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1. Full Text Selection on Codon Bias
by Hershberg, R and Petrov, DA
ANNUAL REVIEW OF GENETICS, ISSN 0066-4197, 2008, Volume 42, Issue 1, pp. 287 - 299
In a wide variety of organisms, Synonymous cottons are used with different frequencies, a phenomenon known as colon bias. Population genetic studies have shown... 
codon bias | USAGE BIAS | MAXIMUM-LIKELIHOOD | DROSOPHILA-MELANOGASTER | PHYLOGENETIC ANALYSIS | ESCHERICHIA-COLI | TRANSLATIONAL ACCURACY | evolution | TRANSFER-RNA GENES | selection | BACILLUS-SUBTILIS | NATURAL-SELECTION | PROTEIN EXPRESSION | GENETICS & HEREDITY | Genetics, Population | Genetic Drift | Animals | Caenorhabditis elegans - genetics | Selection, Genetic | Models, Genetic | Codon - genetics | Mutation | Drosophila melanogaster - genetics | Evolution | Codon bias | Selection | Genetic drift | Codon | Research | Analysis | Natural selection
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2. Full Text Codon degeneracy and amino acid abundance influence the measures of codon usage bias: improved Nc (N̂c) and ENCprime (N̂′c) measures
by Satapathy, Siddhartha Sankar and Sahoo, Ajit Kumar and Ray, Suvendra Kumar and Ghosh, Tapash Chandra
Genes to Cells, ISSN 1356-9597, 03/2017, Volume 22, Issue 3, pp. 277 - 283
Effective number of codons (N^c) and its variant N^′c (effective number of codons prime) are the two widely used methods for measuring unequal usage of... 
BACTERIA | EFFECTIVE NUMBER | MUTATION | GENES | GENETICS & HEREDITY | METHODOLOGICAL WEAKNESS | SYNONYMOUS CODONS | SELECTION | EXPRESSION | CELL BIOLOGY | Amino Acid Sequence | Algorithms | Codon | Open Reading Frames | Bacterial Proteins - genetics | Models, Genetic | Software | Genes
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3. Full Text Codon Bias as a Means to Fine-Tune Gene Expression
by Quax, Tessa E.F and Claassens, Nico J and Söll, Dieter and van der Oost, John
Molecular Cell, ISSN 1097-2765, 07/2015, Volume 59, Issue 2, pp. 149 - 161
The redundancy of the genetic code implies that most amino acids are encoded by multiple synonymous codons. In all domains of life, a biased frequency of... 
HETEROLOGOUS PROTEIN EXPRESSION | TRANSFER-RNA MODIFICATIONS | USAGE | UNICELLULAR ORGANISMS | ELONGATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | IN-VIVO | TRANSLATION INITIATION | GENOME | RIBOSOME | CELL BIOLOGY | Cell Cycle - genetics | Gene Expression | Protein Biosynthesis | Genetic Code | Operon | Humans | Genes, Synthetic | Selection, Genetic | Protein Folding | Genetic Variation | Cell Differentiation - genetics | Animals | RNA, Transfer - genetics | Codon - genetics | Protein biosynthesis | Codon | Genetic translation | Genes | Genomics | Microbiological Laboratory | Microbiologie | Microbiology | VLAG | Laboratorium voor Microbiologie
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4. Full Text Codon Pair Bias Is a Direct Consequence of Dinucleotide Bias
by Kunec, Dusan and Osterrieder, Nikolaus
Cell Reports, ISSN 2211-1247, 01/2016, Volume 14, Issue 1, pp. 55 - 67
Codon pair bias is a remarkably stable characteristic of a species. Although functionally uncharacterized, robust virus attenuation was achieved by recoding of... 
METHYLATION | SEQUENCES | REDUCTION | VIRUS ATTENUATION | DNA | SCALE | CPG | CONTEXT ANALYSIS | GENOME | DEOPTIMIZATION | CELL BIOLOGY | Insecta - virology | Codon - metabolism | Animals | Arboviruses - genetics | Species Specificity | Humans | Models, Genetic | Codon - genetics | Insecta - genetics | Arboviruses - metabolism
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5. Full Text Codon optimality, bias and usage in translation and mRNA decay
by Hanson, G and Coller, J
NATURE REVIEWS MOLECULAR CELL BIOLOGY, ISSN 1471-0072, 01/2018, Volume 19, Issue 1, pp. 20 - 30
The advent of ribosome profiling and other tools to probe mRNA translation has revealed that codon bias-the uneven use of synonymous codons in the... 
ELONGATION RATES | ESCHERICHIA-COLI | PROTEIN EXPRESSION | IN-VIVO | GENE-EXPRESSION | AMINO-ACID STARVATION | OVER-EXPRESSION | GLOBAL ANALYSIS | SYNONYMOUS CODONS | SACCHAROMYCES-CEREVISIAE | CELL BIOLOGY | Proteins - genetics | Animals | Ribosomes - genetics | Humans | RNA, Messenger - genetics | Protein Biosynthesis - genetics | Codon - genetics | RNA Stability - genetics | Homeostasis - genetics | Protein Folding | Genetic research | Messenger RNA | Codon | Properties | Gene expression | Observations | Fidelity | Translation | tRNA | Transcription | Bias | mRNA turnover | Homeostasis | Metabolism | Machinery | Optimization | Proteins | Genetic code | Efficiency | Protein folding | Codon bias | Decay | Dynamic stability | Coupling | Codons | mRNA stability
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6. Full Text Codon bias and heterologous protein expression
by Gustafsson, Claes and Govindarajan, Sridhar and Minshull, Jeremy
Trends in Biotechnology, ISSN 0167-7799, 2004, Volume 22, Issue 7, pp. 346 - 353
The expression of functional proteins in heterologous hosts is a cornerstone of modern biotechnology. Unfortunately, proteins are often difficult to express... 
USAGE BIAS | HIGH-LEVEL EXPRESSION | HUMAN-PAPILLOMAVIRUS TYPE-16 | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ESCHERICHIA-COLI | GENE-EXPRESSION | PICHIA-PASTORIS | INITIATION CODON | MAMMALIAN-CELLS | BACTERIAL EXPRESSION | TRANSFER-RNA ABUNDANCE | Proteins - genetics | Protein Engineering - methods | Gene Expression Regulation - genetics | Cloning, Molecular - methods | Recombinant Proteins - genetics | Codon - genetics | Recombinant Proteins - biosynthesis | Sequence Analysis, DNA - methods
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7. Full Text A general model of Codon bias due to GC mutational bias
by Palidwor, Gareth A and Perkins, Theodore J and Xia, Xuhua
PLoS ONE, ISSN 1932-6203, 2010, Volume 5, Issue 10, p. e13431
Background: In spite of extensive research on the effect of mutation and selection on codon usage, a general model of codon usage bias due to mutational bias... 
RESPECTIVE CODONS | EVOLUTION | TRANSFER-RNAS | USAGE | PROTEIN GENES | ESCHERICHIA-COLI | BIOLOGY | HUMANS | ISOCHORES | MITOCHONDRIAL GENOMES | ABUNDANCE | Models, Theoretical | Markov Chains | Codon | Base Composition | Guanine - chemistry | Mutation | Cytosine - chemistry | Arginine | Analysis | Genomics | Plant genetics | Markov processes | Genetic aspects | Models | Research | Prokaryotes | Bias | Genes | Amino acids | Markov chains | Genomes | Leucine | Physical properties | Correlation analysis | Codon bias | Cyanobacteria | Position measurement | Mathematical models | Codons | Isoleucine | Markov process | Markov models
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8. Full Text Synonymous but not the same: the causes and consequences of codon bias
by Kudla, Grzegorz and Plotkin, Joshua B
Nature Reviews Genetics, ISSN 1471-0056, 01/2011, Volume 12, Issue 1, pp. 32 - 42
Despite their name, synonymous mutations have significant consequences for cellular processes in all taxa. As a result, an understanding of codon bias is... 
USAGE BIAS | TRANSLATIONAL EFFICIENCY | DROSOPHILA-MELANOGASTER | ESCHERICHIA-COLI | NATURAL-SELECTION | PROTEIN EXPRESSION | GENETICS & HEREDITY | GENE-EXPRESSION | GLOBAL ANALYSIS | SECONDARY STRUCTURE | MESSENGER-RNA STABILITY | Gene Expression | Protein Biosynthesis | Animals | Humans | Mice | Codon - genetics | Drosophila Proteins - genetics | Mutation | Genome | Codon | Gene mutations | Reorganization and restructuring | Physiological aspects | Protein biosynthesis | Research | Health aspects | Elongation
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9. Full Text Virus Attenuation by Genome-Scale Changes in Codon Pair Bias
by J. Robert Coleman and Dimitris Papamichail and Steven Skiena and Bruce Futcher and Eckard Wimmer and Steffen Mueller
Science, ISSN 0036-8075, 6/2008, Volume 320, Issue 5884, pp. 1784 - 1787
As a result of the redundancy of the genetic code, adjacent pairs of amino acids can be encoded by as many as 36 different pairs of synonymous codons. A... 
Transcriptional regulatory elements | RNA | Memory interference | Virions | HeLa cells | Viruses | Amino acids | Reports | Codons | Poliovirus | Genetic mutation | POLIOVIRUS | STRATEGY | MULTIDISCIPLINARY SCIENCES | GENES | ERADICATION | DEOPTIMIZATION | Protein Biosynthesis | Humans | Vaccination | Virulence | Cytopathogenic Effect, Viral | Codon | Cloning, Molecular | Poliovirus - genetics | Poliovirus - pathogenicity | Antibodies, Viral - biosynthesis | Genome, Viral | Viral Plaque Assay | Mice, Transgenic | Poliomyelitis - immunology | Hot Temperature | Vaccines, Attenuated - immunology | Algorithms | Animals | Poliovirus - growth & development | Poliovirus Vaccines - genetics | Poliovirus - immunology | Poliomyelitis - virology | Mice | HeLa Cells | Mutation | Poliovirus Vaccines - immunology | Capsid Proteins - genetics | Vaccines, Attenuated - genetics | Genetic engineering | Genetic aspects | Research | Properties | Proteins | Molecular biology | Genomics | Deoxyribonucleic acid--DNA
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10. Full Text Forces that influence the evolution of codon bias
by Paul M. Sharp and Laura R. Emery and Kai Zeng
Philosophical Transactions: Biological Sciences, ISSN 0962-8436, 4/2010, Volume 365, Issue 1544, pp. 1203 - 1212
The frequencies of alternative synonymous codons vary both among species and among genes from the same genome. These patterns have been inferred to reflect the... 
Biological taxonomies | Genetic variation | Escherichia coli | Bacteria | Evolution | Amino acids | Genomes | Codons | Genetic mutation | Transfer RNA | Mutation bias | Population genetics | Selection | Codon usage | ENTEROBACTERIAL GENES | population genetics | USAGE BIAS | bacteria | TRANSLATIONAL ACCURACY | codon usage | REPLICATION ORIENTATION | SYNONYMOUS SUBSTITUTION-RATE | ESCHERICHIA-COLI CHROMOSOME | selection | mutation bias | BIOLOGY | BASE-COMPOSITION | SALMONELLA-TYPHIMURIUM | GENE-EXPRESSION LEVEL | CLOSTRIDIUM-PERFRINGENS | Genes, Bacterial | Protein Biosynthesis | Codon | Escherichia coli - genetics | Selection, Genetic | RNA, Transfer - genetics | Evolution, Molecular | Polymorphism, Genetic | 1001 | 181
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11. Full Text Causes and Effects of N-Terminal Codon Bias in Bacterial Genes
by Daniel B. Goodman and George M. Church and Sriram Kosuri
Science, ISSN 0036-8075, 10/2013, Volume 342, Issue 6157, pp. 475 - 479
Most amino acids are encoded by multiple codons, and codon choice has strong effects on protein expression. Rare codons are enriched at the N terminus of genes... 
Proteins | Messenger RNA | RNA | Protein synthesis | DNA | REPORTS | Amino acids | Bacteria | Libraries | Codons | Free energy | DESIGN | SELECTION | TRANSLATIONAL EFFICIENCY | USAGE | EXPRESSION | MULTIDISCIPLINARY SCIENCES | Codon, Terminator - chemistry | Genes, Bacterial | Gene Library | Codon, Terminator - genetics | Escherichia coli - genetics | Protein Biosynthesis - genetics | Recombinant Proteins - genetics | Recombinant Proteins - biosynthesis | Gene Expression Regulation, Bacterial | Nucleic Acid Conformation | Genes, Reporter | Codon | Escherichia coli | Physiological aspects | Genetic aspects | Research | Bacterial genetics | Gene expression | E coli | Ribonucleic acid--RNA | Bacteriology
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