Computational identification of rare codons of Escherichia coli based on codon pairs preference

[1]  L. Shimkets,et al.  Genome Evolution and the Emergence of Fruiting Body Development in Myxococcus xanthus , 2007, PloS one.

[2]  Surajit Basak,et al.  On the origin of synonymous codon usage divergence between thermophilic and mesophilic prokaryotes , 2007, FEBS letters.

[3]  M. Hubisz,et al.  Patterns of mutation and selection at synonymous sites in Drosophila. , 2007, Molecular biology and evolution.

[4]  Preethi Ragunathan,et al.  Analysis of Structure, Function, and Evolutionary Origin of the Ob Gene Product—Leptin , 2007, Journal of biomolecular structure & dynamics.

[5]  Changlin Zhou,et al.  Expression and purification of ancrod, an anticoagulant drug, in Pichia pastoris. , 2007, Protein expression and purification.

[6]  Susanna K.P. Lau,et al.  Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses , 2007, Virology.

[7]  Han Yu,et al.  Codon usage bias in Chlamydia trachomatis and the effect of codon modification in the MOMP gene on immune responses to vaccination. , 2007, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[8]  Kwan-Hwa Park,et al.  Characterization of a thermostable cyclodextrin glucanotransferase from Pyrococcus furiosus DSM3638 , 2007, Extremophiles.

[9]  Susan Holmes,et al.  Unusual Codon Bias in Vinyl Chloride Reductase Genes of Dehalococcoides Species , 2007, Applied and Environmental Microbiology.

[10]  D. Hickey,et al.  Rapid divergence of codon usage patterns within the rice genome , 2007, BMC Evolutionary Biology.

[11]  Laurent Duret,et al.  No evidence for tissue-specific adaptation of synonymous codon usage in humans. , 2006, Molecular biology and evolution.

[12]  Ian Stansfield,et al.  tRNA properties help shape codon pair preferences in open reading frames , 2006, Nucleic acids research.

[13]  S. Newbury,et al.  Control of mRNA stability in eukaryotes. , 2006, Biochemical Society transactions.

[14]  C. Arraiano,et al.  Drosophila gene tazman, an orthologue of the yeast exosome component Rrp44p/Dis3, is differentially expressed during development , 2005, Developmental dynamics : an official publication of the American Association of Anatomists.

[15]  Manuel A. S. Santos,et al.  Comparative context analysis of codon pairs on an ORFeome scale , 2005, Genome Biology.

[16]  Yizhar Lavner,et al.  Codon bias as a factor in regulating expression via translation rate in the human genome. , 2005, Gene.

[17]  Arnold J Levine,et al.  Tissue-specific codon usage and the expression of human genes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Elmar Wahle,et al.  Messenger RNA Turnover in Eukaryotes: Pathways and Enzymes , 2004, Critical reviews in biochemistry and molecular biology.

[19]  L. Wernisch,et al.  Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. , 2003, Nucleic acids research.

[20]  Araxi O. Urrutia,et al.  The signature of selection mediated by expression on human genes. , 2003, Genome research.

[21]  S. Ehrlich,et al.  Essential Bacillus subtilis genes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Ivan Ivanov,et al.  Missing Codon Pairs in the Genome of Escherichia Coli , 2002, Bioinform..

[23]  Shigehiko Kanaya,et al.  Codon Usage and tRNA Genes in Eukaryotes: Correlation of Codon Usage Diversity with Translation Efficiency and with CG-Dinucleotide Usage as Assessed by Multivariate Analysis , 2001, Journal of Molecular Evolution.

[24]  Stephen J Freeland,et al.  A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes , 2001, Genome Biology.

[25]  W. Tate,et al.  Codon bias at the 3'-side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli. , 2001, Gene.

[26]  K. H. Wolfe,et al.  Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae , 2000, Yeast.

[27]  L. Duret,et al.  tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. , 2000, Trends in genetics : TIG.

[28]  D. Ding,et al.  Corrigendum to: The relationship between synonymous codon usage and protein structure (FEBS 20717) , 1998 .

[29]  J L Oliver,et al.  Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cervisiae and Escherichia coli. , 1998, Nucleic acids research.

[30]  H. Lipshitz,et al.  Control of mRNA stability and translation during Drosophila development. , 1997, Seminars in cell & developmental biology.

[31]  Etsuko N. Moriyama,et al.  Codon Usage Bias and tRNA Abundance in Drosophila , 1997, Journal of Molecular Evolution.

[32]  A. Eyre-Walker,et al.  Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy? , 1996, Molecular biology and evolution.

[33]  G. W. Hatfield,et al.  Codon Pair Utilization Biases Influence Translational Elongation Step Times (*) , 1995, The Journal of Biological Chemistry.

[34]  Mitsuhiro Itaya,et al.  An estimation of minimal genome size required for life , 1995, FEBS letters.

[35]  P. Lio’,et al.  Selection, mutations and codon usage in a bacterial model. , 1995, Journal of theoretical biology.

[36]  F. Studier,et al.  Consecutive low-usage leucine codons block translation only when near the 5' end of a message in Escherichia coli. , 1995, Journal of molecular biology.

[37]  Gabriel Gutiérrez,et al.  Compositional heterogeneity of the Escherichia coli genome: A role for VSP repair? , 1994, Journal of Molecular Evolution.

[38]  Z. Burton,et al.  Importance of codon preference for production of human RAP74 and reconstitution of the RAP30/74 complex. , 1994, Protein expression and purification.

[39]  C. Karrer,et al.  Mass spectrometric analysis of human soluble catechol O-methyltransferase expressed in Escherichia coli. Identification of a product of ribosomal frameshifting and of reactive cysteines involved in S-adenosyl-L-methionine binding. , 1994, European journal of biochemistry.

[40]  H. Akashi.  Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. , 1994, Genetics.

[41]  M. Bulmer,et al.  Reduced synonymous substitution rate at the start of enterobacterial genes. , 1993, Nucleic acids research.

[42]  E. Goldman,et al.  Increased ribosomal accuracy increases a programmed translational frameshift in Escherichia coli. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[43]  J. Kane,et al.  Novel in-frame two codon translational hop during synthesis of bovine placental lactogen in a recombinant strain of Escherichia coli. , 1992, Nucleic acids research.

[44]  Giorgio Bernardi,et al.  Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins , 1991, Journal of Molecular Evolution.

[45]  J. van Duin,et al.  Frameshift suppression at tandem AGA and AGG codons by cloned tRNA genes: assigning a codon to argU tRNA and T4 tRNA(Arg). , 1990, Nucleic acids research.

[46]  R Parker,et al.  Identification and comparison of stable and unstable mRNAs in Saccharomyces cerevisiae , 1990, Molecular and cellular biology.

[47]  U. Brinkmann,et al.  High-level expression of recombinant genes in Escherichia coli is dependent on the availability of the dnaY gene product. , 1989, Gene.

[48]  M Yarus,et al.  Codon contexts from weakly expressed genes reduce expression in vivo. , 1989, Journal of molecular biology.

[49]  C. Kurland,et al.  Codon usage determines translation rate in Escherichia coli. , 1989, Journal of molecular biology.

[50]  G. W. Hatfield,et al.  Nonrandom utilization of codon pairs in Escherichia coli. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[51]  E E Murray,et al.  Codon usage in plant genes. , 1989, Nucleic acids research.

[52]  J. van Duin,et al.  Translation of the sequence AGG-AGG yields 50% ribosomal frameshift. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[53]  Sarah F. Newbury,et al.  Differential mRNA stability controls relative gene expression within a polycistronic operon , 1987, Cell.

[54]  P. Sharp,et al.  The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. , 1987, Nucleic acids research.

[55]  Sarah F. Newbury,et al.  Stabilization of translationally active mRNA by prokaryotic REP sequences , 1987, Cell.

[56]  D. Mullin,et al.  The E. coli dnaY gene encodes an arginine transfer RNA , 1986, Cell.

[57]  M Yarus,et al.  Sense codons are found in specific contexts. , 1985, Journal of molecular biology.

[58]  T. Ikemura.  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. , 1982, Journal of molecular biology.

[59]  J. Bennetzen,et al.  Codon selection in yeast. , 1982, The Journal of biological chemistry.

[60]  T. Ikemura.  Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. , 1981, Journal of molecular biology.

[61]  O. Kuipers,et al.  BMC Bioinformatics , 2006 .

[62]  Ren Zhang,et al.  DEG: a database of essential genes. , 2004, Nucleic acids research.

[63]  Hong-Yu Ou,et al.  EG: a database of essential genes , 2004, Nucleic Acids Res..

[64]  D. Ding,et al.  The relationship between synonymous codon usage and protein structure. , 1998, FEBS letters.

[65]  J. Kane,et al.  Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli. , 1995, Current opinion in biotechnology.

[66]  G Perrière,et al.  NRSub: a non-redundant data base for the Bacillus subtilis genome. , 1994, Nucleic acids research.

[67]  T Gojobori,et al.  Codon usage tabulated from the GenBank genetic sequence data. , 1991, Nucleic acids research.

[68]  M. Zama,et al.  Codon usage and secondary structure of mRNA. , 1990, Nucleic acids symposium series.

[69]  T Gojobori,et al.  Codon usage tabulated from the GenBank Genetic Sequence Data. , 1988, Nucleic acids research.

[70]  T. Ikemura.  Codon usage and tRNA content in unicellular and multicellular organisms. , 1985, Molecular biology and evolution.