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Abbreviation : CAI
Long Form : codon adaptation index
No. Year Title Co-occurring Abbreviation
2019 Evolutionary changes of the novel Influenza D virus hemagglutinin-esterase fusion gene revealed by the codon usage pattern. HEF, IDVs, RCDI, SiD
2019 Genetic Evolution and Molecular Selection of the HE Gene of Influenza C Virus. HE, ICV, RCDI, SiD
2019 Recombinant production of active Streptococcus pneumoniae CysE in E. coli facilitated by codon optimized BL21(DE3)-RIL and detergent. Spn
2018 An in silico study: Novel targets for potential drug and vaccine design against drug resistant H. pylori. MDR
2018 Analysis of codon usage bias of Crimean-Congo hemorrhagic fever virus and its adaptation to hosts. CA, CCHFV, ENC, RSCU
2018 Analysis of synonymous codon usage bias in helicase gene from Autographa californica multiple nucleopolyhedrovirus. AcMNPV, ENC, RSCU
2018 Codon harmonization - going beyond the speed limit for protein expression. ---
2018 Codon usage characteristics of PB2 gene in influenza A H7N9 virus from different host species. COA, ENC, RSCU
2018 Codon usage of HIV regulatory genes is not determined by nucleotide composition. ENC
10  2018 Comparative genome-wide analysis of codon usage of different bacterial species infecting Oryza sativa. CBI, COA, ENC, RSCU
11  2018 Does adaptation to vertebrate codon usage relate to flavivirus emergence potential? ---
12  2018 Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-Specific. HeV, NiV, RCDI, SiD
13  2018 Genome polarity of RNA viruses reflects the different evolutionary pressures shaping codon usage. dsRNA
14  2018 Integrated constraints based analysis of an engineered violacein pathway in Escherichia coli. SP, SYNO, TIR
15  2018 Quantifying codon usage in signal peptides: Gene expression and amino acid usage explain apparent selection for inefficient codons. CUB, tAI
16  2017 A detailed analysis of codon usage patterns and influencing factors in Zika virus. ENC, ZIKV
17  2017 Codon Usage Patterns of Tyrosinase Genes in Clonorchis sinensis. CUB, ENC
18  2017 Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes. SCUO
19  2017 In Silico Analysis of L1/L2 Sequences of Human Papillomaviruses: Implication for Universal Vaccine Design. HPV, pI
20  2017 Recombinant thermo-alkali-stable endoglucanase of Myceliopthora thermophila BJA (rMt-egl): Biochemical characteristics and applicability in enzymatic saccharification of agro-residues. rMt-egl, rMt-egl
21  2017 Translational resistivity/conductivity of coding sequences during exponential growth of Escherichia coli. ---
22  2016 Analysis of single nucleotide polymorphism among Varicella-Zoster Virus and identification of vaccine-specific sites. SNP, VZV
23  2016 Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts. CA, ENC, RSCU, ZIKV
24  2016 Bioinformatics analysis of codon usage patterns and influencing factors in Penaeus monodon nudivirus. ENC, PmNV, RSCU
25  2016 Characterization of codon usage pattern and influencing factors in Japanese encephalitis virus. COA, ENC, JE, JEV, RSCU
26  2016 Cloning and expression of codon-optimized recombinant darbepoetin alfa in Leishmania tarentolae T7-TR. CHO, EPO, RT-PCR
27  2016 Effects of nucleotide usage on the synonymous codon usage patterns of biofilm-associated genes in Haemophilus parasuis. ENC
28  2016 Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome. ENC, Fop, ORFs, PCA, tAI
29  2015 A major controversy in codon-anticodon adaptation resolved by a new codon usage index. ---
30  2015 Analysis of codon usage pattern evolution in avian rotaviruses and their preferred host. AvRV, CUB, ENCs, RSCU, RV
31  2015 Codon bias and gene expression of mitochondrial ND2 gene in chordates. ENC, RSCU
32  2015 Codon-optimized human sodium iodide symporter (opt-hNIS) as a sensitive reporter and efficient therapeutic gene. opt-hNIS, opt-hNIS
33  2015 Data in support of large scale comparative codon usage analysis in Leishmania and Trypanosomatids. ENC, RSCU
34  2015 Design, Construction and Cloning of Truncated ORF2 and tPAsp-PADRE-Truncated ORF2 Gene Cassette From Hepatitis E Virus in the pVAX1 Expression Vector. Fop, HEV, ORF2, PCR, RT-PCR
35  2015 Genome-wide investigation of mRNA lifetime determinants in Escherichia coli cells cultured at different growth rates. ---
36  2015 High-level expression and purification of soluble bioactive recombinant human heparin-binding epidermal growth factor in Escherichia coli. HB-EGF, Ni-NTA
37  2015 Looking into the genome of Thermosynechococcus elongatus (thermophilic cyanobacteria) with codon selection and usage perspective. ---
38  2015 Non-uniqueness of factors constraint on the codon usage in Bombyx mori. A. thaliana, B. mori, C. elegans, D. melanogaster, E. coli, ENC, GRAVY, S. cerevisiae
39  2014 Codon usage bias in human cytomegalovirus and its biological implication. CDS, ENC, HCMV, OR, RSCU
40  2014 Differential codon adaptation between dsDNA and ssDNA phages in Escherichia coli. dsDNA, RSCU, ssDNA
41  2014 Genome comparison of three serovar 5 pathogenic strains of Haemophilus parasuis: insights into an evolving swine pathogen. ABC, LGTs, LSPs, SSGs, TRAP
42  2014 Genome-wide analysis of codon usage and influencing factors in chikungunya viruses. CHIKV, ENC, RSCU
43  2014 Identification, characterization, and utilization of single copy genes in 29 angiosperm genomes. AS, Nc
44  2014 Overall codon usage pattern of enterovirus 71. ENC, EV71, HFMD, RSCU
45  2014 Stress induced MAPK genes show distinct pattern of codon usage in Arabidopsis thaliana, Glycine max and Oryza sativa. MAPK, Nc
46  2013 A detailed comparative analysis on the overall codon usage patterns in West Nile virus. ENC, WNV
47  2013 An improved implementation of effective number of codons (nc). Nc
48  2013 Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data. RSCU
49  2013 Combinational effect of mutational bias and translational selection for translation efficiency in tomato (Solanum lycopersicum) cv. Micro-Tom. CUB, ESTs, nrFLcDNA
50  2013 Comparative genome sequence analysis of Sulfolobus acidocaldarius and 9 other isolates of its genus for factors influencing codon and amino acid usage. SCUO
51  2013 Comprehensive analysis of the overall codon usage patterns in equine infectious anemia virus. EIAV, ENC
52  2013 Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria. ---
53  2013 Evolutionary diversification and characterization of the eubacterial gene family encoding DXR type II, an alternative isoprenoid biosynthetic enzyme. DXR-I, HGT, MEP
54  2013 Evolutionary reconstruction and population genetics analysis of aurora kinases. RSCU
55  2013 Genomic adaptation of the ISA virus to Salmo salar codon usage. ISAV, NS1
56  2013 The evolution of codon usage in structural and non-structural viral genes: the case of Avian coronavirus and its natural host Gallus gallus. CU, Nc, nsp2, RSCU
57  2013 Translation Elongation Rate Measurement of Epstein-Barr Virus Strain GD1. EBV
58  2012 Avian coronavirus spike glycoprotein ectodomain shows a low codon adaptation to Gallus gallus with virus-exclusive codons in strategic amino acids positions. ENC, nt 1-507
59  2012 Comparative study on factors influencing the codon and amino acid usage in Lactobacillus sakei 23K and 13 other lactobacilli. COA, SCUO, tRNAs
60  2012 EuGene: maximizing synthetic gene design for heterologous expression. ---
61  2012 Identification of TTA codon containing genes in Frankia and exploration of the role of tRNA in regulating these genes. ---
62  2011 A novel in silico approach to identify potential therapeutic targets in human bacterial pathogens. ---
63  2011 Codon optimization of the major antigen encoding genes of diverse strains of influenza a virus. HA, NA
64  2011 Prediction and Characterization of Missing Proteomic Data in Desulfovibrio vulgaris. ---
65  2010 A detailed comparative analysis on the overall codon usage pattern in herpesviruses. RSCU
66  2010 Analysis of synonymous codon usage in Zea mays. ---
67  2010 DIGA--a database of improved gene annotation for phytopathogens. TISs
68  2010 Relative codon adaptation index, a sensitive measure of codon usage bias. rCAI
69  2010 Relative codon adaptation: a generic codon bias index for prediction of gene expression. CBIs, RCA, RCBS
70  2009 Mutational bias and gene expression level shape codon usage in Thermobifida fusca YX. RSCU, SCUO
71  2009 Proteomics analysis of Lactobacillus casei Zhang, a new probiotic bacterium isolated from traditional home-made koumiss in Inner Mongolia of China. COG
72  2009 Study of codon bias perspective of fungal xylanase gene by multivariate analysis. RSCU
73  2009 The rapid evolution of signal peptides is mainly caused by relaxed selection on non-synonymous and synonymous sites. SP
74  2008 CAIcal: a combined set of tools to assess codon usage adaptation. ---
75  2008 E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI). eCAI, FAQ
76  2008 HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection. HEG-DB
77  2008 The implication of life style on codon usage patterns and predicted highly expressed genes for three Frankia genomes. ---
78  2007 Analysis of codon usage patterns and predicted highly expressed genes for six phytopathogenic Xanthomonas genomes shows a high degree of conservation. COGs, GAP, PHX
79  2007 Comprehensive analysis of prokaryotic mechanosensation genes: their characteristics in codon usage. ENC, MSC, RSCU
80  2007 Error minimization explains the codon usage of highly expressed genes in Escherichia coli. eAI
81  2007 Prediction of highly expressed genes in microbes based on chromatin accessibility. ---
82  2007 The CAI Analyser Package: inferring gene expressivity from raw genomic data. CAIAP
83  2006 A theoretical analysis of codon adaptation index of the Boophilus microplus bm86 gene directed to the optimization of a DNA vaccine. RSCU
84  2006 Analysis of codon usage pattern in the radioresistant bacterium Deinococcus radiodurans. COA
85  2006 Predicted highly expressed genes in Nocardia farcinica and the implication for its primary metabolism and nocardial virulence. AhpC, PHX, ROS, RP
86  2005 Compositional variation in bacterial genes and proteins with potential expression level. ---
87  2005 JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. ---
88  2005 Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism. PHX
89  2005 The relationship among gene expression, folding free energy and codon usage bias in Escherichia coli. ---
90  2004 Integrated and ultrasensitive gel protein identification. MALDI-MS
91  2004 Intragenic codon bias in a set of mouse and human genes. RCR, TNR
92  2004 Nucleotides downstream of start codons show marked non-randomness in Escherichia coli but not in Bacillus subtilis. Nc
93  2004 Relationship between codon biased genes, microarray expression values and physiological characteristics of Streptococcus pneumoniae. PHE
94  2004 Setting up standards and a reference map for the alkaline proteome of the Gram-positive bacterium Lactococcus lactis. GRAVY, IPG, MALDI-TOF MS
95  2004 Significance of codon usage and irregularities of rare codon distribution in genes for expression of BspLU11III methyltransferases. ---
96  2003 Codon adaptation index as a measure of dominating codon bias. ---
97  2003 Factors affecting codon usage in Yersinia pestis. COA, Nc
98  2003 Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models. ---
99  2003 The effective number of codons for individual amino acids: some codons are more optimal than others. AA, RSCU
100  2003 Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. CUB