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References from Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases. Local targets link to admitted publications; unresolved targets remain external evidence.
Evolution and ecology of plant viruses
2019 · External reference
10.1016/j.tim.2019.03.003
10.1016/j.tim.2019.03.003 · External reference
10.1146/annurev.phyto.35.1.191
10.1146/annurev.phyto.35.1.191 · External reference
10.1128/jvi.02203-10
10.1128/jvi.02203-10 · External reference
10.1016/j.coviro.2012.12.003
10.1016/j.coviro.2012.12.003 · External reference
10.1073/pnas.97.13.6967
10.1073/pnas.97.13.6967 · External reference
10.1146/annurev.ecolsys.110308.120248
10.1146/annurev.ecolsys.110308.120248 · External reference
The evolution of viruses in multi-host fitness landscapes
10.2174/1874357900903010001 · 2009 · External reference
The evolution of viral emergence
10.1073/pnas.0601166103 · 2006 · External reference
10.1038/nrg2053
10.1038/nrg2053 · External reference
The Evolutionary genetics of emerging plant RNA viruses
10.1094/mpmi-09-10-0214 · 2011 · External reference
Evolution and emergence of plant viruses
10.1016/b978-0-12-800098-4.00003-9 · 2014 · External reference
A phylogenomic data-driven exploration of viral origins and evolution
10.1126/sciadv.1500527 · 2015 · External reference
10.1371/journal.pone.0066700
10.1371/journal.pone.0066700 · External reference
Recombination as a motor of host switches and virus emergence: Geminiviruses as case studies
10.1016/j.coviro.2014.12.005 · 2015 · External reference
The ‘emergence’ of turnip mosaic virus was probably a ‘gene-for-quasi-gene’ event
10.1016/j.coviro.2014.12.004 · 2015 · External reference
Re-emergence of Cassava Brown Streak disease in Uganda
10.1094/pd-91-0024 · 2007 · External reference
Symptom evolution following the emergence of maize streak virus
10.7554/elife.51984 · 2020 · External reference
Insect vectors as drivers of plant virus emergence
10.1016/j.coviro.2014.12.008 · 2015 · External reference
Evolution in health and medicine Sackler colloquium: The comparative genomics of viral emergence
10.1073/pnas.0906193106 · 2010 · External reference
10.1016/j.coviro.2015.01.005
10.1016/j.coviro.2015.01.005 · External reference
10.1016/j.virusres.2008.07.028
10.1016/j.virusres.2008.07.028 · External reference
The biogeography of viral emergence: rice yellow mottle virus as a case study
10.1016/j.coviro.2014.12.002 · 2014 · External reference
10.1094/phyto-06-14-0172-r
10.1094/phyto-06-14-0172-r · External reference
Processes of diversification and dispersion of Rice yellow mottle virus inferred from large-scale and high-resolution phylogeographical studies
10.1111/j.1365-294x.2005.02578.x · 2005 · External reference
Diversification of rice yellow mottle virus and related viruses spans the history of agriculture from the neolithic to the present
10.1371/journal.ppat.1000125 · 2008 · External reference
The past, present, and future of barley yellow dwarf management
10.3390/agriculture9010023 · 2019 · External reference
Compositional biases in <scp>RNA</scp> viruses: Causes, consequences and applications
2021 · External reference
10.1093/molbev/msaa247
10.1093/molbev/msaa247 · External reference
Mutation and epistasis in influenza virus evolution
10.3390/v10080407 · 2018 · External reference
10.1371/journal.pone.0056642
10.1371/journal.pone.0056642 · External reference
Base composition and translational selection are insufficient to explain codon usage bias in plant viruses
10.3390/v5010162 · 2013 · External reference
10.1016/j.chom.2012.10.008
10.1016/j.chom.2012.10.008 · External reference
Analysis of codon usage of Horseshoe Bat Hepatitis B virus and its host
10.1016/j.virol.2021.05.008 · 2021 · External reference
10.1177/1176934320918861
10.1177/1176934320918861 · External reference
Comprehensive codon usage analysis of porcine deltacoronavirus
10.1016/j.ympev.2019.106618 · 2019 · External reference
Evolutionary changes of the novel Influenza D virus hemagglutinin-esterase fusion gene revealed by the codon usage pattern
10.1080/21505594.2018.1551708 · 2019 · External reference
Genetic analysis and evolutionary changes of Porcine circovirus 2
10.1016/j.ympev.2019.106520 · 2019 · External reference
Evolution of Potato virus X
10.1016/j.ympev.2021.107336 · 2022 · External reference
Analysis of codon usage bias in potato virus Y non-recombinant strains
10.1016/j.virusres.2020.198077 · 2020 · External reference
Directional mutation pressure and neutral molecular evolution
10.1073/pnas.85.8.2653 · 1988 · External reference
Synonymous codon usage in Saccharomyces cerevisiae
10.1002/yea.320070702 · 1991 · External reference
An evaluation of measures of synonymous codon usage bias
10.1007/pl00006384 · 1998 · External reference
10.1146/annurev.genet.42.110807.091442
10.1146/annurev.genet.42.110807.091442 · External reference
10.1126/science.1155761
10.1126/science.1155761 · External reference
10.1016/0022-2836(85)90239-6
10.1016/0022-2836(85)90239-6 · External reference
Preferred and avoided codon pairs in three domains of life
10.1186/1471-2164-9-463 · 2008 · External reference
10.1016/j.celrep.2015.12.011
10.1016/j.celrep.2015.12.011 · External reference
10.1016/0022-2836(81)90264-3
10.1016/0022-2836(81)90264-3 · External reference
Dinucleotide relative abundance extremes: a genomic signature
10.1016/s0168-9525(00)89076-9 · 1995 · External reference
Dinucleotide and stop codon frequencies in single-stranded RNA viruses
10.1099/0022-1317-78-11-2859 · 1997 · External reference
A genomic perspective on the origin and emergence of SARS-CoV-2
2020 · External reference
The emergence, genomic diversity and global spread of SARS-CoV-2
2021 · External reference
High codon adaptation in citrus tristeza virus to its citrus host
10.1186/1743-422x-9-113 · 2012 · External reference
10.1631/jzus.b0820005
10.1631/jzus.b0820005 · External reference
Codon usage bias amongst plant viruses
10.1007/s00705-003-0186-6 · 2003 · External reference
Molecular characteristics of segment 5, a unique fragment encoding two partially overlapping ORFs in the genome of rice black-streaked dwarf virus
10.1371/journal.pone.0224569 · 2019 · External reference
Rice black-streaked dwarf virus Genome in China: diversification, phylogeny, and selection
10.1094/pdis-12-16-1814-re · 2017 · External reference
The dinucleotide composition of sugarcane mosaic virus is shaped more by protein coding regions than by host species
10.1016/j.meegid.2021.105165 · 2022 · External reference
Phylodynamics and codon usage pattern analysis of broad bean wilt virus 2
2021 · External reference
10.1016/j.meegid.2020.104601
10.1016/j.meegid.2020.104601 · External reference
10.1016/j.ympev.2020.106848
10.1016/j.ympev.2020.106848 · External reference
10.3390/v11080752
10.3390/v11080752 · External reference
Codon usage bias analysis of Citrus tristeza virus: higher codon adaptation to Citrus reticulata host
10.3390/v11040331 · 2019 · External reference
Evolution of rice stripe virus
10.1016/j.ympev.2017.02.002 · 2017 · External reference
Plant virus genome is shaped by specific dinucleotide restrictions that influence viral infection
10.1128/mbio.02818-19 · 2020 · External reference
Genetic evolution and molecular selection of the HE gene of influenza C virus
10.3390/v11020167 · 2019 · External reference
Evolution of codon usage in Zika virus genomes is host and vector specific
10.1038/emi.2016.106 · 2016 · External reference
10.1016/j.ygeno.2021.05.008
10.1016/j.ygeno.2021.05.008 · External reference
10.1371/journal.pbio.3001201
10.1371/journal.pbio.3001201 · External reference
Study on the characteristic codon usage pattern in porcine epidemic diarrhea virus genomes and its host adaptation phenotype
2021 · External reference
Transcription, mRNA export and immune evasion shape the codon usage of viruses
2021 · External reference
10.3390/ijms19082397
10.3390/ijms19082397 · External reference
Phylogeny and synonymous codon usage pattern of Papaya ringspot virus coat protein gene in the sub-Himalayan region of north-east India
10.1139/cjm-2015-0172 · 2015 · External reference
Secondary structure of MS2 phage RNA and bias in code word usage
10.1093/nar/7.7.2073 · 1979 · External reference
10.1016/0022-2836(82)90515-0
10.1016/0022-2836(82)90515-0 · External reference
Expression pattern and surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis
10.1073/pnas.96.8.4482 · 1999 · External reference
10.1016/s0378-1119(99)00320-0
10.1016/s0378-1119(99)00320-0 · External reference
Accounting for background nucleotide composition when measuring codon usage bias: brilliant idea, difficult in practice
10.1093/molbev/msl009 · 2006 · External reference
10.1038/s41559-020-1124-7
10.1038/s41559-020-1124-7 · External reference
Codon pair bias in prokaryotic and eukaryotic genomes
10.1186/1471-2105-6-s3-p4 · 2005 · External reference
10.1016/j.gene.2008.12.016
10.1016/j.gene.2008.12.016 · External reference
Clustering of classical swine fever virus isolates by codon pair bias
10.1186/1756-0500-4-521 · 2011 · External reference
Changes in codon-pair bias of human immunodeficiency virus type 1 have profound effects on virus replication in cell culture
10.1186/1742-4690-10-78 · 2013 · External reference
10.3390/cells10071636
10.3390/cells10071636 · External reference
10.1016/j.virol.2015.07.012
10.1016/j.virol.2015.07.012 · External reference
Attenuation of dengue (and other RNA viruses) with codon pair recoding can be explained by increased CpG/UpA dinucleotide frequencies
10.1073/pnas.1507339112 · 2015 · External reference
10.1016/j.vaccine.2015.11.054
10.1016/j.vaccine.2015.11.054 · External reference
10.1099/jgv.0.001136
10.1099/jgv.0.001136 · External reference
10.1371/journal.ppat.1006857
10.1371/journal.ppat.1006857 · External reference
Zika virus attenuation by codon pair deoptimization induces sterilizing immunity in mouse models
2018 · External reference
A codon-pair bias associated with network interactions in influenza A, B, and C genomes
10.3389/fgene.2021.699141 · 2021 · External reference
The spectrum of genomic signatures: From dinucleotides to chaos game representation
10.1016/j.gene.2004.10.021 · 2005 · External reference
10.1128/jvi.68.5.2889-2897.1994
10.1128/jvi.68.5.2889-2897.1994 · External reference
Heterogeneity of genomes: measures and values
10.1073/pnas.91.26.12837 · 1994 · External reference
Compositional differences within and between eukaryotic genomes
10.1073/pnas.94.19.10227 · 1997 · External reference
Dinucleotide composition in animal RNA viruses is shaped more by virus family than by host species
10.1128/jvi.02381-16 · 2017 · External reference
10.1093/ve/vez038
10.1093/ve/vez038 · External reference
CpG and upA dinucleotides in both coding and non-coding regions of echovirus 7 inhibit replication initiation post-entry
2017 · External reference
10.1038/nature24039
10.1038/nature24039 · External reference
CpG-recoding in Zika virus genome causes host-age-dependent attenuation of infection with protection against lethal heterologous challenge in mice
10.3389/fimmu.2019.03077 · 2020 · External reference
10.1016/j.ympev.2021.107336
10.1016/j.ympev.2021.107336 · External reference
10.1007/bf02099948
10.1007/bf02099948 · External reference
10.1016/j.meegid.2011.08.025
10.1016/j.meegid.2011.08.025 · External reference
Interspecies transmission, genetic diversity, and evolutionary dynamics of pseudorabies virus
10.1093/infdis/jiy731 · 2019 · External reference
10.1177/117693430700300028
10.1177/117693430700300028 · External reference
10.1186/1745-6150-3-38
10.1186/1745-6150-3-38 · External reference
RCDI/eRCDI: a web-server to estimate codon usage deoptimization
10.1186/1756-0500-3-87 · 2010 · External reference
A functional investigation of the suppression of CpG and UpA dinucleotide frequencies in plant RNA virus genomes
10.1038/s41598-019-54853-0 · 2019 · External reference
BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
1999 · External reference
10.1016/s0168-9525(00)02024-2
10.1016/s0168-9525(00)02024-2 · External reference
Unresolved reference
2000 · External reference
DnaSP, DNA polymorphism analyses by the coalescent and other methods
10.1093/bioinformatics/btg359 · 2003 · External reference
10.2144/00286ir01
10.2144/00286ir01 · External reference
10.1093/molbev/msab120
10.1093/molbev/msab120 · External reference
Statistical, computational and visualization methodologies to unveil gene primary structure features
10.1055/s-0038-1634061 · 2006 · External reference
10.1016/j.jmb.2019.04.021
10.1016/j.jmb.2019.04.021 · External reference
Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris
10.1186/s12934-021-01696-y · 2021 · External reference
10.1016/s0021-9258(19)81068-2
10.1016/s0021-9258(19)81068-2 · External reference
10.1093/bioinformatics/btu192
10.1093/bioinformatics/btu192 · External reference
COUSIN (COdon Usage Similarity INdex): A normalized measure of codon usage preferences
10.1093/gbe/evz262 · 2019 · External reference
HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection
10.1093/nar/gkm831 · 2007 · External reference
10.1093/nar/gki376
10.1093/nar/gki376 · External reference
OPTIMIZER: a web server for optimizing the codon usage of DNA sequences
10.1093/nar/gkm219 · 2007 · External reference
stAIcalc: tRNA adaptation index calculator based on species-specific weights
2016 · External reference
The Synthetic Gene Designer: A flexible web platform to explore sequence manipulation for heterologous expression
10.1016/j.pep.2005.10.020 · 2006 · External reference
Synonymous codon pattern of cowpea mild mottle virus sheds light on its host adaptation and genome evolution
10.3390/pathogens11040419 · 2022 · External reference
Synonymous codon usage analysis of three narcissus potyviruses
10.3390/v14050846 · 2022 · External reference
Analysis of synonymous codon usage bias and phylogeny of coat protein gene in banana bract mosaic virus isolates
2017 · External reference
Plant virus genome is shaped by specific dinucleotide restrictions that influence viral infection
2020 · External reference
The adaptation of codon usage of +ssRNA viruses to their hosts
10.1016/j.meegid.2018.05.034 · 2018 · External reference
Analysis on codon usage of CP gene in soybean mosaic virus
2015 · External reference
High-throughput profiling of influenza a virus hemagglutinin gene at single-nucleotide resolution
2014 · External reference
10.1371/journal.pgen.1000742
10.1371/journal.pgen.1000742 · External reference
10.1073/pnas.0400146101
10.1073/pnas.0400146101 · External reference
10.1128/jvi.00524-07
10.1128/jvi.00524-07 · External reference