A new and updated resource for codon usage tables

[1]  Evan Bolton,et al.  Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..

[2]  Luis V. Santana-Quintero,et al.  High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis , 2016, Database J. Biol. Databases Curation.

[3]  H. Schwalbe,et al.  Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations. , 2016, Molecular cell.

[4]  Dennis Eichmann,et al.  Heterologous Gene Expression In Ecoli Methods And Protocols , 2016 .

[5]  T. Tatusova,et al.  The Reference Sequence ( RefSeq ) Database , 2016 .

[6]  Alberto Pallavicini,et al.  Analysis of synonymous codon usage patterns in sixty-four different bivalve species , 2015, PeerJ.

[7]  R. Desrosiers,et al.  Importance of codon usage for the temporal regulation of viral gene expression , 2015, Proceedings of the National Academy of Sciences.

[8]  Seppo Vainio,et al.  ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization , 2015, BMC Bioinformatics.

[9]  Z. Bebők,et al.  Decoding mechanisms by which silent codon changes influence protein biogenesis and function. , 2015, The international journal of biochemistry & cell biology.

[10]  Andrés Iriarte,et al.  Conservation of CFTR codon frequency through primates suggests synonymous mutations could have a functional effect. , 2015, Mutation research.

[11]  Qiang Wang,et al.  Optimized human factor IX expression cassettes for hepatic-directed gene therapy of hemophilia B , 2015, Frontiers of Medicine.

[12]  T. Tuller,et al.  Multiple roles of the coding sequence 5′ end in gene expression regulation , 2014, Nucleic acids research.

[13]  Michael Recht,et al.  Long-term safety and efficacy of factor IX gene therapy in hemophilia B. , 2014, The New England journal of medicine.

[14]  Chih-Yang Wang,et al.  Optimization protein productivity of human interleukin-2 through codon usage, gene copy number and intracellular tRNA concentration in CHO cells. , 2014, Biochemical and biophysical research communications.

[15]  Tamir Tuller,et al.  Modelling the Efficiency of Codon–tRNA Interactions Based on Codon Usage Bias , 2014, DNA research : an international journal for rapid publication of reports on genes and genomes.

[16]  Michele Vendruscolo,et al.  Understanding the influence of codon translation rates on cotranslational protein folding. , 2014, Accounts of chemical research.

[17]  Julie L. Chaney,et al.  Expanding Anfinsen’s Principle: Contributions of Synonymous Codon Selection to Rational Protein Design , 2014, Journal of the American Chemical Society.

[18]  M Madan Babu,et al.  The Hidden Codes That Shape Protein Evolution , 2013, Science.

[19]  Judith Frydman,et al.  Evolutionary conservation of codon optimality reveals hidden signatures of co-translational folding , 2012, Nature Structural &Molecular Biology.

[20]  P. Della Valle,et al.  Hyperfunctional coagulation factor IX improves the efficacy of gene therapy in hemophilic mice. , 2012, Blood.

[21]  Eva Maria Novoa,et al.  Speeding with control: codon usage, tRNAs, and ribosomes. , 2012, Trends in genetics : TIG.

[22]  Catherine Putonti,et al.  CBDB: The codon bias database , 2012, BMC Bioinformatics.

[23]  Somdatta Sinha,et al.  Differential Trends in the Codon Usage Patterns in HIV-1 Genes , 2011, PloS one.

[24]  Jeffrey Heer,et al.  SpanningAspectRatioBank Easing FunctionS ArrayIn ColorIn Date Interpolator MatrixInterpola NumObjecPointI Rectang ISchedu Parallel Pause Scheduler Sequen Transition Transitioner Transiti Tween Co DelimGraphMLCon IData JSONCon DataField DataSc Dat DataSource Data DataUtil DirtySprite LineS RectSprite , 2011 .

[25]  E. Angov Codon usage: Nature's roadmap to expression and folding of proteins , 2011, Biotechnology journal.

[26]  E. Angov,et al.  Adjustment of codon usage frequencies by codon harmonization improves protein expression and folding. , 2011, Methods in molecular biology.

[27]  Norbert Grundmann,et al.  Origin of the 1918 pandemic H1N1 influenza A virus as studied by codon usage patterns and phylogenetic analysis. , 2011, RNA.

[28]  J. Plotkin,et al.  Synonymous but not the same: the causes and consequences of codon bias , 2011, Nature Reviews Genetics.

[29]  Jeffrey Heer,et al.  D³ Data-Driven Documents , 2011, IEEE Transactions on Visualization and Computer Graphics.

[30]  Raul Rabadan,et al.  Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus , 2010, BMC Evolutionary Biology.

[31]  Jan Kubicek,et al.  Gene optimization mechanisms: A multi-gene study reveals a high success rate of full-length human proteins expressed in Escherichia coli , 2010, Protein science : a publication of the Protein Society.

[32]  Nathan Linial,et al.  Codon usage is associated with the evolutionary age of genes in metazoan genomes , 2009, BMC Evolutionary Biology.

[33]  Michal Linial,et al.  Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences , 2009, Molecular systems biology.

[34]  Tobias Warnecke,et al.  Why there is more to protein evolution than protein function: splicing, nucleosomes and dual-coding sequence. , 2009, Biochemical Society transactions.

[35]  Bartek Wilczynski,et al.  Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..

[36]  Patricia P. Chan,et al.  GtRNAdb: a database of transfer RNA genes detected in genomic sequence , 2008, Nucleic Acids Res..

[37]  Patricia L. Clark,et al.  Rare Codons Cluster , 2008, PloS one.

[38]  Randall L. Kincaid,et al.  Heterologous Protein Expression Is Enhanced by Harmonizing the Codon Usage Frequencies of the Target Gene with those of the Expression Host , 2008, PloS one.

[39]  L. Hurst,et al.  How do synonymous mutations affect fitness? , 2007, BioEssays : news and reviews in molecular, cellular and developmental biology.

[40]  Lippincott-Schwartz,et al.  Supporting Online Material Materials and Methods Som Text Figs. S1 to S8 Table S1 Movies S1 to S3 a " Silent " Polymorphism in the Mdr1 Gene Changes Substrate Specificity Corrected 30 November 2007; See Last Page , 2022 .

[41]  L. Hurst,et al.  Hearing silence: non-neutral evolution at synonymous sites in mammals , 2006, Nature Reviews Genetics.

[42]  S. Govindarajan,et al.  Codon bias and heterologous protein expression. , 2004, Trends in biotechnology.

[43]  Zhiyong Zhou,et al.  Enhanced expression of a recombinant malaria candidate vaccine in Escherichia coli by codon optimization. , 2004, Protein expression and purification.

[44]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[45]  L. Wernisch,et al.  Solving the riddle of codon usage preferences: a test for translational selection. , 2004, Nucleic acids research.

[46]  Hidenori Ohnishi,et al.  Optimized gene synthesis and high expression of human interleukin-18. , 2003, Protein expression and purification.

[47]  Laurent Duret,et al.  Evolution of synonymous codon usage in metazoans. , 2002, Current opinion in genetics & development.

[48]  Ricardo Ehrlich,et al.  Silent mutations affect in vivo protein folding in Escherichia coli. , 2002, Biochemical and biophysical research communications.

[49]  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.

[50]  W G Hol,et al.  International Journal for Parasitology 30 (2000) 113±118 Rapid communication , 2000 .

[51]  Toshimichi Ikemura,et al.  Codon usage tabulated from international DNA sequence databases: status for the year 2000 , 2000, Nucleic Acids Res..

[52]  R. Hale,et al.  Codon optimization of the gene encoding a domain from human type 1 neurofibromin protein results in a threefold improvement in expression level in Escherichia coli. , 1998, Protein expression and purification.

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

[54]  W. Hauswirth,et al.  A "humanized" green fluorescent protein cDNA adapted for high-level expression in mammalian cells , 1996, Journal of virology.

[55]  P. Sharp,et al.  DNA sequence evolution: the sounds of silence. , 1995, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

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

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

[58]  P. Sharp,et al.  Codon usage: mutational bias, translational selection, or both? , 1993, Biochemical Society transactions.

[59]  Leszek Kotula,et al.  Evaluation of Foreign Gene Codon Optimization in Yeast: Expression of a Mouse IG Kappa Chain , 1991, Bio/Technology.

[60]  R. Fuchs,et al.  Modification of the coding sequence enhances plant expression of insect control protein genes. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[61]  F. Wright The 'effective number of codons' used in a gene. , 1990, Gene.

[62]  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.

[63]  D. Regier,et al.  Design, synthesis and expression of a human interleukin-2 gene incorporating the codon usage bias found in highly expressed Escherichia coli genes. , 1988, Nucleic acids research.

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

[65]  T. Ikemura Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. , 1981, Journal of molecular biology.

[66]  M. Gouy,et al.  Codon catalog usage and the genome hypothesis. , 1980, Nucleic acids research.

[67]  C. Anfinsen Principles that govern the folding of protein chains. , 1973, Science.