Literature DB >> 23764402

Viral categorization and discovery in human circulation by transcriptome sequencing.

Weihua Wang1, Xiaoan Zhang, Yanjuan Xu, Adrian M Di Bisceglie, Xiaofeng Fan.   

Abstract

Serum is the most common and easily accessible patient specimen in a minimally invasive manner. As a biological resource, RNA in serum has been less explored for its clinical utilization due to prevailing concerns regarding its high degradable nature. In the current study, however, we have documented the use of human serum RNA for viral categorization and discovery through transcriptome sequencing and analysis using well-curated databases and advanced bioinformatic tools. Such an integrated approach may have an immediate application in any clinical situations concerning with viral etiology.
Copyright © 2013 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Multiple displacement amplification; Next-generation sequencing; Viral discovery

Mesh:

Substances:

Year:  2013        PMID: 23764402      PMCID: PMC3709469          DOI: 10.1016/j.bbrc.2013.05.139

Source DB:  PubMed          Journal:  Biochem Biophys Res Commun        ISSN: 0006-291X            Impact factor:   3.575


  36 in total

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Authors:  Roger S Lasken
Journal:  Biochem Soc Trans       Date:  2009-04       Impact factor: 5.407

2.  Isothermal DNA amplification in bioanalysis: strategies and applications.

Authors:  Joonyul Kim; Christopher J Easley
Journal:  Bioanalysis       Date:  2011-01       Impact factor: 2.681

3.  Enhanced protocol for determining the 3' terminus of hepatitis C virus.

Authors:  Xiaoan Zhang; Xiaofeng Fan; Yanjuan Xu; Adrian M Di Bisceglie
Journal:  J Virol Methods       Date:  2010-04-08       Impact factor: 2.014

Review 4.  Metagenomics for the discovery of novel human viruses.

Authors:  Patrick Tang; Charles Chiu
Journal:  Future Microbiol       Date:  2010-02       Impact factor: 3.165

5.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

6.  Artificial and natural duplicates in pyrosequencing reads of metagenomic data.

Authors:  Beifang Niu; Limin Fu; Shulei Sun; Weizhong Li
Journal:  BMC Bioinformatics       Date:  2010-04-13       Impact factor: 3.169

7.  BEDTools: a flexible suite of utilities for comparing genomic features.

Authors:  Aaron R Quinlan; Ira M Hall
Journal:  Bioinformatics       Date:  2010-01-28       Impact factor: 6.937

8.  A new arenavirus in a cluster of fatal transplant-associated diseases.

Authors:  Gustavo Palacios; Julian Druce; Lei Du; Thomas Tran; Chris Birch; Thomas Briese; Sean Conlan; Phenix-Lan Quan; Jeffrey Hui; John Marshall; Jan Fredrik Simons; Michael Egholm; Christopher D Paddock; Wun-Ju Shieh; Cynthia S Goldsmith; Sherif R Zaki; Mike Catton; W Ian Lipkin
Journal:  N Engl J Med       Date:  2008-02-06       Impact factor: 91.245

9.  miRBase: integrating microRNA annotation and deep-sequencing data.

Authors:  Ana Kozomara; Sam Griffiths-Jones
Journal:  Nucleic Acids Res       Date:  2010-10-30       Impact factor: 16.971

10.  Application of proteomics methods for pathogen discovery.

Authors:  Yiming Ye; Eng-Chun Mar; Suxiang Tong; Scott Sammons; Sunan Fang; Larry J Anderson; Dongxia Wang
Journal:  J Virol Methods       Date:  2009-09-12       Impact factor: 2.014

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  4 in total

1.  Template-dependent multiple displacement amplification for profiling human circulating RNA.

Authors:  Weihua Wang; Yi Ren; Yang Lu; Yuan Xu; Seth D Crosby; Adrian M Di Bisceglie; Xiaofeng Fan
Journal:  Biotechniques       Date:  2017-07-01       Impact factor: 1.993

2.  In-depth serum virome analysis in patients with acute liver failure with indeterminate etiology.

Authors:  Yi Ren; Yanjuan Xu; William M Lee; Adrian M Di Bisceglie; Xiaofeng Fan
Journal:  Arch Virol       Date:  2019-11-18       Impact factor: 2.574

3.  Full annotation of serum virome in Chinese blood donors with elevated alanine aminotransferase levels.

Authors:  Gang Li; Zhihua Zhou; Li Yao; Yanjuan Xu; Lan Wang; Xiaofeng Fan
Journal:  Transfusion       Date:  2019-08-08       Impact factor: 3.157

4.  Identification of the transcripts associated with spontaneous HCV clearance in individuals co-infected with HIV and HCV.

Authors:  Yue Chen; Chengli Shen; Debjani Guha; Ming Ding; Scott Kulich; Aiymkul Ashimkhanova; Charles Rinaldo; Eric Seaberg; Joseph B Margolick; Valentina Stosor; Otoniel Martínez-Maza; Phalguni Gupta
Journal:  BMC Infect Dis       Date:  2016-11-22       Impact factor: 3.090

  4 in total

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