DOI: 10.1371/journal.pone.0003412. Rare Codons Cluster

Rare Codons Cluster

10.1371/journal.pone.0003412

Crossref journal-article

Public Library of Science (PLoS)

PLoS ONE (340)

Bibliography

Clarke, T. F., & Clark, P. L. (2008). Rare Codons Cluster. PLoS ONE, 3(10), e3412.

Authors 2

Thomas F. Clarke (first)
Patricia L. Clark (additional)

References 27 Referenced 162

10.1016/S0959-437X(02)00353-2 / Curr Opin Genet Dev / Evolution of synonymous codon usage in metazoans. by L Duret (2002)
10.1093/nar/8.1.197-c / Nucl Acids Res / Codon catalog usage and the genome hypothesis. by R Grantham (1980)
10.1016/0958-1669(95)80082-4 / Curr Op Biotechnol / Effects of rare codon clusters on high-level expression of heterologous proteins in <italic>Escherichia coli</italic>. by JF Kane (1995)
10.1016/0022-2836(91)90575-Q / J Mol Biol / Evidence for horizontal gene transfer in Escherichia coli speciation. by C Medigue (1991)
10.1007/s002390010212 / J Mol Evol / Why are translationally sub-optimal synonymous codons used in <italic>Escherichia coli</italic>? by NG Smith (2001)
10.1093/nar/15.3.1281 / Nucl Acids Res / The Codon Adaptation Index: A measure of directional synonymous codon usage bias, and its potential applications. by PM Sharp (1987)
10.1080/07391102.2002.10506859 / J Biomol Struct Dyn / Distribution of rare triplets along mRNA and their relation to protein folding. by CH Makhoul (2002)
10.1016/S0959-437X(00)00250-1 / Curr Opin Genet Dev / Gene expression and molecular evolution. by H Akashi (2001)
10.1109/TNB.2003.817024 / IEEE Trans Nanobiosci / Folding type specific secondary structure propensities of synonymous codons. by W Gu (2003)
{'key': 'ref10', 'first-page': '549', 'article-title': 'Translation is a non-uniform process. Effect of tRNA availability on the rate of elongation of nascent polypeptide chains.', 'volume': '180', 'author': 'S Varenne', 'year': '1984', 'journal-title': 'J Mol Biol'} / J Mol Biol / Translation is a non-uniform process. Effect of tRNA availability on the rate of elongation of nascent polypeptide chains. by S Varenne (1984)
10.1016/0022-2836(91)90211-N / J Mol Biol / Absolute <italic>in vivo</italic> translation rates of individual codons in <italic>Escherichia coli</italic>: The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate. by MA Sorensen (1991)
10.1093/nar/29.1.123 / Nucleic Acids Res / The Comprehensive Microbial Resource. by JD Peterson (2001)
10.1016/S0014-5793(99)01566-5 / FEBS Lett / Synonymous codon substitutions affect ribosome traffic and protein folding during <italic>in vitro</italic> translation. by AA Komar (1999)
10.1016/S0006-291X(02)00226-7 / Biophys Res Commun / Silent mutations affect <italic>in vivo</italic> protein folding in <italic>Escherichia coli</italic>. Biochem. by P Cortazzo (2002)
10.1002/pro.5560051003 / Protein Sci / Protein secondary structural types are differentially coded on messenger RNA. by TA Thanaraj (1996)
10.1002/pro.5560050814 / Protein Sci / Ribosome-mediated translational pause and protein domain organization. by TA Thanaraj (1996)
10.1186/1471-2164-9-207 / BMC Genomics / Analysis of the distribution of functionally relevant rare codons. by M Widmann (2008)
10.1126/science.1131262 / Science / Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. by AG Nackley (2006)
10.1126/science.1135308 / Science / A “silent” polymorphism in the MDR1 gene changes substrate specificity. by C Kimchi-Sarfaty (2007)
10.1093/oxfordjournals.molbev.a025629 / Mol Biol Evol / Large-scale search for genes on which positive selection may operate. by T Endo (1996)
10.1016/0300-9084(89)90027-8 / Biochimie / The maximum rate of gene expression is dependent on the downstream context of unfavourable codons. by S Varenne (1989)
10.1016/S0022-5193(86)80020-0 / J Theor Biol / Effect of distribution of unfavourable codons on the maximum rate of gene expression by an heterologous organism. by S Varenne (1986)
{'key': 'ref23', 'article-title': 'Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima.', 'author': 'CJ Tsai', 'journal-title': 'J Mol Biol'} / J Mol Biol / Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. by CJ Tsai
10.1042/BC20070037 / Biol Cell / Halting a cellular production line: responses to ribosomal pausing during translation. by JR Buchan (2007)
10.1016/j.ygeno.2006.11.012 / Genomics / hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. by P Lamesch (2007)
10.1093/nar/28.1.292 / Nucl Acids Res / Codon usage tabulated from international DNA sequence databases: status for the year 2000. by Y Nakamura (2000)
10.1074/jbc.M008490200 / J Biol Chem / A newly synthesized, ribosome-bound polypeptide chain adopts conformations dissimilar from early in vitro refolding intermediates. by PL Clark (2001)

Dates

Type	When
Created	16 years, 10 months ago (Oct. 14, 2008, 1:47 p.m.)
Deposited	5 years, 3 months ago (May 8, 2020, 10:31 p.m.)
Indexed	18 hours, 52 minutes ago (Aug. 29, 2025, 6:33 a.m.)
Issued	16 years, 10 months ago (Oct. 15, 2008)
Published	16 years, 10 months ago (Oct. 15, 2008)
Published Online	16 years, 10 months ago (Oct. 15, 2008)

Funders 0

None

BibTeX

@article{Clarke_2008, title={Rare Codons Cluster}, volume={3}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0003412}, DOI={10.1371/journal.pone.0003412}, number={10}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Clarke, Thomas F. and Clark, Patricia L.}, editor={Jin, Dong-Yan}, year={2008}, month=oct, pages={e3412} }

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