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, Sam Zaremba, Sanjeev Kumar, Jon Deitrich, Edward Klem, Richard H. Scheuermann

Research output: Contribution to journalArticle

181 Citations (Scopus)

Abstract

Background The recent emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about other important virus characteristics. Design The Influenza Research Database (IRD, http://www.fludb.org) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. 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 comparative genomics analysis, together with personal log in-protected 'workbench' spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature. Results To demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented. A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross-protective immunity. Phylogenetic and geospatial analysis of sequences from wild bird surveillance samples revealed a possible evolutionary connection between influenza virus from Delaware Bay shorebirds and Alberta ducks. Conclusions The IRD provides a wealth of integrated data and information about influenza virus to support research of the genetic determinants dictating virus pathogenicity, host range restriction and transmission, and to facilitate development of vaccines, diagnostics, and therapeutics.

Original languageEnglish (US)
Pages (from-to)404-416
Number of pages13
JournalInfluenza and other Respiratory Viruses
Volume6
Issue number6
DOIs
StatePublished - Nov 2012

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Orthomyxoviridae
Computational Biology
Human Influenza
Databases
Epitopes
National Institute of Allergy and Infectious Diseases (U.S.)
Research
Viruses
Literature
H1N1 Subtype Influenza A Virus
Alberta
Genetic Research
Ducks
Information Storage and Retrieval
Host Specificity
Influenza A virus
Hemagglutinins
Pandemics
Genomics
Proteomics

Keywords

  • Bioinformatics
  • Epitope
  • Influenza virus
  • Integrated
  • Surveillance

ASJC Scopus subject areas

  • Infectious Diseases
  • Pulmonary and Respiratory Medicine
  • Public Health, Environmental and Occupational Health
  • Epidemiology

Cite this

Influenza Research Database : An integrated bioinformatics resource for influenza research and surveillance. / Squires, R. Burke; Noronha, Jyothi; Hunt, Victoria; García-Sastre, Adolfo; Macken, Catherine; Baumgarth, Nicole; Suarez, David; Pickett, Brett E.; Zhang, Yun; Larsen, Christopher N.; Ramsey, Alvin; Zhou, Liwei; Zaremba, Sam; Kumar, Sanjeev; Deitrich, Jon; Klem, Edward; Scheuermann, Richard H.

In: Influenza and other Respiratory Viruses, Vol. 6, No. 6, 11.2012, p. 404-416.

Research output: Contribution to journalArticle

Squires, RB, Noronha, J, Hunt, V, García-Sastre, A, Macken, C, Baumgarth, N, Suarez, D, Pickett, BE, Zhang, Y, Larsen, CN, Ramsey, A, Zhou, L, Zaremba, S, Kumar, S, Deitrich, J, Klem, E & Scheuermann, RH 2012, 'Influenza Research Database: An integrated bioinformatics resource for influenza research and surveillance', Influenza and other Respiratory Viruses, vol. 6, no. 6, pp. 404-416. https://doi.org/10.1111/j.1750-2659.2011.00331.x
Squires, R. Burke ; Noronha, Jyothi ; Hunt, Victoria ; García-Sastre, Adolfo ; Macken, Catherine ; Baumgarth, Nicole ; Suarez, David ; Pickett, Brett E. ; Zhang, Yun ; Larsen, Christopher N. ; Ramsey, Alvin ; Zhou, Liwei ; Zaremba, Sam ; Kumar, Sanjeev ; Deitrich, Jon ; Klem, Edward ; Scheuermann, Richard H. / Influenza Research Database : An integrated bioinformatics resource for influenza research and surveillance. In: Influenza and other Respiratory Viruses. 2012 ; Vol. 6, No. 6. pp. 404-416.
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abstract = "Background The recent emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about other important virus characteristics. Design The Influenza Research Database (IRD, http://www.fludb.org) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. 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 comparative genomics analysis, together with personal log in-protected 'workbench' spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature. Results To demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented. A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross-protective immunity. Phylogenetic and geospatial analysis of sequences from wild bird surveillance samples revealed a possible evolutionary connection between influenza virus from Delaware Bay shorebirds and Alberta ducks. Conclusions The IRD provides a wealth of integrated data and information about influenza virus to support research of the genetic determinants dictating virus pathogenicity, host range restriction and transmission, and to facilitate development of vaccines, diagnostics, and therapeutics.",
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AU - Macken, Catherine

AU - Baumgarth, Nicole

AU - Suarez, David

AU - Pickett, Brett E.

AU - Zhang, Yun

AU - Larsen, Christopher N.

AU - Ramsey, Alvin

AU - Zhou, Liwei

AU - Zaremba, Sam

AU - Kumar, Sanjeev

AU - Deitrich, Jon

AU - Klem, Edward

AU - Scheuermann, Richard H.

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N2 - Background The recent emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about other important virus characteristics. Design The Influenza Research Database (IRD, http://www.fludb.org) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. 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 comparative genomics analysis, together with personal log in-protected 'workbench' spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature. Results To demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented. A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross-protective immunity. Phylogenetic and geospatial analysis of sequences from wild bird surveillance samples revealed a possible evolutionary connection between influenza virus from Delaware Bay shorebirds and Alberta ducks. Conclusions The IRD provides a wealth of integrated data and information about influenza virus to support research of the genetic determinants dictating virus pathogenicity, host range restriction and transmission, and to facilitate development of vaccines, diagnostics, and therapeutics.

AB - Background The recent emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about other important virus characteristics. Design The Influenza Research Database (IRD, http://www.fludb.org) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. 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 comparative genomics analysis, together with personal log in-protected 'workbench' spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature. Results To demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented. A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross-protective immunity. Phylogenetic and geospatial analysis of sequences from wild bird surveillance samples revealed a possible evolutionary connection between influenza virus from Delaware Bay shorebirds and Alberta ducks. Conclusions The IRD provides a wealth of integrated data and information about influenza virus to support research of the genetic determinants dictating virus pathogenicity, host range restriction and transmission, and to facilitate development of vaccines, diagnostics, and therapeutics.

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