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ViPR: an open bioinformatics database and analysis resource for virology research

Brett E. Pickett, Eva L. Sadat, Yun Zhang, Jyothi M. Noronha, R. Burke Squires, Victoria Hunt, Mengya Liu, Sanjeev Kumar, Sam Zaremba, Zhiping Gu, Liwei Zhou, Christopher N. Larson (+3 others)
2011 Nucleic Acids Research  
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

Brett Pickett, Douglas Greer, Yun Zhang, Lucy Stewart, Liwei Zhou, Guangyu Sun, Zhiping Gu, Sanjeev Kumar, Sam Zaremba, Christopher Larsen, Wei Jen, Edward Klem (+1 others)
2012 Viruses  
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]

Sujal Phadke, Saichetana Macherla, Richard H. Scheuermann
2019 Reference Module in Life Sciences  
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]

Angelin George, John J. Georrge
2019 Zenodo  
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

Deepak Sharma, Pragya Priyadarshini, Sudhanshu Vrati, S. P. Goff
2014 Journal of Virology  
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

Bashar Ibrahim, Dino P. McMahon, Franziska Hufsky, Martin Beer, Li Deng, Philippe Le Mercier, Massimo Palmarini, Volker Thiel, Manja Marz
2018 Virus Research  
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

Joshua B. Singer, Emma C. Thomson, John McLauchlan, Joseph Hughes, Robert J. Gifford
2018 BMC Bioinformatics  
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]

Joshua B Singer, Emma C Thomson, John McLauchlan, Joseph Hughes, Robert J Gifford
2018 bioRxiv   pre-print
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]

Ablesh Gautam, Ashish Tiwari, Yashpal Singh Malik
2019 Recent Advances in Animal Virology  
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

Livia Rossi, Alejandro Escobar-Gutierrez, Paula Rahal
2015 Viruses  
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

Chantal Hulo, Edouard de Castro, Patrick Masson, Lydie Bougueleret, Amos Bairoch, Ioannis Xenarios, Philippe Le Mercier
2010 Nucleic Acids Research  
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

G. Lynn Law, Marcus J. Korth, Arndt G. Benecke, Michael G. Katze
2013 Nature Reviews Microbiology  
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]

Francisco J. Díaz, Luis E. Paternina, Juan David Rodas
2017 Msphere  
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

Brian D. Aevermann, Brett E. Pickett, Sanjeev Kumar, Edward B. Klem, Sudhakar Agnihothram, Peter S. Askovich, Armand Bankhead, Meagen Bolles, Victoria Carter, Jean Chang, Therese R.W. Clauss, Pradyot Dash (+56 others)
2014 Scientific Data  
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]

Jolene Ramsey, Brenley McIntosh, Daniel Renfro, Suzanne A. Aleksander, Sandra LaBonte, Curtis Ross, Adrienne E. Zweifel, Nathan Liles, Shabnam Farrar, Jason J. Gill, Ivan Erill, Sarah Ades (+36 others)
2021 bioRxiv   pre-print
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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