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Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus
Yuri I Wolf, Cecile Viboud, Edward C Holmes, Eugene V Koonin, David J Lipman
Biol Direct. 2006; 1: 34. Published online 2006 October 26. doi: 10.1186/1745-6150-1-34
PMCID:
PMC1647279
Abstract Full Text PDF–477K Supplementary Material
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 Is Cited by the Following 36 Articles in this Archive:
Gnarled-Trunk Evolutionary Model of Influenza A Virus Hemagglutinin
Kimihito Ito, Manabu Igarashi, Yutaka Miyazaki, Teiji Murakami, Syaka Iida, Hiroshi Kida, Ayato Takada
PLoS One. 2011; 6(10): e25953. Published online 2011 October 10. doi: 10.1371/journal.pone.0025953
PMCID:
PMC3189952
Abstract Full Text PDF–1.3M Supplementary Material
Strength and tempo of selection revealed in viral gene genealogies
Trevor Bedford, Sarah Cobey, Mercedes Pascual
BMC Evol Biol. 2011; 11: 220. Published online 2011 July 25. doi: 10.1186/1471-2148-11-220
PMCID:
PMC3199772
Abstract Full Text PDF–1.0M
Positive selection on hemagglutinin and neuraminidase genes of H1N1 influenza viruses
Wenfu Li, Weifeng Shi, Huijie Qiao, Simon YW Ho, Arong Luo, Yanzhou Zhang, Chaodong Zhu
Virol J. 2011; 8: 183. Published online 2011 April 21. doi: 10.1186/1743-422X-8-183
PMCID:
PMC3094300
Abstract Full Text PDF–414K Supplementary Material
Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins
Sergey Kryazhimskiy, Jonathan Dushoff, Georgii A. Bazykin, Joshua B. Plotkin
PLoS Genet. 2011 February; 7(2): e1001301. Published online 2011 February 17. doi: 10.1371/journal.pgen.1001301
PMCID:
PMC3040651
Abstract Full Text PDF–312K Supplementary Material
Projection of seasonal influenza severity from sequence and serological data
Yuri I Wolf, Anastasia Nikolskaya, Joshua L. Cherry, Cecile Viboud, Eugene Koonin, David J. Lipman
PLoS Curr. 2010 December 3; 2: RRN1200. doi: 10.1371/currents.RRN1200
PMCID:
PMC2998708
Abstract Full Text
Global Migration Dynamics Underlie Evolution and Persistence of Human Influenza A (H3N2)
Trevor Bedford, Sarah Cobey, Peter Beerli, Mercedes Pascual
PLoS Pathog. 2010 May; 6(5): e1000918. Published online 2010 May 27. doi: 10.1371/journal.ppat.1000918
PMCID:
PMC2877742
Abstract Full Text PDF–396K Supplementary Material
A two-tiered model for simulating the ecological and evolutionary dynamics of rapidly evolving viruses, with an application to influenza
Katia Koelle, Priya Khatri, Meredith Kamradt, Thomas B. Kepler
J R Soc Interface. 2010 September 6; 7(50): 1257–1274. Published online 2010 March 24. doi: 10.1098/rsif.2010.0007
PMCID:
PMC2894885
Abstract Full Text PDF–1.1M
Modeling gene sequences over time in 2009 H1N1 Influenza A Virus populations
Natalia Goñi, Alvaro Fajardo, Gonzalo Moratorio, Rodney Colina, Juan Cristina
Virol J. 2009; 6: 215. Published online 2009 December 4. doi: 10.1186/1743-422X-6-215
PMCID:
PMC2794274
Abstract Full Text PDF–702K Supplementary Material
Modeling gene sequences over time in 2009 H1N1 Influenza A Virus populations
Natalia Goñi, Alvaro Fajardo, Gonzalo Moratorio, Rodney Colina, Juan Cristina
Virol J. 2009; 6: 215. Published online 2009 December 4. doi: 10.1186/1743-422X-6-215
PMCID:
PMC2794274
Abstract Full Text PDF–702K Supplementary Material
Evolutionary Trends of A(H1N1) Influenza Virus Hemagglutinin Since 1918
Jun Shen, Jianpeng Ma, Qinghua Wang
PLoS One. 2009; 4(11): e7789. Published online 2009 November 17. doi: 10.1371/journal.pone.0007789
PMCID:
PMC2773012
Abstract Full Text PDF–604K Supplementary Material
The Role of Genomics in Tracking the Evolution of Influenza A Virus
Alice Carolyn McHardy, Ben Adams
PLoS Pathog. 2009 October; 5(10): e1000566. Published online 2009 October 26. doi: 10.1371/journal.ppat.1000566
PMCID:
PMC2739293
Abstract Full Text PDF–885K
Influenza A Gradual and Epochal Evolution: Insights from Simple Models
Sébastien Ballesteros, Elisabeta Vergu, Bernard Cazelles
PLoS One. 2009; 4(10): e7426. Published online 2009 October 20. doi: 10.1371/journal.pone.0007426
PMCID:
PMC2759541
Abstract Full Text PDF–1.3M Supplementary Material
Recent Human Influenza A/H3N2 Virus Evolution Driven by Novel Selection Factors in Addition to Antigenic Drift
Matthew J. Memoli, Brett W. Jagger, Vivien G. Dugan, Li Qi, Jadon P. Jackson, Jeffery K. Taubenberger
J Infect Dis. Author manuscript; available in PMC 2010 October 15.
Published in final edited form as: J Infect Dis. 2009 October 15; 200(8): 1232–1241. doi: 10.1086/605893
PMCID:
PMC2778484
Abstract Full Text PDF–2.5M
Evolutionary Dynamics of N-Glycosylation Sites of Influenza Virus Hemagglutinin
Joshua L. Cherry, David J. Lipman, Anastasia Nikolskaya, Yuri I Wolf
PLoS Curr. 2009 August 18; 1: RRN1001. doi: 10.1371/currents.RRN1001
PMCID:
PMC2762648
Abstract Full Text
The Persistent Legacy of the 1918 Influenza Virus
David M. Morens, Jeffery K. Taubenberger, Anthony S. Fauci
N Engl J Med. Author manuscript; available in PMC 2010 January 16.
Published in final edited form as: N Engl J Med. 2009 July 16; 361(3): 225–229. Published online 2009 June 29. doi: 10.1056/NEJMp0904819
PMCID:
PMC2749954
Full Text PDF–480K
Genetic Diversity in the SIR Model of Pathogen Evolution
Isabel Gordo, M. Gabriela M. Gomes, Daniel G. Reis, Paulo R. A. Campos
PLoS ONE. 2009; 4(3): e4876. Published online 2009 March 16. doi: 10.1371/journal.pone.0004876
PMCID:
PMC2653725
Abstract Full Text PDF–463K Supplementary Material
The Population Genetics of dN/dS
Sergey Kryazhimskiy, Joshua B. Plotkin
PLoS Genet. 2008 December; 4(12): e1000304. Published online 2008 December 12. doi: 10.1371/journal.pgen.1000304
PMCID:
PMC2596312
Abstract Full Text PDF–415K Supplementary Material
The pig as a mixing vessel for influenza viruses: Human and veterinary implications
Wenjun Ma, Robert E Kahn, Juergen A Richt
J Mol Genet Med. 2009 January; 3(1): 158–166. Published online 2008 November 27.
PMCID:
PMC2702078
Abstract Full Text PDF–362K
Seasonality of Influenza A(H3N2) Virus: A Hong Kong Perspective (1997–2006)
Julian W. Tang, Karry L. K. Ngai, Wai Y. Lam, Paul K. S. Chan
PLoS ONE. 2008; 3(7): e2768. Published online 2008 July 23. doi: 10.1371/journal.pone.0002768
PMCID:
PMC2481298
Abstract Full Text PDF–140K Supplementary Material
Directionality in the evolution of influenza A haemagglutinin
Sergey Kryazhimskiy, Georgii A Bazykin, Joshua Plotkin, Jonathan Dushoff
Proc Biol Sci. 2008 November 7; 275(1650): 2455–2464. Published online 2008 July 22. doi: 10.1098/rspb.2008.0521
Correction in:
Proc Biol Sci. 2009 August 22; 276(1669): 3035.
PMCID:
PMC2603193
Abstract Full Text PDF–241K Supplementary Material Correction
Toward a Unified Nomenclature System for Highly Pathogenic Avian Influenza Virus (H5N1)
WHO, OIE, FAO H, N, Evolution Working Group
Emerg Infect Dis. 2008 July; 14(7): e1. doi: 10.3201/eid1407.071681
PMCID:
PMC2600337
Full Text
Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation
Leonid Zaslavsky, Yiming Bao, Tatiana A Tatusova
BMC Bioinformatics. 2008; 9: 237. Published online 2008 May 16. doi: 10.1186/1471-2105-9-237
PMCID:
PMC2416652
Abstract Full Text PDF–684K Supplementary Material
Changing Selective Pressure during Antigenic Changes in Human Influenza H3
Benjamin P. Blackburne, Alan J. Hay, Richard A. Goldstein
PLoS Pathog. 2008 May; 4(5): e1000058. Published online 2008 May 2. doi: 10.1371/journal.ppat.1000058
PMCID:
PMC2323114
Abstract Full Text PDF–451K Supplementary Material
The genomic and epidemiological dynamics of human influenza A virus
Andrew Rambaut, Oliver G. Pybus, Martha I. Nelson, Cecile Viboud, Jeffery K. Taubenberger, Edward C. Holmes
Nature. Author manuscript; available in PMC 2009 May 29.
Published in final edited form as: Nature. 2008 May 29; 453(7195): 615–619. Published online 2008 April 16. doi: 10.1038/nature06945
PMCID:
PMC2441973
Abstract Full Text PDF–415K Supplementary Material
The evolution of human influenza A viruses from 1999 to 2006: A complete genome study
Karoline Bragstad, Lars P Nielsen, Anders Fomsgaard
Virol J. 2008; 5: 40. Published online 2008 March 7. doi: 10.1186/1743-422X-5-40
PMCID:
PMC2311284
Abstract Full Text PDF–536K
Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes
Sergey Kryazhimskiy, Georgii A. Bazykin, Jonathan Dushoff
J Virol. 2008 May; 82(10): 4938–4945. Published online 2008 March 5. doi: 10.1128/JVI.02415-07
PMCID:
PMC2346729
Abstract Full Text PDF–247K
Multiple Reassortment Events in the Evolutionary History of H1N1 Influenza A Virus Since 1918
Martha I. Nelson, Cécile Viboud, Lone Simonsen, Ryan T. Bennett, Sara B. Griesemer, Kirsten St. George, Jill Taylor, David J. Spiro, Naomi A. Sengamalay, Elodie Ghedin, Jeffery K. Taubenberger, Edward C. Holmes
PLoS Pathog. 2008 February; 4(2): e1000012. Published online 2008 February 29. doi: 10.1371/journal.ppat.1000012
PMCID:
PMC2262849
Abstract Full Text PDF–444K Supplementary Material
Influenza A H5N1 Immigration Is Filtered Out at Some International Borders
Robert G. Wallace, Walter M. Fitch
PLoS ONE. 2008; 3(2): e1697. Published online 2008 February 27. doi: 10.1371/journal.pone.0001697
PMCID:
PMC2244808
Abstract Full Text PDF–510K Supplementary Material
Genetic and Epidemiological Analysis of Influenza Virus Epidemics in Taiwan during 2003 to 2006
Jhih-Wei Jian, Guang-Wu Chen, Cheng-Tsung Lai, Li-Ching Hsu, Pei-Jer Chen, Steve Hsu-Sung Kuo, Ho-Sheng Wu, Shin-Ru Shih
J Clin Microbiol. 2008 April; 46(4): 1426–1434. Published online 2008 February 6. doi: 10.1128/JCM.01560-07
PMCID:
PMC2292966
Abstract Full Text PDF–577K Supplementary Material
Networks of genomic co-occurrence capture characteristics of human influenza A (H3N2) evolution
Xiangjun Du, Zhuo Wang, Aiping Wu, Lin Song, Yang Cao, Haiying Hang, Taijiao Jiang
Genome Res. 2008 January; 18(1): 178–187. doi: 10.1101/gr.6969007
PMCID:
PMC2134775
Abstract Full Text PDF–1.0M
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