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Influenza Research Database: An integrated bioinformatics resource for influenza virus research

Yun Zhang, Brian D. Aevermann, Tavis K. Anderson, David F. Burke, Gwenaelle Dauphin, Zhiping Gu, Sherry He, Sanjeev Kumar, Christopher N. Larsen, Alexandra J. Lee, Xiaomei Li, Catherine Macken (+16 others)
2016 Nucleic Acids Research  
National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research.  ...  The Influenza Research Database (IRD) is a U.S.  ...  Influenza Research Database (IRD) through the Bioinformatics Resource Centers program (https://www.niaid.nih.gov/labsandresources/ resources/dmid/brc/).  ... 
doi:10.1093/nar/gkw857 pmid:27679478 pmcid:PMC5210613 fatcat:5e2dsqkibbe63dbu3epmgzgeja

Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance

R. Burke Squires, Jyothi Noronha, Victoria Hunt, Adolfo García-Sastre, Catherine Macken, Nicole Baumgarth, David Suarez, Brett E. Pickett, Yun Zhang, Christopher N. Larsen, Alvin Ramsey, Liwei Zhou (+5 others)
2012 Influenza and Other Respiratory Viruses  
IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user-friendly interfaces for data retrieval, visualization and  ...  Design The Influenza Research Database (IRD, http:// www.fludb.org) is a free, open, publicly-accessible resource funded by the U.S.  ...  We have especially benefitted from collaborating with the NIAID-funded Centers of Excellence for Influenza Research and Surveillance (CEIRS) who have been extremely helpful in developing data standards  ... 
doi:10.1111/j.1750-2659.2011.00331.x pmid:22260278 pmcid:PMC3345175 fatcat:wdhncwqhtbehxiqbplxkwk3ry4

Influenza sequence and epitope database

S. Yang, J.-Y. Lee, J. S. Lee, W. P. Mitchell, H.-B. Oh, C. Kang, K. H. Kim
2009 Nucleic Acids Research  
In order to make full use of the wealth of information from such data, we have developed an integrated user friendly relational database, Influenza Sequence and Epitope Database (ISED), that catalogs the  ...  An increasing number of complete genomes of influenza viruses have been sequenced in Asia in recent years.  ...  Significant efforts have been made to build public resources of influenza viruses, such as the Influenza Virus Resource (http://www.ncbi.nlm.nih.gov/genomes/ FLU/FLU.html) at the National Center for Biotechnology  ... 
doi:10.1093/nar/gkn881 pmid:19015128 pmcid:PMC2686482 fatcat:q6en7uc56fekff26kv7wycpncm

Virus Databases ☆ [chapter]

Kathleen McLeod, Chris Upton
2017 Reference Module in Biomedical Sciences  
Acknowledgements The authors would like to thank Chad Smithson for help assembling the collection of virus databases.  ...  This work was supported by a Natural Sciences and Engineering Research Council of Canada Discovery Grant to CU. Conflicts of Interest: The authors are the developers of Virology.ca.  ...  Offering an alternative to the Influenza Virus Resource at NCBI, ViPR also provides the Influenza Research Database (IRD).  ... 
doi:10.1016/b978-0-12-801238-3.95728-3 fatcat:hmkdfmz4urgcdjzgo3jqsohace

Viroinformatics: Databases and Tools [chapter]

Angelin George, John J. Georrge
2019 Zenodo  
More than 100 web servers and databases are currently available, which provides information regarding different viruses, for example, dengue virus, influenza virus, hepatitis virus, human immunodeficiency  ...  This review presents an overview of all the viroinformatics databases and tools developed to contribute to the development of the new potential drug.  ...  decorator =influenza FluGenome Web portal for genotyping influenza A virus https://omictools.com/flugeno me-tool IVDB An integrated information resource and analysis platform for influenza virus  ... 
doi:10.5281/zenodo.4721391 fatcat:u5fprkfyzrddlaev5zamvr4jte

Database and Analytical Resources for Viral Research Community [chapter]

Sujal Phadke, Saichetana Macherla, Richard H. Scheuermann
2019 Reference Module in Life Sciences  
Comprehensive databases such as Viral Pathogen Resource (ViPR, see "Relevant Websites section") and Influenza Research Database (IRD, see "Relevant Websites section") have been instrumental in providing  ...  a one-stop-shop for data and analytical tools for basic and applied research in virology.  ...  capabilities for research on influenza virus.  ... 
doi:10.1016/b978-0-12-809633-8.20995-3 fatcat:dbouvnr6hnebdio7fe6ydpjfn4

BioHealthBase: informatics support in the elucidation of influenza virus host–pathogen interactions and virulence

Burke Squires, Catherine Macken, Adolfo Garcia-Sastre, Shubhada Godbole, Jyothi Noronha, Victoria Hunt, Roger Chang, Christopher N. Larsen, Ed Klem, Kevin Biersack, Richard H. Scheuermann
2007 Nucleic Acids Research  
The BioHealthBase Bioinformatics Resource Center (BRC) (www.biohealthbase.org) is a public bioinformatics database and analysis resource for the study of specific biodefense and public health pathogens-Influenza  ...  The BioHealthBase serves as an collaboration with the Reactome database (www.reactome.org).  ...  ACKNOWLEDGEMENTS We thank the Reactome database project team, especially Marc Gillespie, Peter D'Eustachio and Lincoln Stein for their assistance with the development and deployment of the influenza life  ... 
doi:10.1093/nar/gkm905 pmid:17965094 pmcid:PMC2238987 fatcat:mfh57lpznbesne2gwm54gfylq4

Variations in genome-wide RNAi screens: lessons from influenza research

Yu-Chi Chou, Michael Lai, Yi-Chen Wu, Nai-Chi Hsu, King-Song Jeng, Wen-Chi Su
2015 Journal of Clinical Bioinformatics  
To date, several genome-wide RNAi screens have been successfully performed to identify host factors essential for influenza virus replication.  ...  Taking influenza virus screens as an example, we found that a number of screening parameters may directly or indirectly influence the primary hits identified by the screens.  ...  Miranda Loney for correcting grammatical errors and improving the quality of the manuscript. This work was supported by the Ministry of Science and Technology (MOST 103-2319-B-001-002), Taiwan.  ... 
doi:10.1186/s13336-015-0017-5 pmid:25745555 pmcid:PMC4350949 fatcat:huyk3ib22nd5njux7msxhk57h4

FluKB: A Knowledge-Based System for Influenza Vaccine Target Discovery and Analysis of the Immunological Properties of Influenza Viruses

Christian Simon, Ulrich J. Kudahl, Jing Sun, Lars Rønn Olsen, Guang Lan Zhang, Ellis L. Reinherz, Vladimir Brusic
2015 Journal of Immunology Research  
FluKB is representation of a new generation of databases that integrates data, analytical tools, and analytical workflows that enable comprehensive analysis and automatic generation of analysis reports  ...  FluKB is a knowledge-based system focusing on data and analytical tools for influenza vaccine discovery.  ...  Database [5] , OpenFlu Database [6] , Influenza Research Database (IRD) [7] , and the Immune Epitope Database (IEDB) [8] .  ... 
doi:10.1155/2015/380975 pmid:26504853 pmcid:PMC4609449 fatcat:gracgxsoqrgwzc6xas4535yisy

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  ...  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  ...  The first one to be developed was the Influenza Virus Database (IVDB), and the NCBI Influenza Virus Resource (NCBI-IVR) and Influenza Research Database (IRD) were subsequently concurrently established  ... 
doi:10.1128/jvi.02027-14 pmid:25428870 pmcid:PMC4300767 fatcat:2qgddtkbzzfztiyymbwksd7lvq

The Immune Epitope Database and Analysis Resource [chapter]

A. Sette, H. H. Bui, J. Sidney, P. Bourne, S. Buus, W. Fleri, R. Kubo, O. Lund, D. Nemazee, J. V. Ponomarenko, M. Sathiamurthy, S. Stewart (+3 others)
2006 Lecture Notes in Computer Science  
An analysis resource is linked to the database which hosts various bioinformatics tools to analyze epitope data as well as to predict de novo epitopes.  ...  The Immune Epitope Database and Analysis Resource (IEDB, http://www.immuneepitope.org) is a database specifically devoted to immune epitope data.  ...  An analysis resource is linked to the database that hosts various bioinformatic tools to analyze epitope data (including, for example, population coverage and sequence conservation), as well as tools to  ... 
doi:10.1007/11818564_14 fatcat:rqgwf3jm2rhd3dsv5kozsggc2e

Early observational research and registries during the 2009–2010 influenza A pandemic

Robert A. Fowler, Steven A. R. Webb, Kathy M. Rowan, Charles L. Sprung, B. Taylor Thompson, Adrienne G. Randolph, Philippe Jouvet, Stephen Lapinsky, Lewis Rubinson, Jordi Rello, J. Perren Cobb, Todd W. Rice (+2 others)
2010 Critical Care Medicine  
During the severe acute respiratory syndrome outbreaks in 2003, illness was unexpected, caused by an uncharacterized virus with an uncertain mode of transmission and outcome (1).  ...  C linical research is an essential component of the pandemic response.  ...  At the start of the H1N1 swine influenza pandemic, participating Case Mix Programme units were asked to submit data for confirmed H1N1 cases for rapid analysis and feedback.  ... 
doi:10.1097/ccm.0b013e3181d20c77 pmid:20101176 pmcid:PMC3705715 fatcat:byksgd3safhbdjskjpnfh2dz3m

Development of a Database Course for Bioinformatics

Zhengxin Chena
2012 Procedia Computer Science  
Biology databases (bioDBs) play an ever-increasing role in the post-genome era for bioinformatics education.  ...  offered a course entitled "Database Search and Pattern Discovery" for seniors of our undergraduate Bioinformatics program (which is also available for graduate students majored in Compute Science program  ...  Mark Pauley for developing a website which provided necessary background of biology for students who were not majored in biology and bioinformatics.  ... 
doi:10.1016/j.procs.2012.04.057 fatcat:u5jm6bs7xbfvnhneugr7tbvhym

Investigation into Wuhan Institute of Virology Pathogen Databases

A Anon, B Bostickson, G Demaneuf
2021 Zenodo  
Eventually every single one of the 16 viral pathogen databases managed by the WIV was taken offline.  ...  On the 12th Sep 2019, the main database of samples and viral sequences of the Wuhan Institute of Virology went offline.  ...  It is a comprehensive research center integrating virus resource collection and preservation, virus biotechnology research and development, systematic virology and bioinformatics research. 4.  ... 
doi:10.5281/zenodo.4512260 fatcat:ustze3cpbfgzhi2vfzo6bx2gm4

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  ...  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
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