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VISDB: a manually curated database of viral integration sites in the human genome

2019 Nucleic Acids Research  
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]

Ying Wang, Yuantao Tong, Zeyu Zhang, Rongbin Zheng, Danqi Huang, Jinxuan Yang, Hui Zong, Fanglin Tan, Xiaoyan Zhang
2020 bioRxiv   pre-print
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

Ying Wang, Yuantao Tong, Zeyu Zhang, Rongbin Zheng, Danqi Huang, Jinxuan Yang, Hui Zong, Fanglin Tan, Yujia Xie, Honglian Huang, Xiaoyan Zhang
2021 Nucleic Acids Research  
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

Haodong Xu, Peilin Jia, Zhongming Zhao
2021 Advanced Science  
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

Maria Bousali, Timokratis Karamitros
2022 Microorganisms  
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