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

By Yun Zhang, B. Aevermann, T. Anderson, D. Burke, G. Dauphin, Z. Gu, Sherry He, Sanjeev Kumar, C. Larsen, Alexandra J. Lee and 18 more. Nucleic Acids Res., 2016

326 citations recorded by the source corpus.

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.

Subfields: Epidemiology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fd69bd5b948ff001ae87f6bfa06693398965a9c2

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Citations in the corpus

UniProt: a worldwide hub of protein knowledge (2018, background): “We compiled and curated complete viral genome (proteome) data from INSDC (which feeds into UniProt) as well as a range of other specialized viral genome resources including ViPr (9), IRD (10), the HIV database (https://www.hiv.lanl. gov/), Papillomavirus Episteme (11) and the HCV database (https://h”
Development of a Pan-H1 Influenza Vaccine (2018, background): “The advent of high-throughput DNA sequencing and bioinformatics over the past decade has led to vast databases of viral sequences that have affected human populations across the world and over the past century (28).”
Multistate design of influenza antibodies improves affinity and breadth against seasonal viruses (2019, methodology): “We created homology models of HA proteins from the sequences of 524 viruses in the Influenza Research Database using the RosettaCM multitemplate comparative modeling protocol (14, 15).”