TY - JOUR AU - Alexander, D. J. PY - 2000 DA - 2000// TI - A review of avian influenza in different bird species JO - Vet Microbiol VL - 74 UR - https://doi.org/10.1016/S0378-1135(00)00160-7 DO - 10.1016/S0378-1135(00)00160-7 ID - Alexander2000 ER - TY - JOUR AU - Vanderven, H. A. AU - Petkau, K. AU - Ryan-Jean, K. E. AU - Aldridge, J. R. AU - Webster, R. G. AU - Magor, K. E. PY - 2012 DA - 2012// TI - Avian influenza rapidly induces antiviral genes in duck lung and intestine JO - Mol Immunol VL - 51 UR - https://doi.org/10.1016/j.molimm.2012.03.034 DO - 10.1016/j.molimm.2012.03.034 ID - Vanderven2012 ER - TY - JOUR AU - Cornelissen, J. B. AU - Vervelde, L. AU - Post, J. AU - Rebel, J. M. PY - 2013 DA - 2013// TI - Differences in highly pathogenic avian influenza viral pathogenesis and associated early inflammatory response in chickens and ducks JO - Avian Pathol VL - 42 UR - https://doi.org/10.1080/03079457.2013.807325 DO - 10.1080/03079457.2013.807325 ID - Cornelissen2013 ER - TY - JOUR AU - Sturm-Ramirez, K. M. AU - Ellis, T. AU - Bousfield, B. AU - Bissett, L. AU - Dyrting, K. AU - Rehg, J. E. PY - 2004 DA - 2004// TI - Reemerging H5N1 influenza viruses in Hong Kong in 2002 are highly pathogenic to ducks JO - J Virol VL - 78 UR - https://doi.org/10.1128/JVI.78.9.4892-4901.2004 DO - 10.1128/JVI.78.9.4892-4901.2004 ID - Sturm-Ramirez2004 ER - TY - JOUR AU - Kajihara, M. AU - Sakoda, Y. AU - Soda, K. AU - Minari, K. AU - Okamatsu, M. AU - Takada, A. PY - 2013 DA - 2013// TI - The PB2, PA, HA, NP, and NS genes of a highly pathogenic avian influenza virus A/whooper swan/Mongolia/3/2005 (H5N1) are responsible for pathogenicity in ducks JO - Virol J VL - 10 UR - https://doi.org/10.1186/1743-422X-10-45 DO - 10.1186/1743-422X-10-45 ID - Kajihara2013 ER - TY - JOUR AU - Pantin-Jackwood, M. AU - Swayne, D. E. AU - Smith, D. AU - Shepherd, E. PY - 2013 DA - 2013// TI - Effect of species, breed and route of virus inoculation on the pathogenicity of H5N1 highly pathogenic influenza (HPAI) viruses in domestic ducks JO - Vet Res VL - 44 UR - https://doi.org/10.1186/1297-9716-44-62 DO - 10.1186/1297-9716-44-62 ID - Pantin-Jackwood2013 ER - TY - JOUR AU - Kuchipudi, S. V. AU - Dunham, S. P. AU - Nelli, R. AU - White, G. A. AU - Coward, V. J. AU - Slomka, M. J. PY - 2012 DA - 2012// TI - Rapid death of duck cells infected with influenza: a potential mechanism for host resistance to H5N1 JO - Immunol Cell Biol VL - 90 UR - https://doi.org/10.1038/icb.2011.17 DO - 10.1038/icb.2011.17 ID - Kuchipudi2012 ER - TY - STD TI - CNN article: [http://edition.cnn.com/2013/04/24/world/asia/china-birdflu/index.html] UR - http://edition.cnn.com/2013/04/24/world/asia/china-birdflu/index.html ID - ref8 ER - TY - JOUR AU - Nunes-Alves, C. PY - 2014 DA - 2014// TI - Viral pathogenesis: The pandemic potential of H10N8 JO - Nat Rev Microbiol VL - 12 ID - Nunes-Alves2014 ER - TY - JOUR AU - Gagneux, P. AU - Cheriyan, M. AU - Hurtado-Ziola, N. AU - Linden, E. C. AU - Anderson, D. AU - McClure, H. PY - 2003 DA - 2003// TI - Human-specific regulation of alpha 2-6-linked sialic acids JO - J Biol Chem VL - 278 UR - https://doi.org/10.1074/jbc.M309813200 DO - 10.1074/jbc.M309813200 ID - Gagneux2003 ER - TY - JOUR AU - Matrosovich, M. N. AU - Matrosovich, T. Y. AU - Gray, T. AU - Roberts, N. A. AU - Klenk, H. D. PY - 2004 DA - 2004// TI - Human and avian influenza viruses target different cell types in cultures of human airway epithelium JO - Proc Natl Acad Sci U S A VL - 101 UR - https://doi.org/10.1073/pnas.0308001101 DO - 10.1073/pnas.0308001101 ID - Matrosovich2004 ER - TY - JOUR AU - Kuchipudi, S. V. AU - Nelli, R. AU - White, G. A. AU - Bain, M. AU - Chang, K. C. AU - Dunham, S. PY - 2009 DA - 2009// TI - Differences in influenza virus receptors in chickens and ducks: Implications for interspecies transmission JO - J Mol Genet Med VL - 3 UR - https://doi.org/10.4172/1747-0862.1000026 DO - 10.4172/1747-0862.1000026 ID - Kuchipudi2009 ER - TY - JOUR AU - Hughes, A. L. AU - Friedman, R. PY - 2008 DA - 2008// TI - Genome size reduction in the chicken has involved massive loss of ancestral protein-coding genes JO - Mol Biol Evol VL - 25 UR - https://doi.org/10.1093/molbev/msn207 DO - 10.1093/molbev/msn207 ID - Hughes2008 ER - TY - JOUR AU - Huang, Y. AU - Li, Y. AU - Burt, D. W. AU - Chen, H. AU - Zhang, Y. AU - Qian, W. PY - 2013 DA - 2013// TI - The duck genome and transcriptome provide insight into an avian influenza virus reservoir species JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2657 DO - 10.1038/ng.2657 ID - Huang2013 ER - TY - JOUR AU - Yilmaz, A. AU - Shen, S. X. AU - Adelson, D. L. AU - Xavier, S. AU - Zhu, J. J. PY - 2005 DA - 2005// TI - Identification and sequence analysis of chicken Toll-like receptors JO - Immunogenetics VL - 56 UR - https://doi.org/10.1007/s00251-004-0740-8 DO - 10.1007/s00251-004-0740-8 ID - Yilmaz2005 ER - TY - JOUR AU - Temperley, N. D. AU - Berlin, S. AU - Paton, I. R. AU - Griffin, D. K. PY - 2008 DA - 2008// TI - Evolution of the chicken Toll-like receptor gene family: a story of gene gain and gene loss JO - BMC Genomics VL - 9 UR - https://doi.org/10.1186/1471-2164-9-62 DO - 10.1186/1471-2164-9-62 ID - Temperley2008 ER - TY - JOUR AU - Magor, K. E. AU - Miranzo Navarro, D. AU - Barber, M. R. AU - Petkau, K. AU - Fleming-Canepa, X. AU - Blyth, G. A. PY - 2013 DA - 2013// TI - Defense genes missing from the flight division JO - Dev Comp Immunol VL - 41 UR - https://doi.org/10.1016/j.dci.2013.04.010 DO - 10.1016/j.dci.2013.04.010 ID - Magor2013 ER - TY - JOUR AU - Barber, M. R. AU - Aldridge, J. R. AU - Webster, R. G. AU - Magor, K. E. PY - 2010 DA - 2010// TI - Association of RIG-I with innate immunity of ducks to influenza JO - Proc Natl Acad Sci U S A VL - 107 UR - https://doi.org/10.1073/pnas.1001755107 DO - 10.1073/pnas.1001755107 ID - Barber2010 ER - TY - JOUR AU - Huang, I. C. AU - Bailey, C. C. AU - Weyer, J. L. AU - Radoshitzky, S. R. AU - Becker, M. M. AU - Chiang, J. J. PY - 2011 DA - 2011// TI - Distinct patterns of IFITM-mediated restriction of filoviruses, SARS coronavirus, and influenza A virus JO - PLoS Pathog VL - 7 UR - https://doi.org/10.1371/journal.ppat.1001258 DO - 10.1371/journal.ppat.1001258 ID - Huang2011 ER - TY - JOUR AU - Everitt, A. R. AU - Clare, S. AU - Pertel, T. AU - John, S. P. AU - Wash, R. S. AU - Smith, S. E. PY - 2012 DA - 2012// TI - Gordon SB; GenISIS Investigators; MOSAIC Investigators, Smyth RL, Openshaw PJ, Dougan G, Brass AL, Kellam P: IFITM3 restricts the morbidity and mortality associated with influenza JO - Nature VL - 484 UR - https://doi.org/10.1038/nature10921 DO - 10.1038/nature10921 ID - Everitt2012 ER - TY - JOUR AU - Sällman Almén, M. AU - Bringeland, N. AU - Fredriksson, R. AU - Schiöth, H. B. PY - 2012 DA - 2012// TI - The dispanins: a novel gene family of ancient origin that contains 14 human members JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0031961 DO - 10.1371/journal.pone.0031961 ID - Sällman Almén2012 ER - TY - JOUR AU - Zhang, Z. AU - Liu, J. AU - Li, M. AU - Yang, H. AU - Zhang, C. PY - 2012 DA - 2012// TI - Evolutionary dynamics of the interferon-induced transmembrane gene family in vertebrates JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0049265 DO - 10.1371/journal.pone.0049265 ID - Zhang2012 ER - TY - JOUR AU - Brass, A. L. AU - Huang, I. C. AU - Benita, Y. AU - John, S. P. AU - Krishnan, M. N. AU - Feeley, E. M. PY - 2009 DA - 2009// TI - The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus JO - Cell VL - 139 UR - https://doi.org/10.1016/j.cell.2009.12.017 DO - 10.1016/j.cell.2009.12.017 ID - Brass2009 ER - TY - JOUR AU - Diamond, M. S. AU - Farzan, M. PY - 2013 DA - 2013// TI - The broad-spectrum antiviral functions of IFIT and IFITM proteins JO - Nat Rev Immunol VL - 13 UR - https://doi.org/10.1038/nri3344 DO - 10.1038/nri3344 ID - Diamond2013 ER - TY - JOUR AU - Amini-Bavil-Olyaee, S. AU - Choi, Y. J. AU - Lee, J. H. AU - Shi, M. AU - Huang, I. C. AU - Farzan, M. PY - 2013 DA - 2013// TI - The antiviral effector IFITM3 disrupts intracellular cholesterol homeostasis to block viral entry JO - Cell Host Microbe VL - 13 UR - https://doi.org/10.1016/j.chom.2013.03.006 DO - 10.1016/j.chom.2013.03.006 ID - Amini-Bavil-Olyaee2013 ER - TY - JOUR AU - John, S. P. AU - Chin, C. R. AU - Perreira, J. M. AU - Feeley, E. M. AU - Aker, A. M. AU - Savidis, G. PY - 2013 DA - 2013// TI - The CD225 domain of IFITM3 is required for both IFITM protein association and inhibition of influenza A virus and dengue virus replication JO - J Virol VL - 87 UR - https://doi.org/10.1128/JVI.00481-13 DO - 10.1128/JVI.00481-13 ID - John2013 ER - TY - CHAP AU - Pantin-Jackwood, M. AU - Swayne, D. E. ED - Swayne, D. E. PY - 2008 DA - 2008// TI - Pathobiology of avian influenza virus infections in birds and mammals BT - In Avian Influenza PB - Blackwell Publishing CY - Iowa ID - Pantin-Jackwood2008 ER - TY - JOUR AU - Smith, S. E. AU - Gibson, M. S. AU - Wash, R. S. AU - Ferrara, F. AU - Wright, E. AU - Temperton, N. PY - 2013 DA - 2013// TI - Chicken interferon-inducible transmembrane protein 3 restricts influenza viruses and lyssaviruses in vitro JO - J Virol VL - 87 UR - https://doi.org/10.1128/JVI.01443-13 DO - 10.1128/JVI.01443-13 ID - Smith2013 ER - TY - JOUR AU - Huelsenbeck, J. P. AU - Ronquist, F. PY - 2001 DA - 2001// TI - MRBAYES: Bayesian inference of phylogenetic trees JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.8.754 DO - 10.1093/bioinformatics/17.8.754 ID - Huelsenbeck2001 ER - TY - JOUR AU - Ronquist, F. AU - Huelsenbeck, J. P. PY - 2003 DA - 2003// TI - MrBayes 3: Bayesian phylogenetic inference under mixed models JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg180 DO - 10.1093/bioinformatics/btg180 ID - Ronquist2003 ER - TY - JOUR AU - Pond, S. L. AU - Frost, S. D. PY - 2005 DA - 2005// TI - Datamonkey: rapid detection of selective pressure on individual sites of codon alignments JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti320 DO - 10.1093/bioinformatics/bti320 ID - Pond2005 ER - TY - JOUR AU - Murrell, B. AU - Wertheim, J. O. AU - Moola, S. AU - Weighill, T. AU - Scheffler, K. AU - Pond, S. L. K. PY - 2012 DA - 2012// TI - Detecting individual; sites subject to episodic diversifying selection JO - PLoS Genet VL - 8 UR - https://doi.org/10.1371/journal.pgen.1002764 DO - 10.1371/journal.pgen.1002764 ID - Murrell2012 ER - TY - JOUR AU - Murrell, B. AU - Moola, S. AU - Mabona, A. AU - Weighill, T. AU - Sheward, D. AU - Pond, S. L. K. PY - 2013 DA - 2013// TI - FUBAR: a fast, unconstrained bayesian approximation for Inferring Selection JO - Mol Biol Evol VL - 30 UR - https://doi.org/10.1093/molbev/mst030 DO - 10.1093/molbev/mst030 ID - Murrell2013 ER - TY - JOUR AU - Upla, P. AU - Hyypiä, T. AU - Marjomäk, V. PY - 2009 DA - 2009// TI - Role of lipid rafts in virus infection JO - Future Virol VL - 4 UR - https://doi.org/10.2217/fvl.09.45 DO - 10.2217/fvl.09.45 ID - Upla2009 ER - TY - STD TI - Tanner LB: Lipidomics of influenza virus: implications of host cell choline and sphingolipid metabolism. PhD Thesis. National University of Singapore & University of Basel; 2012. http://www.scholarbank.nus.edu.sg/handle/10635/36115. UR - http://www.scholarbank.nus.edu.sg/handle/10635/36115 ID - ref35 ER - TY - JOUR AU - Jang, H. AU - Boltz, D. AU - McClaren, J. AU - Pani, A. K. AU - Smeyne, M. AU - Korff, A. PY - 2012 DA - 2012// TI - Inflammatory effects of highly pathogenic H5N1 influenza virus infection in the CNS of mice JO - J Neurosci VL - 32 UR - https://doi.org/10.1523/JNEUROSCI.5123-11.2012 DO - 10.1523/JNEUROSCI.5123-11.2012 ID - Jang2012 ER - TY - JOUR AU - Jang, H. AU - Boltz, D. AU - Sturm-Ramirez, K. AU - Shepherd, K. R. AU - Jiao, Y. AU - Webster, R. PY - 2009 DA - 2009// TI - Highly pathogenic H5N1 influenza virus can enter the central nervous system and induce neuroinflammation and neurodegeneration JO - Proc Natl Acad Sci U S A VL - 106 UR - https://doi.org/10.1073/pnas.0900096106 DO - 10.1073/pnas.0900096106 ID - Jang2009 ER - TY - JOUR AU - Wiwanitkit, S. AU - Wiwanitkit, V. PY - 2013 DA - 2013// TI - Brain involvement in H7N9 bird flu: a topic for consideration JO - Arq Neuropsiquiatr VL - 71 UR - https://doi.org/10.1590/0004-282X20130133 DO - 10.1590/0004-282X20130133 ID - Wiwanitkit2013 ER - TY - JOUR AU - Smith, J. AU - Sadeyen, J. R. AU - Paton, I. R. AU - Hocking, P. M. AU - Salmon, N. AU - Fife, M. PY - 2011 DA - 2011// TI - Systems analysis of immune responses in Marek's disease virus-infected chickens identifies a gene involved in susceptibility and highlights a possible novel pathogenicity mechanism JO - J Virol VL - 85 UR - https://doi.org/10.1128/JVI.05499-11 DO - 10.1128/JVI.05499-11 ID - Smith2011 ER - TY - JOUR AU - Chesarino, N. M. AU - McMichael, T. M. AU - Hach, J. C. AU - Yount, J. S. PY - 2014 DA - 2014// TI - Phosphorylation of the antiviral protein interferon-inducible transmembrane protein 3 (IFITM3) dually regulates its endocytosis and ubiquitination JO - J Biol Chem VL - 289 UR - https://doi.org/10.1074/jbc.M114.557694 DO - 10.1074/jbc.M114.557694 ID - Chesarino2014 ER - TY - JOUR AU - Yount, J. S. AU - Moltedo, B. AU - Yang, Y. -. Y. AU - Charron, G. AU - Moran, T. M. AU - Lopez, C. B. PY - 2010 DA - 2010// TI - Palmitoylome profiling reveals S-palmitoylation-dependent antiviral activity of IFITM3 JO - Nat Chem Biol VL - 6 UR - https://doi.org/10.1038/nchembio.405 DO - 10.1038/nchembio.405 ID - Yount2010 ER - TY - JOUR AU - Yount, J. S. AU - Karssemeijer, R. A. AU - Hang, H. C. PY - 2012 DA - 2012// TI - S-palmitoylation and ubiquination differentially regulate IFITM3-mediated resistance to influenza virus JO - J Biol Chem VL - 287 UR - https://doi.org/10.1074/jbc.M112.362095 DO - 10.1074/jbc.M112.362095 ID - Yount2012 ER - TY - JOUR AU - Chutiwitoonchai, N. AU - Hiyoshi, M. AU - Hiyoshi-Yoshidomi, Y. AU - Hashimoto, M. AU - Tokunaga, K. AU - Suzu, S. PY - 2013 DA - 2013// TI - Characteristics of IFITM, the newly identified IFN-inducible anti-HIV-1 family proteins JO - Microbes Infect VL - 15 UR - https://doi.org/10.1016/j.micinf.2012.12.003 DO - 10.1016/j.micinf.2012.12.003 ID - Chutiwitoonchai2013 ER - TY - JOUR AU - Li, K. AU - Markosyan, R. M. AU - Zheng, Y. -. M. AU - Golfetto, O. AU - Bungart, B. AU - Li, M. PY - 2013 DA - 2013// TI - IFITM proteins restrict viral membrane hemifusion JO - PLoS Pathog VL - 9 UR - https://doi.org/10.1371/journal.ppat.1003124 DO - 10.1371/journal.ppat.1003124 ID - Li2013 ER - TY - STD TI - BLAST. [http://blast.ncbi.nlm.nih.gov/Blast.cgi/] UR - http://blast.ncbi.nlm.nih.gov/Blast.cgi/ ID - ref45 ER - TY - STD TI - Genewise. [http://www.ebi.ac.uk/Tools/psa/genewise/] UR - http://www.ebi.ac.uk/Tools/psa/genewise/ ID - ref46 ER - TY - STD TI - SMART. [http://smart.embl-heidelberg.de/] UR - http://smart.embl-heidelberg.de/ ID - ref47 ER - TY - STD TI - SOSUI. [http://bp.nuap.nagoya-u.ac.jp/sosui/] UR - http://bp.nuap.nagoya-u.ac.jp/sosui/ ID - ref48 ER - TY - STD TI - Expasy. [http://www.expasy.org/] UR - http://www.expasy.org/ ID - ref49 ER - TY - STD TI - T-coffee. [http://www.tcoffee.org] UR - http://www.tcoffee.org/ ID - ref50 ER - TY - STD TI - Jalview. [http://www.jalview.org] UR - http://www.jalview.org/ ID - ref51 ER - TY - STD TI - Weblogo. [http://weblogo.threeplusone.com/] UR - http://weblogo.threeplusone.com/ ID - ref52 ER - TY - STD TI - GenBank. [www.ncbi.nlm.nih.gov/] UR - http://www.ncbi.nlm.nih.gov/ ID - ref53 ER - TY - STD TI - Ensembl. [www.ensembl.org/] UR - http://www.ensembl.org/ ID - ref54 ER - TY - STD TI - Avian Phylogenomic Project. [http://phybirds.genomics.org.cn/] UR - http://phybirds.genomics.org.cn/ ID - ref55 ER - TY - STD TI - MUSCLE. [www.ebi.ac.uk] UR - http://www.ebi.ac.uk ID - ref56 ER - TY - STD TI - MrBayes. [http://mrbayes.sourceforge.net/] UR - http://mrbayes.sourceforge.net/ ID - ref57 ER - TY - STD TI - MEGA6. [www.megasoftware.net/] UR - http://www.megasoftware.net/ ID - ref58 ER - TY - STD TI - FigTree. [www.molecularevolution.org] UR - http://www.molecularevolution.org ID - ref59 ER - TY - STD TI - DATAMONKEY. [www.datamonkey.org] UR - http://www.datamonkey.org ID - ref60 ER - TY - JOUR AU - Yang, Z. PY - 2007 DA - 2007// TI - PAML 4: phylogenetic analysis by maximum likelihood JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm088 DO - 10.1093/molbev/msm088 ID - Yang2007 ER - TY - STD TI - Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014;346(6215):1320–31. doi:10.1126/science.1253451. PubMed PMID: 25504713; PubMed Central PMCID: PMC4405904. ID - ref62 ER - TY - JOUR AU - Reed, L. J. AU - Muench, H. PY - 1938 DA - 1938// TI - A simple method for estimating fifty percent endpoints JO - Am J Hyg VL - 27 ID - Reed1938 ER - TY - JOUR AU - Livak, K. J. AU - Schmittgen, T. D. PY - 2001 DA - 2001// TI - Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2 − ΔΔCT Method JO - Methods VL - 25 UR - https://doi.org/10.1006/meth.2001.1262 DO - 10.1006/meth.2001.1262 ID - Livak2001 ER - TY - STD TI - Pathway Express [http://vortex.cs.wayne.edu/ontoexpress/] UR - http://vortex.cs.wayne.edu/ontoexpress/ ID - ref65 ER - TY - STD TI - Ingenuity Pathway Analysis. [http://www.ingenuity.com/] UR - http://www.ingenuity.com/ ID - ref66 ER - TY - STD TI - Expander. [http://acgt.cs.tau.ac.il/expander/] UR - http://acgt.cs.tau.ac.il/expander/ ID - ref67 ER - TY - STD TI - MATLAB and Statistics Toolbox Release 2009, The MathWorks, Inc., Natick, Massachusetts, United States [www.mathworks.co.uk/products/matlab/]. UR - http://www.mathworks.co.uk/products/matlab/ ID - ref68 ER - TY - STD TI - DAVID. [https://david.ncifcrf.gov/] UR - https://david.ncifcrf.gov/ ID - ref69 ER - TY - JOUR AU - Dennis, G. AU - Sherman, B. T. AU - Hosack, D. A. AU - Yang, J. AU - Gao, W. AU - Lane, H. C. PY - 2003 DA - 2003// TI - DAVID. Database for Annotation, Visualization, and Integrated Discovery JO - Genome Biol VL - 4 UR - https://doi.org/10.1186/gb-2003-4-5-p3 DO - 10.1186/gb-2003-4-5-p3 ID - Dennis2003 ER -