Genome Biology

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Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals

JV Chamary and Laurence D Hurst*

Genome Biology 2005, 6:R75 doi:10.1186/gb-2005-6-9-r75

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BioMed Central: 11 citations

Research article   Open Access

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 Genetics 2010, 11:23 (15 April 2010)

Research article   Open Access

Ultraconserved coding regions outside the homeobox of mammalian Hox genes

Zhenguo Lin, Hong Ma, Masatoshi Nei BMC Evolutionary Biology 2008, 8:260 (24 September 2008)

Research article   Open Access

Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures

Nina Stoletzki BMC Evolutionary Biology 2008, 8:224 (31 July 2008)

Research   Open Access

Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases

Jan C Biro Theoretical Biology and Medical Modelling 2008, 5:14 (29 July 2008)

Research article   Open Access

Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures

Jason M Bechtel, Thomas Wittenschlaeger, Trisha Dwyer, Jun Song, Sasi Arunachalam, Sadeesh K Ramakrishnan, Samuel Shepard, Alexei Fedorov BMC Genomics 2008, 9:284 (12 June 2008)

Research article   Open Access

Positive selection for unpreferred codon usage in eukaryotic genomes

Daniel E Neafsey, James E Galagan BMC Evolutionary Biology 2007, 7:119 (18 July 2007)

Research article   Open Access Highly Accessed

Chromatin structure and evolution in the human genome

James GD Prendergast, Harry Campbell, Nick Gilbert, Malcolm G Dunlop, Wendy A Bickmore, Colin AM Semple BMC Evolutionary Biology 2007, 7:72 (9 May 2007)

Transcriptionally active 'open' chromatin and more inert 'closed' regions each have distinct gene mutation rates that may reflect differences in selection pressure and variation in their rates of DNA damage or DNA repair.

Research   Open Access

Developmental stage related patterns of codon usage and genomic GC content: searching for evolutionary fingerprints with models of stem cell differentiation

Lichen Ren, Ge Gao, Dongxin Zhao, Mingxiao Ding, Jingchu Luo, Hongkui Deng Genome Biology 2007, 8:R35 (12 March 2007)

Developmental-stage-related patterns of gene expression correlate with codon usage and genomic GC content in stem cell hierarchies.

Research article   Open Access

Strand bias in complementary single-nucleotide polymorphisms of transcribed human sequences: evidence for functional effects of synonymous polymorphisms

Hui-Qi Qu, Steve G Lawrence, Fan Guo, Jacek Majewski, Constantin Polychronakos BMC Genomics 2006, 7:213 (17 August 2006)

Research   Open Access

Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species

Makedonka Mitreva, Michael C Wendl, John Martin, Todd Wylie, Yong Yin, Allan Larson, John Parkinson, Robert H Waterston, James P McCarter Genome Biology 2006, 7:R75 (14 August 2006)

A codon usage table for 32 nematode species is presented and suggests that total genomic GC content drives codon usage.

Methodology article   Open Access

Genetic algorithm learning as a robust approach to RNA editing site prediction

James Thompson, Shuba Gopal BMC Bioinformatics 2006, 7:145 (16 March 2006)