http://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.”
here 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
I 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
QT:”
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.
no website, github + readthedocs distribution
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003153
QT:”
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
The 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
http://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) .
Y sequencing by Page et al.
Arch Pathol Lab Med. 2009 Sep;133(9):1463-7. doi: 10.1043/1543-2165-133.9.1463.
Henrietta Lacks, HeLa cells, and cell culture contamination.
Lucey BP, Nelson-Rees WA, Hutchins GM.