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ViTa: prediction of host microRNAs targets on viruses

P. W.-C. Hsu, L.-Z. Lin, S.-D. Hsu, J. B.-K. Hsu, H.-D. Huang
2007 Nucleic Acids Research  
Experimentally validated miRNA targets on viruses were derived from literatures. Then, miRanda and TargetScan are utilized to predict miRNA targets within virus genomes.  ...  To investigate regulatory relationships between host miRNAs and related viruses, we present a novel database, namely ViTa, to curate the known virus miRNA genes and the known/putative target sites of human  ...  Funding to pay the Open Access publication charges for this article was provided by National Science Council of the Republic of China. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkl1009 pmid:17148483 pmcid:PMC1761424 fatcat:kkqgrfqjqbexdl33ooeluy3qki

Predicting MicroRNA Mediated Gene Regulation between Human and Viruses

Xin Shu, Xinyuan Zang, Xiaoshuang Liu, Jie Yang, Jin Wang
2018 Cells  
To facilitate an extensive investigation on the interplay among the gene regulatory networks of humans and viruses, we designed a prediction pipeline, mirTarP, that is suitable for miRNA target screening  ...  By applying mirTarP, we constructed the database mirTar, which is a comprehensive miRNA target repository of bidirectional interspecies regulation between viruses and humans.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/cells7080100 pmid:30096814 fatcat:rpyma3btnzf2nb4mg4f2eg4kd4

Host-Virus Interaction: Role of miRNA and Bioinformatics Tools for miRNA Target Prediction

Amit Ranjan Sahu
2015 Advances in Animal and Veterinary Sciences  
This review focuses on the complete interactions between host and viruses and several bioinformatics tools available with us for its interpretation.  ...  At present several bioinformatics tools are available for the prediction of miRNAs and its target sequence through suitable algorithms pertaining to their own method.  ...  ACKNOWLEDGEMENTS The authors acknowledge the financial support provided by Department of Biotechnology (DBT), Government of India.  ... 
doi:10.14737/journal.aavs/2015/3.4s.30.36 fatcat:lp3qh5mduzep3onazrknbo77lq

Viral and Host Genetic and Epigenetic Biomarkers Related to SARS-CoV-2 Cell Entry, Infection Rate, and Disease Severity

Jernej Gaspersic, Vita Dolzan
2022 Biology  
Bioinformatics tools may help to predict the effect of mutations in the spike protein on the binding to the ACE2 receptor and the infectivity of the strain.  ...  Thus, virus and host related genetic and epigenetic biomarkers may help to predict the course of the disease and the response to treatment.  ...  Acknowledgments: We are grateful to David Vogrinc for helpful comments on the article. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biology11020178 pmid:35205046 pmcid:PMC8869311 fatcat:fvgooiai5ffztoynedrfats6bi

VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets

Abid Qureshi, Nishant Thakur, Isha Monga, Anamika Thakur, Manoj Kumar
2014 Database: The Journal of Biological Databases and Curation  
Abstract Viral microRNAs (miRNAs) regulate gene expression of viral and/or host genes to benefit the virus.  ...  Additionally, there is information of 542 antiviral miRNAs encoded by the host against 24 viruses in antiviral miRNA 'AVIRmir'.  ...  Moreover, databases of predicted viral miRNA targets are also available including ViTa-a database of predicted host miRNA targets on the viral genome (44) and RepTar-a repository of predicted cellular  ... 
doi:10.1093/database/bau103 pmid:25380780 pmcid:PMC4224276 fatcat:ocfktn4yonanfeequtyuebhnzi

Cellular versus viral microRNAs in host-virus interaction

Z. Ghosh, B. Mallick, J. Chakrabarti
2008 Nucleic Acids Research  
MicroRNAs (miRNAs) mark a new paradigm of RNAdirected gene expression regulation in a wide spectrum of biological systems.  ...  Here, we summarize the recent updates on miRNA-induced gene-silencing mechanism, modulating host-virus interactions with a glimpse of the miRNA-based antiviral therapy for near future.  ...  We also thank Dr Angshuman Bagchi (Indiana University School of Medicine, Indianapolis, USA), Avijit Guha Roy (University of Buckingham, UK) and our colleagues for critical reading of the manuscript.  ... 
doi:10.1093/nar/gkn1004 pmid:19095692 pmcid:PMC2651794 fatcat:uahvueppavbk7ietrphhjihq7i

Extracellular circulating viral microRNAs: current knowledge and perspectives

Alessandro Laganà, Francesco Russo, Dario Veneziano, Sebastiano Di Bella, Rosalba Giugno, Alfredo Pulvirenti, Carlo M. Croce, Alfredo Ferro
2013 Frontiers in Genetics  
In this work we summarize the current knowledge on viral circulating miRNAs and provide a few examples of computational prediction of their function.  ...  Viruses also encode their own sets of miRNAs, which they use to control the expression of either the host's genes and/or their own.  ...  RepTar and vHoT are databases of predicted interspecies interactions between viral miRNA and host genomes, while ViTa is a database containing predictions of host miRNA targets on viruses (Hsu et al.,  ... 
doi:10.3389/fgene.2013.00120 pmid:23805153 pmcid:PMC3690336 fatcat:tckquwgdjzewnkghrqi7qtsuyi

MicroRNA Mimics or Inhibitors as Antiviral Therapeutic Approaches Against COVID-19

Christine Hum, Julia Loiselle, Nadine Ahmed, Tyler A Shaw, Caroline Toudic, John Paul Pezacki
2021 Drugs  
2 (ACE2), the receptor used by SARS-CoV-2 and SARS-CoV for host cell entry, were also predicted.  ...  We can take advantage of their ability to modulate host-virus interactions through mediating RNA degradation or translational inhibition.  ...  Some viruses can also encode viral miRNAs that can target both host and viral RNA (e). miRNA microRNA, RISC RNA-induced silencing complex miRNAs and the SARS-CoV-2 genome in order to gain insight and direct  ... 
doi:10.1007/s40265-021-01474-5 pmid:33638807 pmcid:PMC7910799 fatcat:ysvsmp6rsbfr7inlmtxsgopl7y

Computational analysis of microRNA-mediated antiviral defense in humans

Yuka Watanabe, Atsuko Kishi, Nozomu Yachie, Akio Kanai, Masaru Tomita
2007 FEBS Letters  
We listed 62 possible human miRNA-targeted viruses from 6 families, most of which consisted of single-stranded RNA viruses.  ...  ones to be targeted by human miRNAs.  ...  Acknowledgements: We thank Kosuke Fujishima and Hikaru Taniguchi (Keio University) for advices on carrying out the computational analysis, and Dr.  ... 
doi:10.1016/j.febslet.2007.08.049 pmid:17825824 fatcat:dh7hlxmld5c47l6bq7hx4s2lya

HPVbase – a knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas

Amit Kumar Gupta, Manoj Kumar
2015 Scientific Reports  
ViTa: prediction of host DOI:10.1093/nar/gkl1009 (2007). 11 Hsu, S. D. et al. miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.  ...  Nucleic Acids Res42, D53-59; DOI:10.1093/nar/gkt1202 (2014). 8 microRNAs targets on viruses. Nucleic Acids Res35, D381-385; org resource: targets and expression.  ... 
doi:10.1038/srep12522 pmid:26205472 pmcid:PMC4513345 fatcat:7nitzq6ryvgwhjrcutyhknvg3y

Computational Prediction of microRNAs and their Targets

Salim A Vinod Chandra
2014 Journal of Proteomics & Bioinformatics  
ViTa investigate regulatory relationships between host microRNAs and related viruses to curate the known virus microRNA genes and the known/putative target sites of human, mice, rat and chicken microRNAs  ...  ViTa [100] and VirMir [101] [102] [103] [104] [105] are providing virus host interaction databases.  ... 
doi:10.4172/jpb.1000320 fatcat:hwxjs3uzerbyzg4plhpeq5nkmu

Bioinformatics Applications in Advancing Animal Virus Research [chapter]

Ablesh Gautam, Ashish Tiwari, Yashpal Singh Malik
2019 Recent Advances in Animal Virology  
ORF) recognition and tools that enable to analyse host-viral interactions, gene prediction in the viral genome, etc.  ...  There have been various research groups that focus on understanding the viruses in terms of their hostviral relationships, pathogenesis and immune evasion.  ...  Acknowledgements All the authors of the manuscript thank and acknowledge their respective universities and institutes. Conflict of Interest There is no conflict of interest.  ... 
doi:10.1007/978-981-13-9073-9_23 fatcat:kmnyd5z7wbeltchxzoscpgtpzm

MicroRNA-like viral small RNA from porcine reproductive and respiratory syndrome virus negatively regulates viral replication by targeting the viral nonstructural protein 2

Na Li, Yunhuan Yan, Angke Zhang, Jiming Gao, Chong Zhang, Xue Wang, Gaopeng Hou, Gaiping Zhang, Jinbu Jia, En-Min Zhou, Shuqi Xiao
2016 OncoTarget  
Many viruses encode microRNAs (miRNAs) that are small non-coding singlestranded RNAs which play critical roles in virus-host interactions.  ...  Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically impactful viruses in the swine industry.  ...  ACKNOWLEDGMENTS This work was supported by National Natural Science Foundation of China (31472173, 31430084), Northwest A&F University talent special fund (Z111021201) and Fundamental Research Fund (2452016046  ... 
doi:10.18632/oncotarget.12703 pmid:27769040 pmcid:PMC5347740 fatcat:gwuwmgclcffudgg2ndvyyfwbre

Unraveling the Web of Viroinformatics: Computational Tools and Databases in Virus Research

Deepak Sharma, Pragya Priyadarshini, Sudhanshu Vrati, S. P. Goff
2014 Journal of Virology  
The availability of more than 100 Web servers and databases embracing all or specific viruses (for example, dengue virus, influenza virus, hepatitis virus, human immunodeficiency virus [HIV], hemorrhagic  ...  However, information about their access and utility is not available at any single source or on any single platform.  ...  ViTa catalogs known host and viral miRNAs as well as known or putative host miRNA targets on viruses (80) . It utilizes miRanda and TargetScan to predict miRNA targets within virus genomes.  ... 
doi:10.1128/jvi.02027-14 pmid:25428870 pmcid:PMC4300767 fatcat:2qgddtkbzzfztiyymbwksd7lvq

Identification of Chicken Pulmonary miRNAs Targeting PB1, PB1-F2, and N40 Genes of Highly Pathogenic Avian Influenza Virus H5N1 in Silico

Amod Kumar, Asaf V.N. Muhasin, Ashwin Ashok Raut, Richa Sood, Anamika Mishra
2014 Bioinformatics and Biology Insights  
Chicken miRNAs gga-mir-133c, gga-mir-1710, and gga-mir-146c* are predicted to target the expression of PB1, PB1-F2, and N40 proteins.  ...  Since these proteins are critical for viral replication and pathogenesis, targeting their expression can be one of the approaches to control and resist HPAI.  ...  The targets identified by our approach were not predicted by the ViTa database, which predicts targets of host miRNAs in viral genes. 25 This might be due to the fact that the target identification tools  ... 
doi:10.4137/bbi.s14631 pmid:25002813 pmcid:PMC4069037 fatcat:cumjz3bt7zbflgksggk6mxduce
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