ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer. (Q52630979)

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scientific article published on 20 March 2018

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English	ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer.	scientific article published on 20 March 2018

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scholarly article

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Europe PubMed Central

PubMed publication ID

4 May 2018

http://europepmc.org/abstract/MED/29579309

ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer (English)

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6283451&resulttype=core&format=json

13 May 2020

cervix uterine cancer

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based on heuristic

inferred from title

5

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Vineet Bafna

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PubMed publication ID

4 May 2018

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Nam-Phuong D Nguyen

1

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6283451&resulttype=core&format=json

13 May 2020

Viraj Deshpande

2

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6283451&resulttype=core&format=json

13 May 2020

Jens Luebeck

3

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6283451&resulttype=core&format=json

13 May 2020

Paul S Mischel

4

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Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6283451&resulttype=core&format=json

13 May 2020

Vineet Bafna

5

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Europe PubMed Central

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13 May 2020

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publication date

20 March 2018

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Europe PubMed Central

PubMed publication ID

4 May 2018

http://europepmc.org/abstract/MED/29579309

Nucleic Acids Research

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Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6283451&resulttype=core&format=json

13 May 2020

46

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6283451&resulttype=core&format=json

13 May 2020

7

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6283451&resulttype=core&format=json

13 May 2020

3309-3325

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Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6283451&resulttype=core&format=json

13 May 2020

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Creative Commons Attribution-NonCommercial 4.0 International

20 March 2018

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April 2022 Public Data File from Crossref

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Integration of human papillomavirus type 16 DNA into the human genome leads to increased stability of E6 and E7 mRNAs: implications for cervical carcinogenesis

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Profile hidden Markov models

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The human papillomavirus type 16 E6 and E7 oncoproteins independently induce numerical and structural chromosome instability.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A comprehensive analysis of HPV integration loci in anogenital lesions combining transcript and genome-based amplification techniques.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The human LINE-1 retrotransposon creates DNA double-strand breaks.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

All APOBEC3 family proteins differentially inhibit LINE-1 retrotransposition

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Viral infections as a cause of cancer (review)

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Fast and accurate short read alignment with Burrows-Wheeler transform

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Circos: an information aesthetic for comparative genomics

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The role of HPV E6 and E7 oncoproteins in HPV-associated cervical carcinogenesis

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Potential mechanisms of endogenous retroviral-mediated genomic instability in human cancer.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Why do viruses cause cancer? Highlights of the first century of human tumour virology

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Hybrid capture and next-generation sequencing identify viral integration sites from formalin-fixed, paraffin-embedded tissue.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

ART: a next-generation sequencing read simulator.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The role of miRNAs in human papilloma virus (HPV)-associated cancers: bridging between HPV-related head and neck cancer and cervical cancer

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The distribution of a germline methylation marker suggests a regional mechanism of LINE-1 silencing by the piRNA-PIWI system

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Hepatitis B virus X protein modulates oncogene Yes-associated protein by CREB to promote growth of hepatoma cells.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

ENCODE data in the UCSC Genome Browser: year 5 update

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Regulation of human papillomavirus gene expression by splicing and polyadenylation

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Long interspersed element-1 (LINE-1): passenger or driver in human neoplasms?

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The role of human endogenous retroviral long terminal repeat sequences in human cancer (Review).

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The landscape of viral expression and host gene fusion and adaptation in human cancer

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Viral-human chimeric transcript predisposes risk to liver cancer development and progression.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Human viral oncogenesis: a cancer hallmarks analysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Profile hidden Markov models for the detection of viruses within metagenomic sequence data

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

TIPP: taxonomic identification and phylogenetic profiling

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Genome-wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology-mediated integration mechanism

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

VERSE: a novel approach to detect virus integration in host genomes through reference genome customization

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

HISAT: a fast spliced aligner with low memory requirements

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Virus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

LINE-1 in cancer: multifaceted functions and potential clinical implications

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Hepatitis B virus-human chimeric transcript HBx-LINE1 promotes hepatic injury via sequestering cellular microRNA-122.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Global burden of cancers attributable to infections in 2012: a synthetic analysis.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

miRNA Expression Profiles of HPV-Infected Patients with Cervical Cancer in the Uyghur Population in China

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Papillomavirus Episteme: a major update to the papillomavirus sequence database

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

HIPPI: highly accurate protein family classification with ensembles of HMMs

1 reference

https://pubmed.ncbi.nlm.nih.gov/29579309

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKY180

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6283451&resulttype=core&format=json

13 May 2020

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6283451&resulttype=core&format=json

13 May 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6283451&resulttype=core&format=json

13 May 2020

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