I recently have noticed on several occasions that the style files in Endnote don't fit the journal requirement. For example, the reference formats for Trends in Genetics and Nucleic Acids Research are just WRONG.
I am using Endnote 7 for Mac. Not sure if others meet similar problems with Endnote.
It seems reasonable to be cautious about Endnote.
Please read our preprint deposited at Genome Biology. Please share your comments here, or by email.
Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences
Yi Xing and Christopher Lee
Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles,CA 90095-1570, USA
Correspondence: Christopher Lee. E-mail: leec@mbi.ucla.edu
Recently, it was proposed that alternative splicing may act as a mechanism for opening accelerated paths of evolution, by reducing negative selection pressure, but there has been little evidence so far whether this could produce adaptive benefit. Here we employ metrics of very different types of selection pressures (e.g. against amino acid mutations (Ka/Ks); against mutations at synonymous sites (Ks); and for protein reading-frame preservation) to address this question via genome-wide analyses of human, chimpanzee, mouse, and rat. These data show that alternative splicing relaxes Ka/Ks selection pressure up to seven-fold, but intriguingly that this effect is accompanied by a strong increase in selection pressure against synonymous mutations, which propagates into the adjacent intron, and correlates strongly with the alternative splicing level observed for each exon. These effects are highly local to the alternatively spliced exon. Comparisons of these four genomes consistently show an increase in the density of amino acid mutations (Ka) in alternatively spliced exons, and a decrease in the density of synonymous mutations (Ks). This selection pressure against synonymous mutations in alternatively spliced exons was accompanied in all four genomes by a striking increase in selection pressure for protein reading-frame preservation, and both increased markedly with increasing evolutionary age. Restricting our analysis to a subset of exons with strong evidence for biologically functional alternative splicing produced identical results. Thus alternative splicing apparently can create evolutionary “hotspots” within a protein sequence, and these events have evidently been selected for during mammalian evolution.
The final program and presentations have been put up by NAS here.
The audio streams for most talks are up. You can click "Presentation" to listen to them.
This is a very nice meeting. Enjoy!
Frontiers in Bioinformatics: Unsolved Problems and Challenges
Organized by Samuel Karlin, David Eisenberg and Russ Altman
Auditorium, Beckman Center of the National Academies
100 Academy Drive, Irvine, CA
October 16-17, 2004
Monday, April 4th,2005
Hopefully I'll deliver a good talk!
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