Mining for viral fragments in methylation enriched sequencing data.

PubWeight™: 0.81‹?›

🔗 View Article (PMC 4316777)

Published in Front Genet on February 04, 2015

Authors

Klaas Mensaert1, Wim Van Criekinge2, Olivier Thas1, Ed Schuuring3, Renske D M Steenbergen4, G Bea A Wisman5, Tim De Meyer1

Author Affiliations

1: Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University Ghent, Belgium.
2: Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University Ghent, Belgium ; Department of Pathology, VU University Medical Center Amsterdam, Netherlands.
3: Department of Pathology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen Groningen, Netherlands.
4: Department of Pathology, VU University Medical Center Amsterdam, Netherlands.
5: Department of Gynecologic Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen Groningen, Netherlands.

Articles cited by this

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12

Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int J Cancer (2010) 90.16

Human papillomavirus is a necessary cause of invasive cervical cancer worldwide. J Pathol (1999) 40.46

Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2006) 18.85

Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science (2008) 16.60

Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet (2012) 15.21

Quality control and preprocessing of metagenomic datasets. Bioinformatics (2011) 13.84

Global burden of cancers attributable to infections in 2008: a review and synthetic analysis. Lancet Oncol (2012) 9.28

CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics (2012) 8.32

Worldwide distribution of human papillomavirus types in cytologically normal women in the International Agency for Research on Cancer HPV prevalence surveys: a pooled analysis. Lancet (2005) 7.09

The European Nucleotide Archive. Nucleic Acids Res (2010) 6.48

A general primer GP5+/GP6(+)-mediated PCR-enzyme immunoassay method for rapid detection of 14 high-risk and 6 low-risk human papillomavirus genotypes in cervical scrapings. J Clin Microbiol (1997) 6.09

GP5+/6+ PCR followed by reverse line blot analysis enables rapid and high-throughput identification of human papillomavirus genotypes. J Clin Microbiol (2002) 5.63

Comparative oncogenomics identifies NEDD9 as a melanoma metastasis gene. Cell (2006) 4.68

A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. Proc Natl Acad Sci U S A (2001) 4.62

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res (2011) 4.33

Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res (2013) 3.61

Excessive CpG island hypermethylation in cancer cell lines versus primary human malignancies. Hum Mol Genet (2001) 3.58

MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res (2009) 3.29

Bacteriophage survival: multiple mechanisms for avoiding the deoxyribonucleic acid restriction systems of their hosts. Microbiol Rev (1983) 3.13

New adenovirus species found in a patient presenting with gastroenteritis. J Virol (2007) 2.63

A strategy to estimate unknown viral diversity in mammals. MBio (2013) 2.48

The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer. Genome Res (2009) 1.87

Metagenomics and the molecular identification of novel viruses. Vet J (2010) 1.75

VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue. Bioinformatics (2012) 1.71

Landscape of DNA virus associations across human malignant cancers: analysis of 3,775 cases using RNA-Seq. J Virol (2013) 1.68

A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environ Microbiol Rep (2011) 1.64

Viral oncoproteins target the DNA methyltransferases. Oncogene (2006) 1.59

Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing. PLoS One (2012) 1.54

Transition of human papillomavirus type 16 and 18 transfected human foreskin keratinocytes towards immortality: activation of telomerase and allele losses at 3p, 10p, 11q and/or 18q. Oncogene (1996) 1.53

Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl Trop Dis (2012) 1.52

Prophylaxis of cervical cancer and related cervical disease: a review of the cost-effectiveness of vaccination against oncogenic HPV types. J Manag Care Pharm (2010) 1.31

FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes. Bioinformatics (2011) 1.31

HERV-K(HML-2), the Best Preserved Family of HERVs: Endogenization, Expression, and Implications in Health and Disease. Front Oncol (2013) 1.30

Differential methylation of Epstein-Barr virus latency promoters facilitates viral persistence in healthy seropositive individuals. J Virol (1999) 1.28

Clinical implications of (epi)genetic changes in HPV-induced cervical precancerous lesions. Nat Rev Cancer (2014) 1.24

Assessment of gene promoter hypermethylation for detection of cervical neoplasia. Int J Cancer (2006) 1.23

Library construction for next-generation sequencing: overviews and challenges. Biotechniques (2014) 1.20

MBD-seq as a cost-effective approach for methylome-wide association studies: demonstration in 1500 case--control samples. Epigenomics (2012) 1.16

Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing. PLoS One (2013) 1.15

Vaccines to prevent infections by oncoviruses. Annu Rev Microbiol (2010) 1.14

Clinical course of recurrent respiratory papillomatosis: Comparison between aggressiveness of human papillomavirus-6 and human papillomavirus-11. Head Neck (2014) 1.13

Presence and role of cytosine methylation in DNA viruses of animals. Nucleic Acids Res (2008) 1.13

Computational tools for viral metagenomics and their application in clinical research. Virology (2012) 1.13

From deep sequencing to viral tagging: recent advances in viral metagenomics. Bioessays (2013) 1.03

Methylation of episomal plasmids as a barrier to transient gene expression via a synthetic delivery vector. Biomol Eng (2001) 1.01

Epstein-Barr virus-associated lymphoproliferative disorders. Postepy Hig Med Dosw (Online) (2013) 0.98

The microbiota of the human genitourinary tract: trying to see the forest through the trees. Trans Am Clin Climatol Assoc (2012) 0.98

Viral expression associated with gastrointestinal adenocarcinomas in TCGA high-throughput sequencing data. Hum Genomics (2013) 0.92

The prognostic value of global DNA hypomethylation in cancer: a meta-analysis. PLoS One (2014) 0.91

Methylation-specific digital karyotyping of HPV16E6E7-expressing human keratinocytes identifies novel methylation events in cervical carcinogenesis. J Pathol (2013) 0.90

Human Papillomavirus 16, 18, 31 and 45 viral load, integration and methylation status stratified by cervical disease stage. BMC Cancer (2014) 0.89

Epigenetic mechanisms in virus-induced tumorigenesis. Clin Epigenetics (2011) 0.88

Epigenetic mechanisms in human adenovirus type 12 oncogenesis. Semin Cancer Biol (2009) 0.85

Herpesviruses as possible cofactors in HPV-16-related oncogenesis. Acta Biochim Pol (2009) 0.84