Tag codon_bias [57 articles] Export

Recent papers classified by the tag codon_bias.

	Natural Selection on Synonymous Sites Is Correlated With Gene Length and Recombination in Drosophila [My Copy] Genetics In Genetics, Vol. 151, No. 1. (1 January 1999), pp. 239-249. by Josep M. Comeron, Martin Kreitman, Montserrat Aguade posted to synonymous_substitution recombination_rate gene_length drosophila codon_bias by daveGerrard on 2009-12-08 16:04:48 as
	Developmental Stage and Level of Codon Usage Bias in Drosophila [My Copy] Mol Biol Evol, Vol. 25, No. 11. (1 November 2008), pp. 2269-2277. by Saverio Vicario, Christopher E. Mason, Kevin P. White, Jeffrey R. Powell posted to drosophila developmental_stage codon_bias by daveGerrard on 2009-12-01 13:47:33 as
	Selection on Codon Bias [My Copy] Annual Review of Genetics, Vol. 42, No. 1. (2008), pp. 287-299. by Ruth Hershberg, Dmitri A. Petrov posted to review mutation_patterns codon_bias by daveGerrard on 2009-12-01 13:45:30 as along with 2 people codonusage timflutre
	X-Linked Genes Evolve Higher Codon Bias in Drosophila and Caenorhabditis [My Copy] Genetics, Vol. 171, No. 1. (1 September 2005), pp. 145-155. by Nadia D. Singh, Jerel C. Davis, Dmitri A. Petrov posted to x_chromosome drosophila codon_bias c_elegans by daveGerrard on 2009-12-01 10:25:59 as along with 1 person PetrovLab
	Evolution of codon usage bias inâDrosophila [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 94, No. 15. (22 July 1997), pp. 7784-7790. by Jeffrey R. Powell, Etsuko N. Moriyama posted to drosophila comparative_genomics codon_bias by daveGerrard on 2009-12-01 09:49:36 as along with 4 people hrogers operon gpalidwor skumagai
	Hill-Robertson Interference is a Minor Determinant of Variations in Codon Bias Across Drosophila melanogaster and Caenorhabditis elegans Genomes [My Copy] Mol Biol Evol, Vol. 19, No. 9. (1 September 2002), pp. 1399-1406. by Gabriel Marais, Gwenael Piganeau posted to hill_robertson drosophila codon_bias c_elegans by daveGerrard on 2009-12-01 09:39:13 as along with 2 people and 1 group thegoose2 tharris C. elegans / WormBase
	Protein Evolution and Codon Usage Bias on the Neo-Sex Chromosomes of Drosophila miranda [My Copy] Genetics, Vol. 165, No. 3. (1 November 2003), pp. 1221-1232. by Doris Bachtrog posted to sex_chromosomes rate_of_evolution neo_x miranda efficacy_of_selection drosophila codon_bias by daveGerrard on 2009-12-01 09:35:51 as along with 1 person and 1 group penka Nie
	Codon Bias and Noncoding GC Content Correlate Negatively with Recombination Rate on the Drosophila X Chromosome [My Copy] Journal of Molecular Evolution, Vol. 61, No. 3. (28 September 2005), pp. 315-324. by Nadia Singh, Jerel Davis, Dmitri Petrov posted to x_chromosome recombination gc_content drosophila codon_bias by daveGerrard on 2009-12-01 09:34:56 as along with 1 person PetrovLab
	Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 98, No. 10. (8 May 2001), pp. 5688-5692. by Gabriel Marais, Dominique Mouchiroud, Laurent Duret posted to recombination_rate mutation_patterns drosophila codon_bias chromosomes c_elegans by daveGerrard on 2009-12-01 09:24:09 as along with 3 people and 1 group thegoose2 tharris operon C. elegans / WormBase
	Strong Regional Heterogeneity in Base Composition Evolution on the Drosophila X Chromosome [My Copy] Genetics, Vol. 174, No. 1. (1 September 2006), pp. 349-362. by Wen-Ya Ko, Shengfu Piao, Hiroshi Akashi posted to x_chromosomes drosophila codon_bias by daveGerrard on 2009-11-30 17:02:29 as along with 1 person and 1 group dpollard EisenLab
	Codon usage in twelve species of Drosophila [My Copy] BMC Evolutionary Biology, Vol. 7, No. 1. (15 November 2007), 226. by Saverio Vicario, Etsuko Moriyama, Jeffrey Powell posted to drosophila codon_bias by daveGerrard on 2009-11-30 16:58:49 as along with 2 people hrogers cjeans
	Climbing Mount Probable: Mutation as a Cause of Nonrandomness in Evolution [My Copy] J Hered, Vol. 100, No. 5. (1 September 2009), pp. 637-647. by Arlin Stoltzfus, Lev Y. Yampolsky posted to evolution codon_bias biased_mutation amino_acid_substitution by biomcgary on 2009-11-13 21:13:06 as
	Universal function-specificity of codon usage. [My Copy] Nucleic acids research (22 September 2009), gkp792. by Hamed Shateri S. Najafabadi, Hani Goodarzi, Reza Salavati posted to trna codon_bias by hrogers on 2009-09-28 10:32:16 as along with 1 person saunders
	The Evolution of Gene Expression QTL in Saccharomyces cerevisiae [My Copy] PLoS ONE, Vol. 2, No. 8. (2007), e678. by James Ronald, Joshua M. Akey posted to yeast variation selection_purifying selection_positive selection qtl essentiality eqtl codon_bias by biomcgary on 2009-08-21 17:24:48 as along with 1 person myzhang
	Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome [My Copy] Genome Biology, Vol. 3, No. 12. (2002) by Casey Bergman, Barret Pfeiffer, Diego R. Limas, et al.Roger Hoskins, Andreas Gnirke, Chris Mungall, Adrienne Wang, Brent Kronmiller, Joanne Pacleb, Soo Park, Mark Stapleton, Kenneth Wan, Reed George, Pieter de Jong, Juan Botas, Gerald Rubin, Susan Celniker posted to trna genomics drosophila codon_bias codon by hrogers on 2009-08-19 12:43:46 as along with 5 people and 2 groups indigoviolet dpollard nklee cisevol brant EisenLab cis-regulatory-evolution
	Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. [My Copy] PLoS genetics, Vol. 5, No. 7. (3 July 2009), e1000548. by Joanna L. Parmley, Martijn A. Huynen posted to codon codon_bias trna by hrogers on 2009-07-13 20:07:02 as along with 4 people saunders danatcaret bpcusack djkt
	General Rules for Optimal Codon Choice [My Copy] PLoS Genet, Vol. 5, No. 7. (10 July 2009), e1000556. by Ruth Hershberg, Dmitri A. Petrov posted to codon_bias by kiekyon on 2009-07-11 05:37:33 as along with 4 people and 1 group codonusage GustavoLacerda stajich djkt Mycology
	Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes [My Copy] Genome Research, Vol. 19, No. 2. (February 2009), pp. 234-242. by David Alvarez-Ponce, Montserrat Aguadé, Julio Rozas posted to codon_bias dn_ds drosophila interactions network path_analysis rate_of_evolution by daveGerrard to the group BergmanLab on 2009-07-10 11:39:12 as along with 3 people adiel Schmidtc MaxH
	Gene Expression and Protein Length Influence Codon Usage and Rates of Sequence Evolution in Populus tremula [My Copy] Mol Biol Evol, Vol. 24, No. 3. (1 March 2007), pp. 836-844. by Par K. Ingvarsson posted to codon_bias dn_ds expression_level gene_length path_analysis poplar rate_of_evolution by daveGerrard to the group BergmanLab on 2009-07-10 11:32:26 as along with 1 person natstreet
	Coding-sequence determinants of gene expression in Escherichia coli. [My Copy] Science (New York, N.Y.), Vol. 324, No. 5924. (10 April 2009), pp. 255-258. by Grzegorz Kudla, Andrew W. Murray, David Tollervey, Joshua B. Plotkin posted to codon_bias transcriptional_regulation by emptyhb on 2009-05-20 10:15:07 as along with 35 people and 1 group daveGerrard pmalkus codonusage balabu yyfwuhan dbikard kinestetika samgj dswan bpcusack sameersoi dpsuslo8 anwazo Vincent_Rouilly kintoki erel10 michaelbarton fenghezi VGreiff ramanuja austin twatanab coela polivares rpatward lizbiogen jdbowes operon jasontsai absterga jbhiatt jjray kshundyak zwang friendpine BergmanLab
	Divergence of the yellow gene between Drosophila melanogaster and D. subobscura: recombination rate, codon bias and synonymous substitutions. [My Copy] Genetics, Vol. 147, No. 1. (September 1997), pp. 165-175. by A. Munté, M. Aguadé, C. Segarra posted to arthropod codon_bias doctorate drosophila genomics by operon on 2009-05-08 05:29:30 as
	How can the low levels of DNA sequence variation in regions of the drosophila genome with low recombination rates be explained? [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 91, No. 15. (19 July 1994), pp. 6815-6818. by R. R. Hudson posted to arthropod codon_bias doctorate drosophila genomics by operon on 2009-05-08 05:29:16 as
	Differential selection on gene translation efficiency between the filamentous fungus Ashbya gossypii and yeasts [My Copy] BMC Evolutionary Biology, Vol. 8 (29 December 2008), 343. by Huifeng, Zhenglong Gu posted to ashbya codon_bias genome by stajich to the group Mycology on 2008-12-30 05:39:38 as
	Codon usage and the origin of P elements. [My Copy] Molecular biology and evolution, Vol. 17, No. 3. (March 2000), pp. 467-468. by E. Lerat, C. Biémont, P. Capy posted to arthropod codon_bias drosophila evolution transposon by operon on 2008-12-04 20:27:54 as
	Preferential duplication of conserved proteins in eukaryotic genomes. [My Copy] PLoS biology, Vol. 2, No. 3. (March 2004) by J. C. Davis, D. A. Petrov posted to aggregation codon_bias evolution_rate evolutionary_constraint gene_duplication gene_function genome_duplication sequence_divergence by biomcgary on 2008-11-12 22:51:03 as
	Do disparate mechanisms of duplication add similar genes to the genome? [My Copy] Trends in Genetics, Vol. In Press, Corrected Proof by Jerel C. Davis, Dmitri A. Petrov posted to codon_bias convergent_evolution evolution_rate gene_duplication gene_function genome_duplication by biomcgary on 2008-11-12 22:42:14 as along with 6 people and 2 groups Retchless dchughes mikemacpherson nirfriedman PetrovLab bpcusack G4ID Genetics-of-Gambling
	Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cervisiae and Escherichia coli [My Copy] Nucl. Acids Res., Vol. 26, No. 19. (1 October 1998), 4540. by A. Marin, F. Gonzalez, G. Gutierrez, J. L. Oliver posted to arthropod codon_bias doctorate drosophila evolution gene genometrics genomics phylogenetics by operon on 2008-10-30 13:38:21 as
	Codon Optimization Increases Steady-State mRNA Levels in Aspergillus oryzae Heterologous Gene Expression [My Copy] Appl. Environ. Microbiol., Vol. 74, No. 21. (1 November 2008), pp. 6538-6546. by Masafumi Tokuoka, Mizuki Tanaka, Kazuhisa Ono, Shinobu Takagi, Takahiro Shintani, Katsuya Gomi posted to aspergillus codon_bias engineering gene_expression nmd by stajich to the group Mycology on 2008-10-27 22:37:36 as
	Five Drosophila Genomes Reveal Nonneutral Evolution and the Signature of Host Specialization in the Chemoreceptor Superfamily [My Copy] Genetics, Vol. 177, No. 3. (1 November 2007), pp. 1395-1416. by Carolyn S. Mcbride, Roman J. Arguello, Brian C. O'Meara posted to arthropod codon_bias doctorate drosophila evolution genomics phylogenetics selection by operon on 2008-10-21 05:14:52 as along with 1 person smbe2008
	Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage. [My Copy] Mol Biol Evol (3 January 2008) by Ziheng Yang, Rasmus Nielsen posted to codon_bias doctorate evolution genomics phylogenetics selection by operon on 2008-10-21 05:14:28 as along with 4 people and 1 group BioNica stajich cjeans gjuggler Mycology
	Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. [My Copy] Genetics, Vol. 136, No. 3. (March 1994), pp. 927-935. by H. Akashi posted to arthropod codon_bias doctorate drosophila evolution genomics phylogenetics selection by operon on 2008-10-21 05:13:55 as along with 4 people codonusage hrogers bjorns skumagai
	Patterns of Synonymous Codon Usage in Drosophila melanogaster Genes With Sex-Biased Expression [My Copy] Genetics, Vol. 170, No. 4. (1 August 2005), pp. 1691-1700. by Tina M. Hambuch, John Parsch posted to arthropod codon_bias doctorate drosophila evolution genomics phylogenetics selection by operon on 2008-10-21 04:55:26 as along with 2 people and 1 group CharlesM penka Nie
	Patterns of Codon Usage in two Ciliates that Reassign the Genetic Code: Tetrahymena thermophila and Paramecium tetraurelia. [My Copy] Protist (18 January 2008) by Hannah M W M. Salim, Karen L L. Ring, Andre R O R. Cavalcanti posted to codon_bias codon_reassignment codon_usage genetic_code paramecium_tetraurelia tetrahymena_thermophila by scherrer on 2008-10-16 17:54:54 as along with 1 person operon
	SCUMBLE: a method for systematic and accurate detection of codon usage bias by maximum likelihood estimation [My Copy] Nucl. Acids Res., Vol. 36, No. 11. (1 June 2008), pp. 3819-3827. by Morten Kloster, Chao Tang posted to bioinformatics codon_bias methods by stajich to the group Mycology on 2008-07-28 06:18:17 as along with 1 person GustavoLacerda
	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. [My Copy] Journal of molecular biology, Vol. 158, No. 4. (15 July 1982), pp. 573-597. by T. Ikemura posted to codon_bias fungi by cisevol to the group BergmanLab on 2008-04-25 12:49:50 as along with 3 people danatcaret michaelbarton bjorns
	Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes. [My Copy] Nucleic Acids Res, Vol. 22, No. 15. (11 August 1994), pp. 3174-3180. by J. R. Lobry, C. Gautier posted to codon_bias by operon on 2008-04-12 07:01:25 as along with 2 people bjorns michaelbarton
	Coevolution of codon usage and transfer RNA abundance [My Copy] Nature, Vol. 325, No. 6106. (19 February 1987), pp. 728-730. by Michael Bulmer posted to codon_bias by operon on 2008-04-12 07:00:32 as along with 2 people codonusage Retchless
	The relationship between synonymous codon usage and protein structure. [My Copy] FEBS Lett, Vol. 434, No. 1-2. (28 August 1998), pp. 93-96. by T. Xie, D. Ding, X. Tao, D. Dafu posted to codon_bias doctorate by operon on 2008-04-12 05:55:47 as along with 1 person saunders
	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 [My Copy] Journal of Molecular Biology, Vol. 151, No. 3. (25 September 1981), pp. 389-409. by Toshimichi Ikemura posted to codon_bias master by operon on 2008-04-12 04:55:17 as along with 1 person karfunkel
	Codon usage between genomes is constrained by genome-wide mutational processes [My Copy] PNAS, Vol. 101, No. 10. (9 March 2004), pp. 3480-3485. by Swaine L. Chen, William Lee, Alison K. Hottes, Lucy Shapiro, Harley H. Mcadams posted to codon_bias master by operon on 2008-03-29 21:23:57 as along with 3 people and 1 group codonusage azazello wenhan MBLAB
	Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure. [My Copy] PLoS ONE, Vol. 2, No. 9. (2007) by G. Moura, M. Pinheiro, J. Arrais, et al.A. C. Gomes, L. Carreto, A. Freitas, J. L. Oliveira, M. A. Santos posted to codon_bias master by operon on 2008-03-29 21:23:36 as along with 1 person codonusage
	Codon adaptation index as a measure of dominating codon bias [My Copy] Bioinformatics, Vol. 19, No. 16. (1 November 2003), pp. 2005-2015. by A. Carbone, A. Zinovyev, F. Kepes posted to codon_bias master by operon on 2008-03-29 21:22:52 as along with 3 people Retchless marenzelleria aaronsmith
	Codon Bias Signatures, Organization of Microorganisms in Codon Space, and Lifestyle [My Copy] Molecular Biology and Evolution, Vol. 22, No. 3. (March 2005), pp. 547-561. by A. Carbone, F. Kepes, A. Zinovyev posted to codon_bias master by operon on 2008-03-29 21:22:45 as along with 2 people marenzelleria aaronsmith
	The Mystery of Two Straight Lines in Bacterial Genome Statistics [My Copy] Bulletin of Mathematical Biology, Vol. 69, No. 7. (14 October 2007), pp. 2429-2442. by A. Gorban, A. Zinovyev posted to codon_bias master by operon on 2008-03-29 21:22:36 as along with 1 person codonusage
	Codon usage in bacteria: correlation with gene expressivity. [My Copy] Nucleic Acids Res, Vol. 10, No. 22. (25 November 1982), pp. 7055-7074. by M. Gouy, C. Gautier posted to codon_bias master by operon on 2008-03-29 21:21:38 as
	Rapid divergence of codon usage patterns within the rice genome. [My Copy] BMC Evol Biol, Vol. 7 Suppl 1 (2007) by H. C. Wang, D. A. Hickey posted to codon_bias master by operon on 2008-03-21 02:04:10 as
	Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes [My Copy] BMC Evolutionary Biology, Vol. 4, No. 1. (2004) by Xiu F. Wan, Dong Xu, Andris Kleinhofs, Jizhong Zhou posted to codon_bias evolution master by operon on 2008-03-21 01:53:40 as along with 3 people saunders codonusage msafi
	Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. [My Copy] Mol Biol Evol, Vol. 19, No. 6. (June 2002), pp. 908-917. by Z. Yang, R. Nielsen posted to codon_bias master by operon on 2008-03-10 02:35:53 as along with 5 people and 2 groups clearbluespring skembel stevanspringer stajich Garamonfok FAB-lab Mycology
	Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates [My Copy] Bioinformatics In Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i319-327. by Itay Mayrose, Adi Doron-Faigenboim, Eran Bacharach, Tal Pupko posted to codon_bias doctorate master selection by operon on 2008-03-09 23:14:15 as along with 2 people MRCBIRD tale
	A Strong Effect of AT Mutational Bias on Amino Acid Usage in Buchnera is Mitigated at High-Expression Genes [My Copy] Mol Biol Evol, Vol. 19, No. 9. (1 September 2002), pp. 1575-1584. by Carmen Palacios, Jennifer J. Wernegreen posted to codon_bias evolution master reduction by operon on 2008-03-09 22:34:55 as

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drosophila	21
evolution	17
master	14
genomics	13
doctorate	10
arthropod	8
selection	8
phylogenetics	7
rate_of_evolution	5
comparative_genomics	4
dn_ds	4
hgt	4
path_analysis	4
base_composition	3
c_elegans	3
gene_expression	3
gene_length	3
genometrics	3
phylogeny	3
prokaryote	3
protein_sequence	3
sequence_comparison	3
trna	3
ashbya	2
aspergillus	2
bioinformatics	2
codon	2
design	2
engineering	2
evolution_rate	2
expression_level	2
fungi	2
gene_duplication	2
gene_function	2
genome	2
genome_duplication	2
hfsp_synopsis	2
interactions	2
methods	2
mutation_patterns	2
network	2
nmd	2
poplar	2
recombination_rate	2
x_chromosome	2
adaptation	1
aggregation	1
amino_acid_substitution	1
bacteria	1
biased_mutation	1
chromosomes	1
codon_reassignment	1
codon_usage	1
comparative	1
convergent_evolution	1
developmental_stage	1
e_coli	1
efficacy_of_selection	1
eqtl	1
essentiality	1
evolutionary_constraint	1
gc	1
gc_content	1
gene	1
genetic_code	1
hill_roberts	1
hill_robertson	1
horizontal_transfer	1
immunology	1
metabolic_cost	1
miranda	1
mutation	1
neo_x	1
paramecium_tetraurelia	1
qtl	1
recombination	1
reduction	1
review	1
selection_positive	1
selection_purifying	1
sequence_divergence	1
sex_chromosomes	1
synonymous_substitution	1
tetrahymena_thermophila	1
transcriptional_regulation	1
translation	1
transposon	1
vaccine	1
variation	1
x_chromosomes	1
yeast	1

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