http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2651.html
Network-based stratification of tumor mutations
Matan Hofree,
John P Shen,
Hannah Carter,
Andrew Gross
& Trey Ideker
Nature Methods(2013)doi:10.1038/nmeth.2651
Archive for the 'SciLit' Category
Network-based stratification of tumor mutations
September 21, 2013Distributed variation prefers the golden mean – Gene Expression | DiscoverMagazine.com
September 16, 2013#Variation prefers the golden mean: Moderate selection involves many loci v weak & strong, few http://bit.ly/18MgU6p via @drbachinsky
Moderate selection, many loci; Weak or strong selection, few loci.
http://blogs.discovermagazine.com/gnxp/2013/09/distributed-variation-prefers-the-golden-mean/#.UjJTHmSG1MF
Systematic identification of trans eQTLs as putative drivers of known disease associations
September 15, 2013http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2756.html
“They found SNPs that regulate one gene (Ikaros) in different cell types, meaning they found different cis-regulatory regions for a single gene, that map to different pathways…. they used the cell-type specific information from ENCODE data.”
Papers about retroduplications (variable pseudogenes)
September 13, 2013here are three more relevant papers about retroduplications :
http://www.nature.com/nmeth/journal/v9/n2/full/nmeth.1810.html http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003242 http://genomebiology.com/content/14/3/R22
Cancer on left and right sides
September 13, 2013I guess it is peer-reviewed paper
http://www.jaad.org/article/S0190-9622(10)00614-6/abstract
Skin cancer correlates with handedness of car driving
Human chimp increase in segmental duplications
September 1, 2013QT:”
Our results suggest that the evolutionary properties of copy-number mutation differ significantly from other forms of genetic mutation and, in contrast to the hominid slowdown of single-base-pair mutations, there has been a genomic burst of duplication activity at this period during human evolution.
”
http://www.nature.com/nature/journal/v457/n7231/full/nature07744.html
This is a paper on increased rates of segmental duplications along the lineage to human and chimp.
This should have some implications for pseudogene numbers between organisms.
GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations
September 1, 2013no website, github + readthedocs distribution
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003153
Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants : Nature : Nature Publishing Group
August 31, 2013QT:”
We estimate that approximately 73% of all protein-coding SNVs and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000–10,000 years.
”
6,515 #exomes reveals the recent origin of most human protein-coding variants: ~75% #SNVs arose in last ~7.5K yrs
http://www.nature.com/nature/journal/v493/n7431/full/nature11690.html
Analysis of the bread wheat genome using whole-genome shotgun sequencing : Nature : Nature Publishing Group
August 31, 2013The bread #wheat genome using… shotgun sequencing: ~5X human, from 3 diff. component genomes, many #pseudogenes
http://www.nature.com/nature/journal/v491/n7426/full/nature11650.html
Gene intolerance scores in a Plos Gen paper
August 26, 2013http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003709#pgen-1003709-g006
This paper discusses gene intolerance score — very similar to depletion of common polymorphisms. They don’t analyze non-coding regions — this is using exome data only. Blue for tolerant and red for intolerant (see Figure 1) .
linkstream2 microblog 