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; Colin Mahaffey; Brett E. Pickett; Brian Reardon; Thomas Smith; Lucy Stewart; Christian Suloway; Guangyu Sun; Lei Tong; Amy L. Vincent; Bryan Walters; Sam Zaremba; Hongtao Zhao; Liwei Zhou; Christian Zmasek; Edward B. Klem; Richard H. Scheuermann

doi:10.1093/nar/gkw857

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, Colin Mahaffey, Brett E. Pickett, Brian Reardon, Thomas Smith, Lucy Stewart, Christian Suloway, Guangyu Sun, Lei TongAmy L. Vincent, Bryan Walters, Sam Zaremba, Hongtao Zhao, Liwei Zhou, Christian Zmasek, Edward B. Klem, Richard H. Scheuermann^*

^*Corresponding author for this work

Centre for Host Microbiome Interactions

Research output: Contribution to journal › Article › peer-review

265 Citations (Scopus)

Abstract

The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics and therapeutics against influenza virus by providing a comprehensive collection of influenza-related data integrated from various sources, a growing suite of analysis and visualization tools for data mining and hypothesis generation, personal workbench spaces for data storage and sharing, and active user community support. Here, we describe the recent improvements in IRD including the use of cloud and high performance computing resources, analysis and visualization of user-provided sequence data with associated metadata, predictions of novel variant proteins, annotations of phenotype-associated sequence markers and their predicted phenotypic effects, hemagglutinin (HA) clade classifications, an automated tool for HA subtype numbering conversion, linkouts to disease event data and the addition of host factor and antiviral drug components. All data and tools are freely available without restriction from the IRD website at https://www.fludb.org.

Original language	English
Pages (from-to)	D466-D474
Journal	Nucleic Acids Research
Volume	45
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkw857
Publication status	Published - 1 Jan 2017

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10.1093/nar/gkw857

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Zhang, Y., Aevermann, B. D., Anderson, T. K., Burke, D. F., Dauphin, G., Gu, Z., He, S., Kumar, S., Larsen, C. N., Lee, A. J., Li, X., MacKen, C., Mahaffey, C., Pickett, B. E., Reardon, B., Smith, T., Stewart, L., Suloway, C., Sun, G., ... Scheuermann, R. H. (2017). Influenza Research Database: An integrated bioinformatics resource for influenza virus research. Nucleic Acids Research, 45(D1), D466-D474. https://doi.org/10.1093/nar/gkw857

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title = "Influenza Research Database: An integrated bioinformatics resource for influenza virus research",

abstract = "The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics and therapeutics against influenza virus by providing a comprehensive collection of influenza-related data integrated from various sources, a growing suite of analysis and visualization tools for data mining and hypothesis generation, personal workbench spaces for data storage and sharing, and active user community support. Here, we describe the recent improvements in IRD including the use of cloud and high performance computing resources, analysis and visualization of user-provided sequence data with associated metadata, predictions of novel variant proteins, annotations of phenotype-associated sequence markers and their predicted phenotypic effects, hemagglutinin (HA) clade classifications, an automated tool for HA subtype numbering conversion, linkouts to disease event data and the addition of host factor and antiviral drug components. All data and tools are freely available without restriction from the IRD website at https://www.fludb.org.",

author = "Yun Zhang and Aevermann, {Brian D.} and Anderson, {Tavis K.} and Burke, {David F.} and Gwenaelle Dauphin and Zhiping Gu and Sherry He and Sanjeev Kumar and Larsen, {Christopher N.} and Lee, {Alexandra J.} and Xiaomei Li and Catherine MacKen and Colin Mahaffey and Pickett, {Brett E.} and Brian Reardon and Thomas Smith and Lucy Stewart and Christian Suloway and Guangyu Sun and Lei Tong and Vincent, {Amy L.} and Bryan Walters and Sam Zaremba and Hongtao Zhao and Liwei Zhou and Christian Zmasek and Klem, {Edward B.} and Scheuermann, {Richard H.}",

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year = "2017",

month = jan,

day = "1",

doi = "10.1093/nar/gkw857",

language = "English",

volume = "45",

pages = "D466--D474",

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Zhang, Y, Aevermann, BD, Anderson, TK, Burke, DF, Dauphin, G, Gu, Z, He, S, Kumar, S, Larsen, CN, Lee, AJ, Li, X, MacKen, C, Mahaffey, C, Pickett, BE, Reardon, B, Smith, T, Stewart, L, Suloway, C, Sun, G, Tong, L, Vincent, AL, Walters, B, Zaremba, S, Zhao, H, Zhou, L, Zmasek, C, Klem, EB & Scheuermann, RH 2017, 'Influenza Research Database: An integrated bioinformatics resource for influenza virus research', Nucleic Acids Research, vol. 45, no. D1, pp. D466-D474. https://doi.org/10.1093/nar/gkw857

TY - JOUR

T1 - Influenza Research Database

T2 - An integrated bioinformatics resource for influenza virus research

AU - Zhang, Yun

AU - Aevermann, Brian D.

AU - Anderson, Tavis K.

AU - Burke, David F.

AU - Dauphin, Gwenaelle

AU - Gu, Zhiping

AU - He, Sherry

AU - Kumar, Sanjeev

AU - Larsen, Christopher N.

AU - Lee, Alexandra J.

AU - Li, Xiaomei

AU - MacKen, Catherine

AU - Mahaffey, Colin

AU - Pickett, Brett E.

AU - Reardon, Brian

AU - Smith, Thomas

AU - Stewart, Lucy

AU - Suloway, Christian

AU - Sun, Guangyu

AU - Tong, Lei

AU - Vincent, Amy L.

AU - Walters, Bryan

AU - Zaremba, Sam

AU - Zhao, Hongtao

AU - Zhou, Liwei

AU - Zmasek, Christian

AU - Klem, Edward B.

AU - Scheuermann, Richard H.

PY - 2017/1/1

Y1 - 2017/1/1

N2 - The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics and therapeutics against influenza virus by providing a comprehensive collection of influenza-related data integrated from various sources, a growing suite of analysis and visualization tools for data mining and hypothesis generation, personal workbench spaces for data storage and sharing, and active user community support. Here, we describe the recent improvements in IRD including the use of cloud and high performance computing resources, analysis and visualization of user-provided sequence data with associated metadata, predictions of novel variant proteins, annotations of phenotype-associated sequence markers and their predicted phenotypic effects, hemagglutinin (HA) clade classifications, an automated tool for HA subtype numbering conversion, linkouts to disease event data and the addition of host factor and antiviral drug components. All data and tools are freely available without restriction from the IRD website at https://www.fludb.org.

AB - The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics and therapeutics against influenza virus by providing a comprehensive collection of influenza-related data integrated from various sources, a growing suite of analysis and visualization tools for data mining and hypothesis generation, personal workbench spaces for data storage and sharing, and active user community support. Here, we describe the recent improvements in IRD including the use of cloud and high performance computing resources, analysis and visualization of user-provided sequence data with associated metadata, predictions of novel variant proteins, annotations of phenotype-associated sequence markers and their predicted phenotypic effects, hemagglutinin (HA) clade classifications, an automated tool for HA subtype numbering conversion, linkouts to disease event data and the addition of host factor and antiviral drug components. All data and tools are freely available without restriction from the IRD website at https://www.fludb.org.

UR - http://www.scopus.com/inward/record.url?scp=85016149394&partnerID=8YFLogxK

U2 - 10.1093/nar/gkw857

DO - 10.1093/nar/gkw857

M3 - Article

C2 - 27679478

AN - SCOPUS:85016149394

SN - 0305-1048

VL - 45

SP - D466-D474

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -

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

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