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Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
JV Chamary, Laurence D Hurst
Genome Biol. 2005; 6(9): R75. Published online 2005 August 16. doi: 10.1186/gb-2005-6-9-r75
PMCID:
PMC1242210
Abstract Full Text PDF–386K Supplementary Material

Is Cited by the Following 56 Articles in this Archive:

Codon usage bias as a function of generation time and life expectancy
Rami N Mahdi, Eric C Rouchka
Bioinformation. 2012; 8(3): 158–162. Published online 2012 February 3.
PMCID:
PMC3283889
Abstract Full Text PDF–261K Supplementary Material
Polymorphism in Osteopontin Gene (SPP1) Is Associated with Asthma and Related Phenotypes in a Puerto Rican Population
Mehrdad Arjomandi, Josh M. Galanter, Shweta Choudhry, Celeste Eng, Donglei Hu, Kenneth Beckman, Rocío Chapela, José R. Rodríguez-Santana, William Rodríguez-Cintrón, Jean Ford, Pedro C. Avila, Esteban G. Burchard
Pediatr Allergy Immunol Pulmonol. 2011 December; 24(4): 207–214. doi: 10.1089/ped.2011.0095
PMCID:
PMC3255512
Abstract Full Text PDF–178K Supplementary Material
Widespread signatures of recent selection linked to nucleosome positioning in the human lineage
James G.D. Prendergast, Colin A.M. Semple
Genome Res. 2011 November; 21(11): 1777–1787. doi: 10.1101/gr.122275.111
PMCID:
PMC3205563
Abstract Full Text PDF–1.7M
Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
Michael F. Lin, Pouya Kheradpour, Stefan Washietl, Brian J. Parker, Jakob S. Pedersen, Manolis Kellis
Genome Res. 2011 November; 21(11): 1916–1928. doi: 10.1101/gr.108753.110
PMCID:
PMC3205576
Abstract Full Text PDF–1.6M
Statistics and Truth in Phylogenomics
Sudhir Kumar, Alan J. Filipski, Fabia U. Battistuzzi, Sergei L. Kosakovsky Pond, Koichiro Tamura
Mol Biol Evol. 2012 February; 29(2): 457–472. Published online 2011 August 26. doi: 10.1093/molbev/msr202
PMCID:
PMC3258035
Free in PMC on 2013/02/01
Codon usage: Nature's roadmap to expression and folding of proteins
Evelina Angov
Biotechnol J. 2011 June; 6(6): 650–659. doi: 10.1002/biot.201000332
PMCID:
PMC3166658
Abstract Full Text PDF–295K
The surprising negative correlation of gene length and optimal codon use - disentangling translational selection from GC-biased gene conversion in yeast
Nina Stoletzki
BMC Evol Biol. 2011; 11: 93. Published online 2011 April 11. doi: 10.1186/1471-2148-11-93
PMCID:
PMC3096941
Abstract Full Text PDF–272K
Synonymous Mutations in the Core Gene Are Linked to Unusual Serological Profile in Hepatitis C Virus Infection
Agata Budkowska, Athanassios Kakkanas, Eric Nerrienet, Olga Kalinina, Patrick Maillard, Srey Viseth Horm, Geena Dalagiorgou, Niki Vassilaki, Urania Georgopoulou, Michelle Martinot, Amadou Alpha Sall, Penelope Mavromara
PLoS One. 2011; 6(1): e15871. Published online 2011 January 6. doi: 10.1371/journal.pone.0015871
Correction in:
PLoS One. 2011; 6(1): 10.1371/annotation/cfafce35-02ca-43df-9d06-3c22fc92d349.
PMCID:
PMC3017048
Abstract Full Text PDF–1.4M Correction
Translationally optimal codons associate with aggregation-prone sites in proteins
Yaelim Lee, Tong Zhou, Gian Gaetano Tartaglia, Michele Vendruscolo, Claus O. Wilke
Proteomics. Author manuscript; available in PMC 2011 December 1.
Published in final edited form as: Proteomics. 2010 December; 10(23): 4163–4171. doi: 10.1002/pmic.201000229
PMCID:
PMC3037288
Abstract Full Text PDF–393K Supplementary Material
Synonymous but not the same: the causes and consequences of codon bias
Joshua B. Plotkin, Grzegorz Kudla
Nat Rev Genet. Author manuscript; available in PMC 2011 April 12.
Published in final edited form as: Nat Rev Genet. 2011 January; 12(1): 32–42. Published online 2010 November 23. doi: 10.1038/nrg2899
PMCID:
PMC3074964
Abstract Full Text PDF–709K
Ultraconserved cDNA segments in the human transcriptome exhibit resistance to folding and implicate function in translation and alternative splicing
J. Fah Sathirapongsasuti, Nuankanya Sathira, Yutaka Suzuki, Curtis Huttenhower, Sumio Sugano
Nucleic Acids Res. 2011 March; 39(6): 1967–1979. Published online 2010 November 8. doi: 10.1093/nar/gkq949
PMCID:
PMC3064809
Abstract Full Text PDF–9.2M Supplementary Material
Significant Selective Constraint at 4-Fold Degenerate Sites in the Avian Genome and Its Consequence for Detection of Positive Selection
Axel Künstner, Benoit Nabholz, Hans Ellegren
Genome Biol Evol. 2011; 3: 1381–1389. Published online 2010 October 31. doi: 10.1093/gbe/evr112
PMCID:
PMC3242499
Abstract Full Text PDF–185K
Adaptive Evolution of the Chlamydia trachomatis Dominant Antigen Reveals Distinct Evolutionary Scenarios for B- and T-cell Epitopes: Worldwide Survey
Alexandra Nunes, Paulo J. Nogueira, Maria J. Borrego, João P. Gomes
PLoS One. 2010; 5(10): e13171. Published online 2010 October 5. doi: 10.1371/journal.pone.0013171
PMCID:
PMC2950151
Abstract Full Text PDF–1.8M Supplementary Material
A Synonymous Single Nucleotide Polymorphism in ΔF508 CFTR Alters the Secondary Structure of the mRNA and the Expression of the Mutant Protein
Rafal A. Bartoszewski, Michael Jablonsky, Sylwia Bartoszewska, Lauren Stevenson, Qun Dai, John Kappes, James F. Collawn, Zsuzsa Bebok
J Biol Chem. 2010 September 10; 285(37): 28741–28748. Published online 2010 July 13. doi: 10.1074/jbc.M110.154575
PMCID:
PMC2937902
Abstract Full Text Supplementary Material
Polymorphisms in the gene encoding bovine interleukin-10 receptor alpha are associated with Mycobacterium avium ssp. paratuberculosis infection status
Chris P Verschoor, Sameer D Pant, Qiumei You, Flavio S Schenkel, David F Kelton, Niel A Karrow
BMC Genet. 2010; 11: 23. Published online 2010 April 15. doi: 10.1186/1471-2156-11-23
PMCID:
PMC2873551
Abstract Full Text PDF–680K
Detecting Positive and Purifying Selection at Synonymous Sites in Yeast and Worm
Tong Zhou, Wanjun Gu, Claus O. Wilke
Mol Biol Evol. 2010 August; 27(8): 1912–1922. Published online 2010 March 15. doi: 10.1093/molbev/msq077
PMCID:
PMC2915641
Abstract Full Text PDF–541K Supplementary Material
Fine-Tuning Translation Kinetics Selection as the Driving Force of Codon Usage Bias in the Hepatitis A Virus Capsid
Lluís Aragonès, Susana Guix, Enric Ribes, Albert Bosch, Rosa M. Pintó
PLoS Pathog. 2010 March; 6(3): e1000797. Published online 2010 March 5. doi: 10.1371/journal.ppat.1000797
PMCID:
PMC2832697
Abstract Full Text PDF–697K Supplementary Material
The IGF1 small dog haplotype is derived from Middle Eastern grey wolves
Melissa M Gray, Nathan B Sutter, Elaine A Ostrander, Robert K Wayne
BMC Biol. 2010; 8: 16. Published online 2010 February 24. doi: 10.1186/1741-7007-8-16
Correction in:
BMC Biol. 2010; 8: 118.
PMCID:
PMC2837629
Abstract Full Text PDF–964K Supplementary Material Correction
Allele Interaction – Single Locus Genetics Meets Regulatory Biology
Arne B. Gjuvsland, Erik Plahte, Tormod Ådnøy, Stig W. Omholt
PLoS One. 2010; 5(2): e9379. Published online 2010 February 23. doi: 10.1371/journal.pone.0009379
PMCID:
PMC2826424
Abstract Full Text PDF–343K Supplementary Material
A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes
Wanjun Gu, Tong Zhou, Claus O. Wilke
PLoS Comput Biol. 2010 February; 6(2): e1000664. Published online 2010 February 5. doi: 10.1371/journal.pcbi.1000664
PMCID:
PMC2816680
Abstract Full Text PDF–362K Supplementary Material
Experimentally Increased Codon Bias in the Drosophila Adh Gene Leads to an Increase in Larval, But Not Adult, Alcohol Dehydrogenase Activity
Winfried Hense, Nathan Anderson, Stephan Hutter, Wolfgang Stephan, John Parsch, David B. Carlini
Genetics. 2010 February; 184(2): 547–555. doi: 10.1534/genetics.109.111294
PMCID:
PMC2828731
Abstract Full Text PDF–818K
Measuring and Detecting Molecular Adaptation in Codon Usage Against Nonsense Errors During Protein Translation
Michael A. Gilchrist, Premal Shah, Russell Zaretzki
Genetics. 2009 December; 183(4): 1493–1505. doi: 10.1534/genetics.109.108209
PMCID:
PMC2787434
Abstract Full Text PDF–2.0M
Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA Sequencing
Takatsugu Kan, Bogdan C. Paun, Yuriko Mori, Fumiaki Sato, Zhe Jin, James P. Hamilton, Tetsuo Ito, Yulan Cheng, Stefan David, Alexandru V. Olaru, Jian Yang, Rachana Agarwal, John M. Abraham, Stephen J. Meltzer
Bioinform Biol Insights. 2007; 1: 1–16. Published online 2009 November 24.
PMCID:
PMC2287164
Abstract Full Text PDF–705K Supplementary Material
Universal function-specificity of codon usage
Hamed Shateri Najafabadi, Hani Goodarzi, Reza Salavati
Nucleic Acids Res. 2009 November; 37(21): 7014–7023. Published online 2009 November. doi: 10.1093/nar/gkp792
PMCID:
PMC2790905
Abstract Full Text PDF–8.3M Supplementary Material
Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin
Jesse D. Bloom, Matthew J. Glassman
PLoS Comput Biol. 2009 April; 5(4): e1000349. Published online 2009 April 17. doi: 10.1371/journal.pcbi.1000349
PMCID:
PMC2664478
Abstract Full Text PDF–1.4M
Translationally Optimal Codons Associate with Structurally Sensitive Sites in Proteins
Tong Zhou, Mason Weems, Claus O. Wilke
Mol Biol Evol. 2009 July; 26(7): 1571–1580. Published online 2009 April 6. doi: 10.1093/molbev/msp070
PMCID:
PMC2734146
Abstract Full Text PDF–234K Supplementary Material
Evidence of bias towards buffered codons in human transcripts
Rami N. Mahdi, Eric C. Rouchka
Proc IEEE Int Symp Signal Proc Inf Tech. Author manuscript; available in PMC 2010 July 10.
Published in final edited form as: Proc IEEE Int Symp Signal Proc Inf Tech. 2008 December 16; 2008: 29–34. doi: 10.1109/ISSPIT.2008.4775640
PMCID:
PMC2901532
Abstract Full Text PDF–444K
Detecting Clusters of Mutations
Tong Zhou, Peter J. Enyeart, Claus O. Wilke
PLoS ONE. 2008; 3(11): e3765. Published online 2008 November 19. doi: 10.1371/journal.pone.0003765
PMCID:
PMC2582452
Abstract Full Text PDF–1.7M Supplementary Material
Synonymous Genes Explore Different Evolutionary Landscapes
Guillaume Cambray, Didier Mazel
PLoS Genet. 2008 November; 4(11): e1000256. Published online 2008 November 14. doi: 10.1371/journal.pgen.1000256
PMCID:
PMC2575237
Abstract Full Text PDF–481K Supplementary Material
The Impact of the Nucleosome Code on Protein-Coding Sequence Evolution in Yeast
Tobias Warnecke, Nizar N. Batada, Laurence D. Hurst
PLoS Genet. 2008 November; 4(11): e1000250. Published online 2008 November 7. doi: 10.1371/journal.pgen.1000250
PMCID:
PMC2570795
Abstract Full Text PDF–324K Supplementary Material
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