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VISDB: a manually curated database of viral integration sites in the human genome
2019
Nucleic Acids Research
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Here, we systematically collected and manually curated all VISs reported in the literature and publicly available data resources to construct the Viral Integration Site DataBase (VISDB, https://bioinfo.uth.edu ...
Virus integration into the human genome occurs frequently and represents a key driving event in human disease. ...
and Mr Baochen Yang for their help of web page development. ...
doi:10.1093/nar/gkz867
pmid:31598702
pmcid:PMC6943068
fatcat:xws3aqvhxbddblibp7utrvmroq
ViMIC: A Database of Human Disease-related Virus Mutations, Integration Sites and Cis-effects
[article]
2020
bioRxiv
pre-print
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To address these challenges, we built a database of human disease-related Virus Mutations, Integration sites and Cis-effects (ViMIC), which specialize in three features: virus mutation sites, viral integration ...
Molecular mechanisms of virus-related diseases involve multiple factors, including viral mutation accumulation and integration of a viral genome into the host DNA. ...
Shipeng Chen for reading the manuscript. ...
doi:10.1101/2020.10.28.359919
fatcat:jjxo7xe57jabxpzn3ewednxxdy
ViMIC: a database of human disease-related virus mutations, integration sites and cis-effects
2021
Nucleic Acids Research
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A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
To address these challenges, we built a pilot database of human disease-related Virus Mutations, Integration sites and Cis-effects (ViMIC), which specializes in three features: virus mutation sites, viral ...
Molecular mechanisms of virus-related diseases involve multiple factors, including viral mutation accumulation and integration of a viral genome into the host DNA. ...
Firstly, the viral integration sites in the human genome were derived from VISDB (76 264 curated VISs) and from the PubMed literature (29 360 VISs, 48 articles) that reported disease-related viral integration ...
doi:10.1093/nar/gkab779
pmid:34500462
pmcid:PMC8728280
fatcat:p5ex756gtnekpo72wvghqasbrq
DeepVISP: Deep Learning for Virus Site Integration Prediction and Motif Discovery
2021
Advanced Science
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Here, a new deep convolutional neural network (CNN) model is developed with attention architecture, namely DeepVISP, for accurately predicting oncogenic virus integration sites (VISs) in the human genome ...
A user-friendly web server is developed for predicting putative oncogenic VISs in the human genome using DeepVISP. ...
The funder had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. ...
doi:10.1002/advs.202004958
pmid:33977077
pmcid:PMC8097320
fatcat:2senb23k5nc27gphia3t75hrwi
Hepatitis B Virus Integration into Transcriptionally Active Loci and HBV-Associated Hepatocellular Carcinoma
2022
Microorganisms
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In the present study, we investigated whether HBV preferentially integrates parts of its genome in specific genes and evaluated the contribution of the integrations in HCC development per gene. ...
Hepatitis B Virus (HBV) DNA integrations into the human genome are considered major causative factors to HBV-associated hepatocellular carcinoma development. ...
The present study included manually curated integration sites, as are those provided by the VISDB database [54] , thus the biases occurring from using data from independent research studies, whose results ...
doi:10.3390/microorganisms10020253
pmid:35208708
pmcid:PMC8879149
fatcat:wy2s2j62irbmnnddmtkt7ixhpi