indenbirken, K Reumann… - Scientific reports, 2019 - nature.com
We describe DAMIAN, an open source bioinformatics tool designed for the identification of
pathogenic microorganisms in diagnostic samples. By using authentic clinical samples and …

The human virome: implications for clinical practice in transplantation medicine

SK Tan, DA Relman, BA Pinsky - Journal of Clinical Microbiology, 2017 - Am Soc Microbiol
Advances in DNA sequencing technology have provided an unprecedented opportunity to
study the human virome. Transplant recipients and other immunocompromised hosts are at …

High diversity of picornaviruses in rats from different continents revealed by deep sequencing

TA Hansen, S Mollerup, N Nguyen… - Emerging microbes & …, 2016 - Taylor & Francis
Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an
important component in containment of such emerging viral diseases is rapid and reliable …

Medical laboratory scientist: a new partner in biomarker research

J Smith, CC Qvist, KK Jacobsen… - Personalized Medicine, 2017 - Taylor & Francis
Commentary Smith, Qvist, Jacobsen & Larsen new multiplex ligationdependent probe
amplifica tion (MLPA) technique, which is proposed to be reli able, costeffective and robust …

Potential prognostic impact of EBV RNA‐seq reads in gastric cancer: a reanalysis of The Cancer Genome Atlas cohort

D Sadato, M Ogawa, C Hirama, T Hishima… - FEBS Open …, 2020 - Wiley Online Library
Epstein–Barr virus (EBV)‐associated gastric cancer (EBVaGC), whose prognosis remains
controversial, is diagnosed by in situ hybridization of EBV‐derived EBER1/2 small RNAs. In …