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Virus Variation Resource—recent updates and future directions

J. Rodney Brister, Yiming Bao, Sergey A. Zhdanov, Yuri Ostapchuck, Vyacheslav Chetvernin, Boris Kiryutin, Leonid Zaslavsky, Michael Kimelman, Tatiana A. Tatusova
2013 Nucleic Acids Research  
Together these enhancements should support enhanced usability and the inclusion of new viruses in the future.  ...  Virus Variation (http://www.ncbi.nlm.nih.gov/gen omes/VirusVariation/) is a comprehensive, webbased resource designed to support the retrieval and display of large virus sequence datasets.  ...  FUTURE DIRECTIONS The long term plan is to increase the coverage of virus sequences in the Virus Variation Resource.  ... 
doi:10.1093/nar/gkt1268 pmid:24304891 pmcid:PMC3965055 fatcat:uyjd4rsizzdtbe7nd4vektt3p4

Virus Variation Resource – improved response to emergent viral outbreaks

Eneida L. Hatcher, Sergey A. Zhdanov, Yiming Bao, Olga Blinkova, Eric P. Nawrocki, Yuri Ostapchuck, Alejandro A. Schäffer, J. Rodney Brister
2016 Nucleic Acids Research  
This manuscript describes a series of features and functionalities recently added to the Virus Variation Resource.  ...  The resource is located at http://www.ncbi.nlm.nih.gov/genome/ viruses/variation/ and includes modules for seven viral groups: influenza virus, Dengue virus, West Nile virus, Ebolavirus, MERS coronavirus  ...  FUTURE DIRECTIONS The Virus Variation Resource described here provides a number of features that improve the usability of archival sequence data.  ... 
doi:10.1093/nar/gkw1065 pmid:27899678 pmcid:PMC5210549 fatcat:rmk3lbtajzed3a3nqyfz2eh3by

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  
and other viruses.  ...  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  ...  All these data are updated with each bimonthly release and are directly searchable using intuitive web-based user interfaces. Data from direct submission.  ... 
doi:10.1093/nar/gkr859 pmid:22006842 pmcid:PMC3245011 fatcat:7z5uulanrrbohb5qhzuuens3ci

CHIKVPRO – a protein sequence annotation database for chikungunya virus

Akaash Kumar Mishra, Chakresh Kumar Jain, Apurva Agrawal, Saransh Jain Kumar Sambhav Jain, Namrata Dudha, Kapila Kumar, Sanjeev K. Sharma, Sanjay Gupta
2010 Bioinformation  
In the recent past, there has been a resurgence of interest in Chikungunya virus (CHIKV) attributed to massive outbreaks of Chikungunya fever in the South-East Asia Region.  ...  Hereby we submit a database "CHIKVPRO" containing structural and functional annotation of Chikungunya virus proteins (25 strains) submitted in the NCBI repository.  ...  The database shall be updated timely as more data on viral proteins is generated through our ongoing experimental analysis and future sequence submissions.  ... 
doi:10.6026/97320630005004 pmid:21346870 pmcid:PMC3039996 fatcat:mvk2itqzvfho7bpcbrlfplrore

Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence

Mayya Sedova, Lukasz Jaroszewski, Arghavan Alisoltani, Adam Godzik, Arne Elofsson
2020 Bioinformatics  
Motivation As the COVID-19 pandemics is spreading around the world, the SARS-CoV-2 virus is evolving with mutations that potentially change and fine-tune functions of the proteins coded in its genome.  ...  Results Coronavirus3D website integrates data on the SARS-CoV-2 virus mutations with information about 3D structures of its proteins, allowing users to visually analyze the mutations in their 3D context  ...  Acknowledgments We acknowledge efforts of the teams at PDB, CNCB, GISAID and NextStrain for maintaining and distributing information on COVID-19 and all the individual laboratories that make their results  ... 
doi:10.1093/bioinformatics/btaa550 pmid:32470119 pmcid:PMC7314196 fatcat:pazcmhr4kzb6niobi6voc452xa

A review on viral data sources and search systems for perspective mitigation of COVID-19

Anna Bernasconi, Arif Canakoglu, Marco Masseroli, Pietro Pinoli, Stefano Ceri
2020 Briefings in Bioinformatics  
future pandemics.  ...  In this context, we review the data integration efforts required for accessing and searching genome sequences and metadata of SARS-CoV2, the virus responsible for the COVID-19 disease, which have been  ...  This research is funded by the ERC Advanced Grant 693174 GeCo (datadriven Genomic Computing) and by the EIT Digital innovation activity 20663 "DATA against COVID-19".  ... 
doi:10.1093/bib/bbaa359 pmid:33348368 fatcat:v255kcgjfzhorgzwjtfxxygujy

Hepitopes: A live interactive database of HLA class I epitopes in hepatitis B virus

Sheila Lumley, Howard Noble, Martin J. Hadley, Liz Callow, Amna Malik, Yi Yi Chua, Owen J. Duffey, Natalia Grolmusova, Arvind Kumar, Samuel Ravenscroft, Jonathan I. Spencer, Christoph Neumann-Haefelin (+5 others)
2016 Wellcome Open Research  
Over time, we will continue to http://www.expmedndm.ox.ac.uk/hepitopes refine and update this resource, as well as inviting contributions from others in the field to support its development.  ...  Desmond CP, Bartholomeusz A, Gaudieri S, et al.: A systematic review of T-cell epitopes in hepatitis B virus: identification, genotypic variation and relevance to antiviral therapeutics.  ...  Acknowledgements We are grateful to John Rowlands in the Nuffield Department of Medicine for his support in setting up and maintaining the Hepitopes website.  ... 
doi:10.12688/wellcomeopenres.9952.1 pmid:27976751 pmcid:PMC5142601 fatcat:wh7agd4tifhlhbx5a5uwtmfmnq

ONE YEAR OF THE COVID-19 PANDEMIC: NURSING RESEARCH PRIORITIES FOR THE NEW NORMAL ERA

Joko Gunawan, Yupin Aungsuroch, Mary L Fisher
2020 Belitung Nursing Journal  
Funding The author received no financial support for the research, authorship, and/or publication of this article.  ...  In recent months of the pandemic, science is providing policy makers with updated data related to the virus' impact on its victims, transmission factors, and the effectiveness of mitigation strategies.  ...  Finally, these ten research priorities are expected to be the future nursing research direction in the new normal era. They should be viewed as a positive step for the nursing agenda in each country.  ... 
doi:10.33546/bnj.1255 fatcat:ks6wgysxmzhqzp7v3d2mp67lwa

Epidemiological characteristics of human-infective RNA viruses

Mark E. J. Woolhouse, Liam Brierley
2018 Scientific Data  
This database can be used in comparative studies of human-infective RNA viruses to identify the characteristics of viruses most likely to pose the greatest public health threat, both now and in the future  ...  route(s) and host range.  ...  For example, there is huge variation in the epidemiology of subtypes of Influenza A virus: contrast the human influenza viruses such as H1N1 and H3N2 with avian influenza viruses such as H5N1 and H7N9  ... 
doi:10.1038/sdata.2018.17 pmid:29461515 pmcid:PMC5819479 fatcat:6h23k7cjx5bp7adfybfog7znqe

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  ...  to new genomes, and store or share results from any search or analysis within personal private 'Workbench' spaces for future access.  ...  Meng, Slobodan Paessler, Colin Parrish, Richard Whitley, and John Young, for their guidance and suggestions as well as Dr. Alison Yao for expert oversight of the BRC program.  ... 
doi:10.3390/v4113209 pmid:23202522 pmcid:PMC3509690 fatcat:xadmxig4lvcihb24fqtgp3mh24

NCBI Viral Genomes Resource

J. Rodney Brister, Danso Ako-adjei, Yiming Bao, Olga Blinkova
2014 Nucleic Acids Research  
The resource can be accessed at http://www.ncbi.nlm.nih.gov/genome/viruses/ and catalogs all publicly available virus genome sequences and curates reference genome sequences.  ...  Recent technological innovations have ignited an explosion in virus genome sequencing that promises to fundamentally alter our understanding of viral biology and profoundly impact public health policy.  ...  ACKNOWLEDGEMENT We would like to thank Vyacheslav Chetvernin, Boris Fedorov, Sergey Resenchuck, Igor Tolstoy, Tatiana Tatusova and Jim Ostell for their development and support.  ... 
doi:10.1093/nar/gku1207 pmid:25428358 pmcid:PMC4383986 fatcat:l3xxswkwgfha7bpz3bsxbzzwbi

Ab and T cell epitopes of influenza A virus, knowledge and opportunities

H.-H. Bui, B. Peters, E. Assarsson, I. Mbawuike, A. Sette
2007 Proceedings of the National Academy of Sciences of the United States of America  
The Immune Epitope Database and Analysis Resources (IEDB) (www.immuneepitope.org) was recently developed to capture epitope related data.  ...  At the same time, the analysis illustrates gaps in our collective knowledge that should inspire directions for further study of immunity against the influenza A virus.  ...  Specifically, the revealed gaps in our collective knowledge might inspire and guide directions for future research in the study of immunity against the influenza A virus.  ... 
doi:10.1073/pnas.0609330104 pmid:17200302 pmcid:PMC1765443 fatcat:bp2aveekezhgrojvlpxxoqj76e

Bioinformatics Applications in Advancing Animal Virus Research [chapter]

Ablesh Gautam, Ashish Tiwari, Yashpal Singh Malik
2019 Recent Advances in Animal Virology  
Various databases that organize information on animal and human viruses have also been described.  ...  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  ...  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

Improving influenza vaccine virus selectionReport of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14-16 June 2010

William K. Ampofo, Norman Baylor, Sarah Cobey, Nancy J. Cox, Sharon Daves, Steven Edwards, Neil Ferguson, Gary Grohmann, Alan Hay, Jacqueline Katz, Kornnika Kullabutr, Linda Lambert (+10 others)
2011 Influenza and Other Respiratory Viruses  
The World Health Organization retains copyright and all other rights in the manuscript of this article as submitted for publication.  ...  in a population could help to establish well-characterized banks of age-stratified representative sera as a national, regional and global resource, while providing direct evidence of the specific benefits  ...  global resource.  ... 
doi:10.1111/j.1750-2659.2011.00277.x pmid:21819547 pmcid:PMC4954460 fatcat:7b74c4kukrh65eqn42y24ct7jy

Robust Reactions to Potential Day-Zero Worms Through Cooperation and Validation [chapter]

K. Anagnostakis, S. Ioannidis, A. D. Keromytis, M. B. Greenwald
2006 Lecture Notes in Computer Science  
Our experiments show that distributed algorithms are better able to balance effectiveness against viruses with reduced cost in computation and communication when faced with false alarms.  ...  Cooperative defensive systems communicate and cooperate in their response to worm attacks, but determine the presence of a worm attack solely on local information.  ...  Acknowledgements This work was supported in part by the National Science Foundation under grants ITR CNS-0426623, DUE-0417085 and CCR-0331584.  ... 
doi:10.1007/11836810_31 fatcat:7rcpuqt5u5aurhnyzry72ehv3i
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