tetano
Editor, Senior Moderator
Influenza Other Respi Viruses. 2012 Jan 20. doi: 10.1111/j.1750-2659.2011.00331.x. [Epub ahead of print]
Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance.
Squires RB, Noronha J, Hunt V, Garc?a-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.
Source
Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA Department of Microbiology, Mount Sinai School of Medicine, New York, NY, USA Department of Medicine, Division of Infectious Diseases, Mount Sinai School of Medicine, New York, NY, USA Global Health and Emerging Pathogens Institute, Mount Sinai School of Medicine, New York, NY, USA Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA Center for Comparative Medicine, University of California, Davis, CA, USA Southeast Poultry Research Lab, US Department of Agriculture, Athens, GA, USA Vecna Technologies, Greenbelt, MD, USA Northrop Grumman Information Systems, Health IT Systems, Rockville, MD, USA Division of Biomedical Informatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Abstract
Please cite this paper as: Squires et al. (2012) Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza and Other Respiratory Viruses DOI: 10.1111/j.1750-2659.2011.00331.x. 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.
? 2012 Blackwell Publishing Ltd.
PMID:
22260278
[PubMed - as supplied by publisher]
http://www.ncbi.nlm.nih.gov/pubmed/22260278
Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance.
Squires RB, Noronha J, Hunt V, Garc?a-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.
Source
Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA Department of Microbiology, Mount Sinai School of Medicine, New York, NY, USA Department of Medicine, Division of Infectious Diseases, Mount Sinai School of Medicine, New York, NY, USA Global Health and Emerging Pathogens Institute, Mount Sinai School of Medicine, New York, NY, USA Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA Center for Comparative Medicine, University of California, Davis, CA, USA Southeast Poultry Research Lab, US Department of Agriculture, Athens, GA, USA Vecna Technologies, Greenbelt, MD, USA Northrop Grumman Information Systems, Health IT Systems, Rockville, MD, USA Division of Biomedical Informatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Abstract
Please cite this paper as: Squires et al. (2012) Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza and Other Respiratory Viruses DOI: 10.1111/j.1750-2659.2011.00331.x. 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.
? 2012 Blackwell Publishing Ltd.
PMID:
22260278
[PubMed - as supplied by publisher]
http://www.ncbi.nlm.nih.gov/pubmed/22260278