Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments.

[1]  Gavin J. D. Smith,et al.  No evidence for intra-segment recombination of 2009 H1N1 influenza virus in swine. , 2012, Gene.

[2]  E. Holmes,et al.  Why do RNA viruses recombine? , 2011, Nature Reviews Microbiology.

[3]  Edward C. Holmes,et al.  Guidelines for Identifying Homologous Recombination Events in Influenza A Virus , 2010, PloS one.

[4]  Edward C. Holmes,et al.  Mixed Infection and the Genesis of Influenza Virus Diversity , 2009, Journal of Virology.

[5]  J. Archer,et al.  Molecular Mechanisms of Recombination Restriction in the Envelope Gene of the Human Immunodeficiency Virus , 2009, PLoS pathogens.

[6]  M. Zazzi,et al.  Recombination analysis and structure prediction show correlation between breakpoint clusters and RNA hairpins in the pol gene of human immunodeficiency virus type 1 unique recombinant forms. , 2008, The Journal of general virology.

[7]  Cheng-qiang He,et al.  Homologous recombination evidence in human and swine influenza A viruses. , 2008, Virology.

[8]  Cheng-qiang He,et al.  Homologous recombination as an evolutionary force in the avian influenza A virus. , 2008, Molecular biology and evolution.

[9]  R. Rabadán,et al.  Anomalies in the Influenza Virus Genome Database: New Biology or Laboratory Errors? , 2008, Journal of Virology.

[10]  Jonathan A. Runstadler,et al.  The Evolutionary Genetics and Emergence of Avian Influenza Viruses in Wild Birds , 2008, PLoS pathogens.

[11]  E. Holmes,et al.  Homologous Recombination Is Very Rare or Absent in Human Influenza A Virus , 2008, Journal of Virology.

[12]  C. Hon,et al.  Evolutionary analyses of European H1N2 swine influenza A virus by placing timestamps on the multiple reassortment events. , 2008, Virus research.

[13]  T. Tatusova,et al.  The Influenza Virus Resource at the National Center for Biotechnology Information , 2007, Journal of Virology.

[14]  Gavin J. D. Smith,et al.  The Genesis and Evolution of H9N2 Influenza Viruses in Poultry from Southern China, 2000 to 2005 , 2007, Journal of Virology.

[15]  David Posada,et al.  An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets , 2007, Genetics.

[16]  Edward C Holmes,et al.  Avian influenza virus exhibits rapid evolutionary dynamics. , 2006, Molecular biology and evolution.

[17]  Gavin J. D. Smith,et al.  Emergence and predominance of an H5N1 influenza variant in China , 2006, Proceedings of the National Academy of Sciences.

[18]  F. Lei,et al.  New Genotype of Avian Influenza H5N1 Viruses Isolated from Tree Sparrows in China , 2005, Journal of Virology.

[19]  Hualan Chen,et al.  Evolution of H9N2 influenza viruses from domestic poultry in Mainland China. , 2005, Virology.

[20]  Yoshihiro Kawaoka,et al.  The origins of new pandemic viruses: the acquisition of new host ranges by canine parvovirus and influenza A viruses. , 2005, Annual review of microbiology.

[21]  David Posada,et al.  RDP2: recombination detection and analysis from sequence alignments , 2005, Bioinform..

[22]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[23]  B. Murphy,et al.  Arguments for live flavivirus vaccines , 2004, The Lancet.

[24]  R. Howe,et al.  hGISA: seek and ye shall find , 2004, The Lancet.

[25]  W. Messer,et al.  Arguments for live flavivirus vaccines , 2004, The Lancet.

[26]  Y Li,et al.  The evolution of H5N1 influenza viruses in ducks in southern China. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[27]  H. Kida,et al.  Phylogenetic Analysis of Neuraminidase Gene of H9N2 Influenza Viruses Prevalent in Chickens in China during 1995–2002 , 2003, Virus Genes.

[28]  Edward C Holmes,et al.  Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. , 2003, The Journal of general virology.

[29]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[30]  R. Nielsen,et al.  Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. , 2003, Genetics.

[31]  James I Mullins,et al.  Potential impact of recombination on sitewise approaches for detecting positive natural selection. , 2003, Genetical research.

[32]  S. Shafikhani.  Factors affecting PCR-mediated recombination. , 2002, Environmental microbiology.

[33]  O. Pybus,et al.  Questioning the evidence for genetic recombination in the 1918 "Spanish flu" virus. , 2002, Science.

[34]  Edward C. Holmes,et al.  Rates of Molecular Evolution in RNA Viruses: A Quantitative Phylogenetic Analysis , 2002, Journal of Molecular Evolution.

[35]  Y. Guan,et al.  H5N1 influenza viruses isolated from geese in Southeastern China: evidence for genetic reassortment and interspecies transmission to ducks. , 2002, Virology.

[36]  E. Paradis,et al.  Revealing the demographic histories of species using DNA sequences , 2001 .

[37]  K. Crandall,et al.  Evaluation of methods for detecting recombination from DNA sequences: Computer simulations , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[38]  D. Posada,et al.  Unveiling the molecular clock in the presence of recombination. , 2001, Molecular biology and evolution.

[39]  J. Hein,et al.  Recombination and the molecular clock. , 2000, Molecular biology and evolution.

[40]  J. Hein,et al.  Consequences of recombination on traditional phylogenetic analysis. , 2000, Genetics.

[41]  R. Webster,et al.  Characterization of the Influenza A Virus Gene Pool in Avian Species in Southern China: Was H6N1 a Derivative or a Precursor of H5N1? , 2000, Journal of Virology.

[42]  David E. Swayne,et al.  Continued Circulation in China of Highly Pathogenic Avian Influenza Viruses Encoding the Hemagglutinin Gene Associated with the 1997 H5N1 Outbreak in Poultry and Humans , 2000, Journal of Virology.

[43]  Darren Martin,et al.  RDP: detection of recombination amongst aligned sequences , 2000, Bioinform..

[44]  S. Sawyer,et al.  Possible emergence of new geminiviruses by frequent recombination. , 1999, Virology.

[45]  E. Holmes,et al.  Evolutionary aspects of recombination in RNA viruses. , 1999, The Journal of general virology.

[46]  Hidetoshi Shimodaira,et al.  Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference , 1999, Molecular Biology and Evolution.

[47]  E. Holmes,et al.  Phylogenetic evidence for recombination in dengue virus. , 1999, Molecular biology and evolution.

[48]  K. Lole,et al.  Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination , 1999, Journal of Virology.

[49]  I. Brown,et al.  Multiple genetic reassortment of avian and human influenza A viruses in European pigs, resulting in the emergence of an H1N2 virus of novel genotype. , 1998, The Journal of general virology.

[50]  C. Wilson,et al.  Stimulation and suppression of PCR-mediated recombination. , 1998, Nucleic acids research.

[51]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[52]  R. Webster,et al.  Evolution and ecology of influenza A viruses. , 1992, Current topics in microbiology and immunology.

[53]  John Maynard Smith,et al.  Analyzing the mosaic structure of genes , 1992, Journal of Molecular Evolution.

[54]  A. Meyerhans,et al.  DNA recombination during PCR. , 1990, Nucleic acids research.

[55]  S. Frost,et al.  Detecting signatures of selection from DNA sequences using Datamonkey. , 2009, Methods in molecular biology.

[56]  Konrad Scheffler,et al.  Robust inference of positive selection from recombining coding sequences , 2006, Bioinform..

[57]  K. Crandall,et al.  Recombination in evolutionary genomics. , 2002, Annual review of genetics.