TY - JOUR AU - Neumann, G. AU - Brownlee, G. G. AU - Fodor, E. AU - Kawaoka, Y. PY - 2004 DA - 2004// TI - Orthomyxovirus: replication, transcription, and polyadenylation JO - Curr Top Microbiol Immunol VL - 283 ID - Neumann2004 ER - TY - JOUR AU - Ahn, I. AU - Son, H. S. PY - 2007 DA - 2007// TI - Comparative study of the hemagglutinin and neuraminidase genes of Influenza A virus H3N2, H9N2 and H5N1 subtypes using bioinformatics techniques JO - Can J Microbiol VL - 53 UR - https://doi.org/10.1139/W07-044 DO - 10.1139/W07-044 ID - Ahn2007 ER - TY - JOUR AU - Wolf, Y. L. AU - Viboud, C. AU - Holmes, E. C. AU - Koonin, E. V. AU - Lipman, D. J. PY - 2006 DA - 2006// TI - Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus JO - Biol Direct VL - 1 UR - https://doi.org/10.1186/1745-6150-1-34 DO - 10.1186/1745-6150-1-34 ID - Wolf2006 ER - TY - JOUR AU - Hillerman, M. R. PY - 2002 DA - 2002// TI - Realities and enigmas of human viral influenza: pathogenesis, epidemiology and control JO - Vaccine VL - 20 UR - https://doi.org/10.1016/S0264-410X(02)00254-2 DO - 10.1016/S0264-410X(02)00254-2 ID - Hillerman2002 ER - TY - JOUR AU - De Jong, J. C. AU - Rimmelzwaan, G. F. AU - Fouchier, R. A. AU - Osterhaus, A. D. PY - 2000 DA - 2000// TI - Influenza virus: a master of metamorphosis JO - J Infection VL - 40 UR - https://doi.org/10.1053/jinf.2000.0652 DO - 10.1053/jinf.2000.0652 ID - De Jong2000 ER - TY - JOUR AU - Ferguson, N. M. AU - Galvani, A. P. AU - Bush, R. M. PY - 2003 DA - 2003// TI - Ecological and immunological determinants of influenza evolution JO - Nature VL - 422 UR - https://doi.org/10.1038/nature01509 DO - 10.1038/nature01509 ID - Ferguson2003 ER - TY - BOOK PY - 2009 DA - 2009// TI - Pandemic (H1N1). Influenza-like illness in the United States and Mexico. 24 April 2009 ID - ref7 ER - TY - JOUR PY - 2009 DA - 2009// TI - Update: infections with a swine-origin influenza A (H1N1) virus – United States and other countries, April 28th, 2009 JO - Morb Mortal Wkly Rep VL - 58 ID - ref8 ER - TY - JOUR AU - Smith, G. J. D. AU - Vijaykrishna, D. AU - Bahl, J. AU - Lycett, S. J. AU - Worobey, M. AU - Pybus, O. G. AU - Ma, S. K. AU - Cheung, C. L. AU - Raghwani, J. AU - Bhatt, S. AU - Peiris, J. S. M. AU - Guan, Y. AU - Rambaut, A. PY - 2009 DA - 2009// TI - Origins and evolutionary genomics of the 2009 swine-origin H1N1 Influenza A epidemic JO - Nature VL - 459 UR - https://doi.org/10.1038/nature08182 DO - 10.1038/nature08182 ID - Smith2009 ER - TY - JOUR AU - Gorman, O. T. AU - Bean, W. J. AU - Kawaoka, Y. AU - Donatelli, I. AU - Guo, Y. J. AU - Webster, R. G. PY - 1991 DA - 1991// TI - Evolution of influenza A virus nucleocapsid genes: implications for the origins of H1N1 human and classical swine viruses JO - J Virol VL - 65 ID - Gorman1991 ER - TY - JOUR AU - Stoletzki, N. AU - Eyre-Walker, A. PY - 2007 DA - 2007// TI - Synonymous codon usage in Escherichia coli: selection for translational accuracy JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msl166 DO - 10.1093/molbev/msl166 ID - Stoletzki2007 ER - TY - JOUR AU - Wong, E. AU - Smith, D. K. AU - Rabadan, R. AU - Peiris, M. AU - Poon, L. PY - 2010 DA - 2010// TI - Codon usage bias and the evolution of Influenza A viruses. Codon usage biases of Influenza virus JO - Evol Biol VL - 10 ID - Wong2010 ER - TY - JOUR AU - Ikemura, T. PY - 1982 DA - 1982// TI - Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs JO - J Mol Biol VL - 158 UR - https://doi.org/10.1016/0022-2836(82)90250-9 DO - 10.1016/0022-2836(82)90250-9 ID - Ikemura1982 ER - TY - JOUR AU - Sharp, P. M. AU - Li, W. H. PY - 1986 DA - 1986// TI - An evolutionary perspective on synonymous codon usage in unicellular organisms JO - J Mol Evol VL - 24 UR - https://doi.org/10.1007/BF02099948 DO - 10.1007/BF02099948 ID - Sharp1986 ER - TY - JOUR AU - Kryazhimskiy, S. AU - Bazykin, G. A. AU - Dushoff, J. PY - 2008 DA - 2008// TI - Natural selection for nucleotide usage at synonymous and non-synonymous sites in the influenza A genes JO - J Virol VL - 82 UR - https://doi.org/10.1128/JVI.02415-07 DO - 10.1128/JVI.02415-07 ID - Kryazhimskiy2008 ER - TY - JOUR AU - Zhou, T. AU - Gu, W. AU - Ma, J. AU - Sun, X. AU - Lu, Z. PY - 2005 DA - 2005// TI - Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses JO - Biosystems VL - 81 UR - https://doi.org/10.1016/j.biosystems.2005.03.002 DO - 10.1016/j.biosystems.2005.03.002 ID - Zhou2005 ER - TY - JOUR AU - Comeron, J. M. AU - Aguade, M. PY - 1998 DA - 1998// TI - An evaluation of measures of synonymous codon usage bias JO - J Mol Evol VL - 47 UR - https://doi.org/10.1007/PL00006384 DO - 10.1007/PL00006384 ID - Comeron1998 ER - TY - BOOK AU - Greenacre, M. PY - 1984 DA - 1984// TI - Theory and applications of correspondence analysis PB - Academic CY - London ID - Greenacre1984 ER - TY - JOUR AU - Tao, P. AU - Dai, L. AU - Luo, M. AU - Tang, F. AU - Tien, P. AU - Pan, Z. PY - 2009 DA - 2009// TI - Analysis of synonymous codon usage in classical swine fever virus JO - Virus Genes VL - 38 UR - https://doi.org/10.1007/s11262-008-0296-z DO - 10.1007/s11262-008-0296-z ID - Tao2009 ER - TY - JOUR AU - Crick, F. H. C. PY - 1966 DA - 1966// TI - Codon-anticodon pairing – Wobble hypothesis JO - J Mol Biol VL - 19 UR - https://doi.org/10.1016/S0022-2836(66)80022-0 DO - 10.1016/S0022-2836(66)80022-0 ID - Crick1966 ER - TY - JOUR AU - Chan, P. P. AU - Lowe, T. M. PY - 2009 DA - 2009// TI - GtRNAdb: a database of transfer RNA genes detected in genomic sequence JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn787 DO - 10.1093/nar/gkn787 ID - Chan2009 ER - TY - JOUR AU - Li, Z. P. AU - Ying, D. Q. AU - Li, P. AU - Li, F. AU - Bo, X. C. AU - Wang, S. Q. PY - 2010 DA - 2010// TI - Analysis of synonymous codon usage bias in 09H1N1 JO - Vir Sin VL - 25 UR - https://doi.org/10.1007/s12250-010-3123-3 DO - 10.1007/s12250-010-3123-3 ID - Li2010 ER - TY - JOUR AU - Woo, P. C. Y. AU - Wong, B. H. L. AU - Huang, Y. AU - Lau, S. K. P. AU - Yuen, K. PY - 2007 DA - 2007// TI - Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in Coronaviruses JO - Virology VL - 369 UR - https://doi.org/10.1016/j.virol.2007.08.010 DO - 10.1016/j.virol.2007.08.010 ID - Woo2007 ER - TY - JOUR AU - Zhong, J. AU - Li, Y. AU - Zhao, S. AU - Liu, S. AU - Zhang, Z. PY - 2007 DA - 2007// TI - Mutation pressures shapes codon usage in the GC-rich genome of foot-and-mouth disease virus JO - Virus Genes VL - 35 UR - https://doi.org/10.1007/s11262-007-0159-z DO - 10.1007/s11262-007-0159-z ID - Zhong2007 ER - TY - JOUR AU - Jia, R. AU - Cheng, A. AU - Wang, M. AU - Xin, H. AU - Guo, Y. AU - Zhu, D. AU - Qi, X. AU - Zhao, L. AU - Ge, H. AU - Chen, X. PY - 2009 DA - 2009// TI - Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus JO - Virus Genes VL - 38 UR - https://doi.org/10.1007/s11262-008-0295-0 DO - 10.1007/s11262-008-0295-0 ID - Jia2009 ER - TY - JOUR AU - Liu, W. Q. AU - Zhang, J. AU - Zhang, Y. Q. AU - Zhou, J. H. AU - Chen, H. T. AU - Ma, L. N. AU - Ding, Y. Z. AU - Liu, Y. PY - 2011 DA - 2011// TI - Compare the differences of synonymous codon usage between the two species within cardiovirus JO - Virology J VL - 8 UR - https://doi.org/10.1186/1743-422X-8-325 DO - 10.1186/1743-422X-8-325 ID - Liu2011 ER - TY - JOUR AU - Shackelton, L. A. AU - Parrish, C. R. AU - Holmes, E. C. PY - 2006 DA - 2006// TI - Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses JO - J Mol Evol VL - 62 UR - https://doi.org/10.1007/s00239-005-0221-1 DO - 10.1007/s00239-005-0221-1 ID - Shackelton2006 ER - TY - JOUR AU - Dorn, A. AU - Kippenberger, S. PY - 2008 DA - 2008// TI - Clinical application of CpG-, non-CpG, and antisense oligodeoxynucleotides as immunomodulators JO - Curr Opin Mol Ther VL - 10 ID - Dorn2008 ER - TY - JOUR AU - Lobo, F. P. AU - Mota, B. E. F. AU - Pena, S. D. J. AU - Azevedo, V. AU - Macedo, A. M. AU - Tauch, A. AU - Machado, C. R. AU - Franco, G. R. PY - 2009 DA - 2009// TI - Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts JO - PLoS One VL - 4 UR - https://doi.org/10.1371/journal.pone.0006282 DO - 10.1371/journal.pone.0006282 ID - Lobo2009 ER - TY - JOUR AU - Greenbaum, B. D. AU - Levine, A. J. AU - Bhanot, G. AU - Rabadan, R. PY - 2008 DA - 2008// TI - Patterns of evolution and host gene mimicry in influenza and other RNA viruses JO - PLoS Pathog VL - 4 UR - https://doi.org/10.1371/journal.ppat.1000079 DO - 10.1371/journal.ppat.1000079 ID - Greenbaum2008 ER - TY - JOUR AU - Rabadan, R. AU - Levine, A. J. AU - Robins, H. PY - 2006 DA - 2006// TI - Comparison of avian and human influenza A viruses reveals a mutational bias on the viral genomes JO - J Virol VL - 80 UR - https://doi.org/10.1128/JVI.01414-06 DO - 10.1128/JVI.01414-06 ID - Rabadan2006 ER - TY - JOUR AU - Rothberg, P. G. AU - Wimmer, E. PY - 1981 DA - 1981// TI - Mononucleotide and dinucleotide frequencies and codon usage in poliovirus RNA JO - Nucleic Acids Res VL - 9 UR - https://doi.org/10.1093/nar/9.23.6221 DO - 10.1093/nar/9.23.6221 ID - Rothberg1981 ER - TY - JOUR AU - Karlin, S. AU - Doerfler, W. AU - Cardon, L. R. PY - 1996 DA - 1996// TI - Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses? JO - J Virol VL - 68 ID - Karlin1996 ER - TY - JOUR AU - Martínez-Gómez, M. AU - López-Tort, F. AU - Volotao-Ede, M. AU - Recarey, R. AU - Moratorio, G. AU - Musto, H. AU - Leite JP Cristina, J. PY - 2011 DA - 2011// TI - Analysis of human P[4]G2 rotavirus strains isolated in Brazil reveals codon usage bias and strong compositional constraints JO - Infec Genet Evol VL - 11 UR - https://doi.org/10.1016/j.meegid.2011.01.006 DO - 10.1016/j.meegid.2011.01.006 ID - Martínez-Gómez2011 ER - TY - JOUR AU - D’Andrea, L. AU - Pintó, R. M. AU - Bosch, A. AU - Musto, H. AU - Cristina, J. PY - 2011 DA - 2011// TI - A detailed comparative analysis on the overall codon usage patterns in hepatitis A virus JO - Virus Res VL - 157 UR - https://doi.org/10.1016/j.virusres.2011.01.012 DO - 10.1016/j.virusres.2011.01.012 ID - D’Andrea2011 ER - TY - JOUR AU - Vetsigian, K. AU - Goldenfeld, N. PY - 2009 DA - 2009// TI - Genome rhetoric and the emergence of compositional bias JO - Proc Nat Acad Sci USA VL - 106 UR - https://doi.org/10.1073/pnas.0810122106 DO - 10.1073/pnas.0810122106 ID - Vetsigian2009 ER - TY - JOUR AU - Sharp, P. M. AU - Cowe, E. AU - Higgins, D. G. AU - Shields, D. C. AU - Wolfe, K. H. AU - Wright, F. PY - 1988 DA - 1988// TI - Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens: a review of the considerable within-species diversity JO - Nucleic Acids Res VL - 16 UR - https://doi.org/10.1093/nar/16.17.8207 DO - 10.1093/nar/16.17.8207 ID - Sharp1988 ER - TY - JOUR AU - Ikemura, T. PY - 1985 DA - 1985// TI - Codon usage and tRNA content in unicellular and multicellular organisms JO - Mol Biol Evol VL - 2 ID - Ikemura1985 ER - TY - JOUR AU - van Weringh, A. AU - Ragonnet-Cronin, M. AU - Pranckeviciene, E. AU - Pavon-Eternod, M. AU - Kleiman, L. AU - Xia, X. PY - 2011 DA - 2011// TI - HIV-1 modulates the tRNA pool to improve translation efficiency JO - Mol Biol and Evol VL - 28 UR - https://doi.org/10.1093/molbev/msr005 DO - 10.1093/molbev/msr005 ID - van Weringh2011 ER - TY - JOUR AU - Ngumbela, K. C. AU - Ryan, K. P. AU - Sivamurthy, R. AU - Brockman, M. A. AU - Gandhi, R. T. AU - Bhardwaj, N. AU - Kavanagh, D. G. PY - 2008 DA - 2008// TI - Quantitative effect of suboptimal codon usage on translational efficiency of mRNA encoding HIV-1 gag in intact T cells JO - PLoS ONE VL - 3 UR - https://doi.org/10.1371/journal.pone.0002356 DO - 10.1371/journal.pone.0002356 ID - Ngumbela2008 ER - TY - JOUR AU - Coleman, J. R. AU - Papamichail, D. AU - Skiena, S. AU - Futcher, B. AU - Wimmer, E. AU - Muller, S. PY - 2008 DA - 2008// TI - Virus attenuation by genome-scale changes in codon pair bias JO - Science VL - 320 UR - https://doi.org/10.1126/science.1155761 DO - 10.1126/science.1155761 ID - Coleman2008 ER - TY - JOUR AU - Burns, C. C. AU - Shaw, J. AU - Campagnoli, R. AU - Jorba, J. AU - Vincent, A. AU - Quay, J. AU - Kew, O. PY - 2006 DA - 2006// TI - Modulation of poliovirus replicative fitness in HeLa cells by deoptimization of synonymous codon usage in the capsid region JO - J Virol VL - 80 UR - https://doi.org/10.1128/JVI.80.7.3259-3272.2006 DO - 10.1128/JVI.80.7.3259-3272.2006 ID - Burns2006 ER - TY - JOUR AU - Mueller, S. AU - Papamichail, D. AU - Coleman, J. R. AU - Skiena, S. AU - Wimmer, E. PY - 2006 DA - 2006// TI - Reduction of the rate of poliovirus protein synthesis through large-scale codon deoptimization causes attenuation of viral virulence by lowering specific infectivity JO - J Virol VL - 80 UR - https://doi.org/10.1128/JVI.00738-06 DO - 10.1128/JVI.00738-06 ID - Mueller2006 ER - TY - JOUR AU - Coleman, J. R. AU - Papamichail, D. AU - Skiena, S. AU - Futcher, B. AU - Wimmer, E. AU - Mueller, S. PY - 2008 DA - 2008// TI - Virus attenuation by genome-scale changes in codon pair bias JO - Science VL - 320 UR - https://doi.org/10.1126/science.1155761 DO - 10.1126/science.1155761 ID - Coleman2008 ER - TY - CHAP AU - Bull, J. J. AU - Molineux, I. J. AU - Wilke, C. O. PY - 2012 DA - 2012// TI - Slow fitness recovery in a codon-modified viral genome BT - Mol Biol Evol ID - Bull2012 ER - TY - JOUR AU - Mueller, S. AU - Coleman, J. R. AU - Papamichail, D. AU - Ward, C. B. AU - Nimnaual, A. AU - Futcher, B. AU - Skiena, S. AU - Wimmer, E. PY - 2010 DA - 2010// TI - Live attenuated Influenza virus vaccines by computer-aided rational design JO - Nature Biotech VL - 28 UR - https://doi.org/10.1038/nbt.1636 DO - 10.1038/nbt.1636 ID - Mueller2010 ER - TY - JOUR AU - Burns, C. C. AU - Campagnoli, R. AU - Shaw, J. AU - Vincent, A. AU - Jorba, J. AU - Kew, O. PY - 2009 DA - 2009// TI - Genetic inactivation of poliovirus infectivity by increasing the frequencies of CpG and UpA dinucleotides within and across synonymous capsid region codons JO - J Virol VL - 83 UR - https://doi.org/10.1128/JVI.00508-09 DO - 10.1128/JVI.00508-09 ID - Burns2009 ER - TY - JOUR AU - Wimmer, E. AU - Paul, A. V. PY - 2011 DA - 2011// TI - Synthetic poliovirus and other designer viruses: what have we learned from them? JO - Ann Rev Microbiol VL - 65 UR - https://doi.org/10.1146/annurev-micro-090110-102957 DO - 10.1146/annurev-micro-090110-102957 ID - Wimmer2011 ER - TY - JOUR AU - Wimmer, E. AU - Mueller, S. AU - Tumpey, T. M. AU - Taubenberger, J. K. PY - 2009 DA - 2009// TI - Synthetic viruses: a new opportunity to understand and prevent viral disease JO - Nature Biotech VL - 27 UR - https://doi.org/10.1038/nbt.1593 DO - 10.1038/nbt.1593 ID - Wimmer2009 ER - TY - JOUR AU - Bao, Y. AU - Bolotov, D. AU - Dernovoy, B. AU - Kiryutin, L. AU - Zaslavsky, L. AU - Tatusova, T. AU - Ostell, J. AU - Lipman, D. PY - 2008 DA - 2008// TI - The Influenza Virus Resource at the National Center for Biotechnology Information JO - J Virol VL - 82 UR - https://doi.org/10.1128/JVI.02005-07 DO - 10.1128/JVI.02005-07 ID - Bao2008 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: a multiple sequence alignment method with reduced time and space complexity JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-113 DO - 10.1186/1471-2105-5-113 ID - Edgar2004 ER - TY - JOUR AU - Nakamura, Y. AU - Gojobori, T. AU - Ikemura, T. PY - 2000 DA - 2000// TI - Codon usage tabulated from international DNA sequence databases: status for the year 2000 JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.292 DO - 10.1093/nar/28.1.292 ID - Nakamura2000 ER - TY - STD TI - Wessa P: Office for Research Development and Education, version 1.1.23-r7. Free Statistics Software. URL: http://www.wessa.net., UR - http://www.wessa.net ID - ref53 ER -