Networks of genomic co-occurrence capture characteristics of human influenza A (H3N2) evolution

@article{citeulike:1995192, abstract = {The recent availability of full genomic sequence data for a large number of human influenza A (H3N2) virus isolates over many years provides us an opportunity to analyze human influenza virus evolution by considering all gene segments simultaneously. However, such analysis requires development of new computational models that can capture the complex evolutionary features over the entire genome. By analyzing nucleotide co-occurrence over the entire genome of human H3N2 viruses, we have developed a network model to describe H3N2 virus evolutionary patterns and dynamics. The network model effectively captures the evolutionary antigenic features of H3N2 virus at the whole-genome level and accurately describes the complex evolutionary patterns between individual gene segments. Our analyses show that the co-occurring nucleotide modules apparently underpin the dynamics of human H3N2 evolution and that amino acid substitutions corresponding to nucleotide co-changes cluster preferentially in known antigenic regions of the viral HA. Therefore, our study demonstrates that nucleotide co-occurrence networks represent a powerful method for tracking influenza A virus evolution and that cooperative genomic interaction is a major force underlying influenza virus evolution. 10.1101/gr.6969007}, author = {Du, Xiangjun and Wang, Zhuo and Wu, Aiping and Song, Lin and Cao, Yang and Hang, Haiying and Jiang, Taijiao }, citeulike-article-id = {1995192}, doi = {http://dx.doi.org/10.1101/gr.6969007}, journal = {Genome Res.}, keywords = {evolution, genome, influenza, network}, month = {November}, pages = {gr.6969007+}, posted-at = {2008-01-03 03:56:21}, priority = {2}, title = {Networks of genomic co-occurrence capture characteristics of human influenza A (H3N2) evolution}, url = {http://dx.doi.org/10.1101/gr.6969007}, year = {2007} }

TY - JOUR ID - citeulike:1995192 L3 - citeulike-article-id:1995192 TI - Networks of genomic co-occurrence capture characteristics of human influenza A (H3N2) evolution JF - Genome Res. SP - gr.6969007 N2 - The recent availability of full genomic sequence data for a large number of human influenza A (H3N2) virus isolates over many years provides us an opportunity to analyze human influenza virus evolution by considering all gene segments simultaneously. However, such analysis requires development of new computational models that can capture the complex evolutionary features over the entire genome. By analyzing nucleotide co-occurrence over the entire genome of human H3N2 viruses, we have developed a network model to describe H3N2 virus evolutionary patterns and dynamics. The network model effectively captures the evolutionary antigenic features of H3N2 virus at the whole-genome level and accurately describes the complex evolutionary patterns between individual gene segments. Our analyses show that the co-occurring nucleotide modules apparently underpin the dynamics of human H3N2 evolution and that amino acid substitutions corresponding to nucleotide co-changes cluster preferentially in known antigenic regions of the viral HA. Therefore, our study demonstrates that nucleotide co-occurrence networks represent a powerful method for tracking influenza A virus evolution and that cooperative genomic interaction is a major force underlying influenza virus evolution. 10.1101/gr.6969007 KW - evolution KW - genome KW - influenza KW - network AU - Du, Xiangjun AU - Wang, Zhuo AU - Wu, Aiping AU - Song, Lin AU - Cao, Yang AU - Hang, Haiying AU - Jiang, Taijiao PY - 2007/11/21/ UR - http://dx.doi.org/10.1101/gr.6969007 ER -