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ViPR: an open bioinformatics database and analysis resource for virology research
2011
Nucleic Acids Research
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The Virus Pathogen Database and Analysis Resource (ViPR, www.ViPRbrc.org) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy ...
ViPR tools and data are available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens ...
the Bioinformatics Resource Centers (BRC) for Infectious Diseases program (5, 6) to develop open, integrated online resources for data about human pathogens. ...
doi:10.1093/nar/gkr859
pmid:22006842
pmcid:PMC3245011
fatcat:7z5uulanrrbohb5qhzuuens3ci
Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community
2012
Viruses
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The NIAID-sponsored Virus Pathogen Database and Analysis Resource (ViPR, www.viprbrc.org) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses, including ...
All of the data and integrated analysis and visualization tools in ViPR are made available without charge as a service to the Coronaviridae research community to facilitate the research and development ...
Acknowledgments We would like to thank the primary data providers for their extensive work to generate data and their willingness to share their data with public data repositories like ViPR. ...
doi:10.3390/v4113209
pmid:23202522
pmcid:PMC3509690
fatcat:xadmxig4lvcihb24fqtgp3mh24
Database and Analytical Resources for Viral Research Community
[chapter]
2019
Reference Module in Life Sciences
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a one-stop-shop for data and analytical tools for basic and applied research in virology. ...
For example, data and bioinformatics tools from ViPR and IRD have facilitated research into detection and diagnostics of viral pathogens, prediction of viral hosts and environmental reservoirs, viral evolution ...
Virus Pathogen Database and Analysis Resource (ViPR) and Influenza Research Database (IRD) For the remainder of this article, we focus on describing two related database and analytical resources available ...
doi:10.1016/b978-0-12-809633-8.20995-3
fatcat:dbouvnr6hnebdio7fe6ydpjfn4
Viroinformatics: Databases and Tools
[chapter]
2019
Zenodo
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The amalgamation of virology and Bioinformatics has led to the development of a new field known as viroinformatics. ...
This review presents an overview of all the viroinformatics databases and tools developed to contribute to the development of the new potential drug. ...
Bioinformatics research works, including data analysis, development of tools and databases on the microorganisms, are growing gradually (Abouelwafa et al., 2017; George et al., 2018; George et al., 2017 ...
doi:10.5281/zenodo.4721391
fatcat:u5fprkfyzrddlaev5zamvr4jte
Unraveling the Web of Viroinformatics: Computational Tools and Databases in Virus Research
2014
Journal of Virology
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Therefore, a compendium of various computational tools and resources dedicated specifically to virology is presented in this article. ...
The beginning of the second century of research in the field of virology (the first virus was discovered in 1898) was marked by its amalgamation with bioinformatics, resulting in the birth of a new domain—viroinformatics ...
VIRUS-CENTERED RESOURCES AND THE VIRUS PATHOGEN DATABASE AND ANALYSIS RESOURCE (ViPR) Influenza virus. ...
doi:10.1128/jvi.02027-14
pmid:25428870
pmcid:PMC4300767
fatcat:2qgddtkbzzfztiyymbwksd7lvq
A new era of virus bioinformatics
2018
Virus Research
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Bringing together the expertise of bioinformaticians and virologists is crucial, since very specific but fundamental computational approaches are required for virus research, particularly in an era of ...
We end by presenting an overview of current technologies, and by outlining some of the major challenges and advantages that bioinformatics will bring to the field of virology. ...
The Virus Variation Resource (VVR) is a selection of web interfaces, analysis and visualization tools for virus sequence datasets [17] . ...
doi:10.1016/j.virusres.2018.05.009
pmid:29751021
fatcat:vwynvtttp5f3nl252bmreht3xq
GLUE: a flexible software system for virus sequence data
2018
BMC Bioinformatics
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GLUE (Genes Linked by Underlying Evolution) is a data-centric bioinformatics environment for building such resources. ...
To facilitate interpretation, such data must be organised and processed within scalable computing resources that encapsulate virology expertise. ...
The funding bodies did not play any role in the design of the study or collection, analysis and interpretation of data or in writing the manuscript. ...
doi:10.1186/s12859-018-2459-9
pmid:30563445
pmcid:PMC6299651
fatcat:bzbl2tx3gbelljsfeh5lnqhpcy
GLUE: A flexible software system for virus sequence data
[article]
2018
bioRxiv
pre-print
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GLUE (Genes Linked by Underlying Evolution) is a data-centric bioinformatics environment for building such resources. ...
To facilitate interpretation, such data must be organised and processed within scalable computing resources that encapsulate virology expertise. ...
Guangzhou Blood Center who contributed some metadata improvements for Genotype 6 sequences and to David Robertson and Massimo Palmarini who provided valuable feedback on the manuscript. ...
doi:10.1101/269274
fatcat:fgwenomdtbc2pawsso6evatxuu
Bioinformatics Applications in Advancing Animal Virus Research
[chapter]
2019
Recent Advances in Animal Virology
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The chapter will converse on overview of the current advances, online and downloadable tools and databases in the field of bioinformatics that will enable the researchers to study animal viruses at gene ...
The chapter further provides information on the tools that can be used to study viral epidemiology, phylogenetic analysis, structural modelling of proteins, epitope recognition and open reading frame ( ...
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
Advanced Molecular Surveillance of Hepatitis C Virus
2015
Viruses
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Importantly, implementation of comprehensive global databases and data mining are also needed for the proper study of the mechanisms responsible for HCV transmission. ...
OPEN ACCESS Viruses 2015, 7 1154 ...
The Virus Pathogen Database and Analysis Resource (ViPR) supports virology researchers studying select agents and other significant public health pathogens belonging to 14 virus families including HCV ...
doi:10.3390/v7031153
pmid:25781918
pmcid:PMC4379565
fatcat:rm4rgqzlynfvfdibkuuy3etley
ViralZone: a knowledge resource to understand virus diversity
2010
Nucleic Acids Research
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Our aim is to provide a comprehensive resource bridging together textbook knowledge with genomic and proteomic sequences. ...
ViralZone web resource (www.expasy.org/viralzone/) provides fact sheets on all known virus families/genera with easy access to sequence data. ...
Funding for open access charge: Swiss Institute of Bioinformatics. ...
doi:10.1093/nar/gkq901
pmid:20947564
pmcid:PMC3013774
fatcat:zjnv3ybpb5co3fltrprv4zv2ka
Systems virology: host-directed approaches to viral pathogenesis and drug targeting
2013
Nature Reviews Microbiology
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Moreover, an understanding of viral protein function has paved the way for the development of antiviral drugs that target viral enzymatic activities. ...
Anyone who has taken an undergraduate virology course is familiar with subject matter focused on the structure of viral genomes and the molecular events associated with multistep viral life cycles. ...
Josset for generating the networks in figure 3 , and M. Heise and M. Ferris for providing the data used in box 3. ...
doi:10.1038/nrmicro3036
pmid:23728212
pmcid:PMC4028060
fatcat:yk674zd7hzevladttnwmdgrjdi
An Approach to the Identification and Phylogenetic Analysis of Emerging and Hemorrhagic Fever Viruses
[chapter]
2017
Msphere
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An important aspect of virological surveillance is the identification of the detected viruses. ...
Here we will describe general approaches to identify hemorrhagic viral agents through phylogenetic analysis of cDNA sequences obtained during surveillance activities. ...
Another useful database for research in
hemorrhagic fever viruses is the Virus Pathogen Resource
(ViPR) available at http://www.viprbrc.org/. ...
doi:10.1007/978-1-4939-6981-4_2
pmid:28986823
fatcat:s2gd72qvwrg5dpsyywry5qi6d4
A comprehensive collection of systems biology data characterizing the host response to viral infection
2014
Scientific Data
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Database (www.fludb.org) and the Virus Pathogen Resource (www.viprbrc.org). ...
Study validation was demonstrated via experimental quality control measures and meta-analysis of independent experiments performed under similar conditions. ...
The Influenza Research Database (IRD, www. fludb.org) and the Virus Pathogen Resource (ViPR, www.viprbrc.org) also received generous support from the NIAID under N01AI40041. ...
doi:10.1038/sdata.2014.33
pmid:25977790
pmcid:PMC4410982
fatcat:7n47nith2ndg7njw2o5iks3rtq
Crowdsourcing biocuration: the Community Assessment of Community Annotation with Ontologies (CACAO)
[article]
2021
bioRxiv
pre-print
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Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. ...
AbstractExperimental data about known gene functions curated from the primary literature have enormous value for research scientists in understanding biology. ...
., ViPR: an open bioinformatics database and analysis resource for 532 virology research. Nucleic Acids Res 40, D593-8 (2011). 533 48. Y. ...
doi:10.1101/2021.04.30.440339
fatcat:ni6k25anrnb7nlfgkqp46tlixq
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