linkstream2 microblog

~8%

http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004525

High-throughput functional testing of ENCODE segmentation predictions

http://genome.cshlp.org/content/early/2014/07/17/gr.173518.114.abstract?papetoc

Interesting but addressing mappability issue is key! Might want to also use a non-analytic stat test….
Compared to wavelets, non-independence betw. scales, perhaps key for allowing pruning.

Multiscale representation of #genomic signals. Fold changes & peaks at different scales; better expression prediction
http://www.nature.com/nmeth/journal/v11/n6/full/nmeth.2924.html

DUX4 binding to #retroelements creates promoters that are active… Highlights #chipseq binding sites in #repeats
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003947 http://www.ncbi.nlm.nih.gov/pubmed/?term=24278031
PLoS Genet. 2013 Nov;9(11):e1003947. doi:
10.1371/journal.pgen.1003947. Epub 2013 Nov 21.
DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis.
Young JM, Whiddon JL, Yao Z, Kasinathan B, Snider L, Geng LN, Balog J, Tawil R, van der Maarel SM, Tapscott SJ.

Deletion of introns and other intergenic regions

Total Synthesis of a Functional Designer Eukaryotic Chromosome

http://www.sciencemag.org/content/early/2014/03/26/science.1249252

http://syntheticyeast.org/

QT:{{”
We found that ~15% of human codons are dual-use codons (“duons”) that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias.
“}}

http://www.sciencemag.org/content/342/6164/1325.summary
http://www.sciencemag.org/content/342/6164/1367.abstract

Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions
L Ward & M Kellis
http://www.sciencemag.org/content/337/6102/1675.abs

In general we know that conservation across species and within humans are correlated. In this paper the authors focus on emphasize the exceptions to this trend. They show that although only ~5% of the human genome is conserved across mammals, regulatory regions in an additional 4% of the genomes are conserved amongst humans. They also show that some elements are conserved across mammals but lack functional activity from ENCODE data and also do not show purifying selection amongst humans. The authors pinpoint regulatory regions near color vision and nerve-growth genes for that show human-specific constraint. This has been criticized in various publications since there are other genes that are higher up in the authors’ list but harder to explain for lineage-specific constraint.

http://www.ncbi.nlm.nih.gov/pubmed/23925245

Contains a personal-genome like construction for HeLa
with 100X shotgun and then paired ends used for variant discovery and sequencing of pools of fosmid clones for haplotype resolution. Finally, low-freq. somatic and passage variants layered onto this.

Haplotype-resolved genome… of #HeLa: Has mapping of #ENCODE RNA- & chIP-seq against a personal genome
http://dx.doi.org/10.1038/nature12213 via @aemonten

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.”

Mattick & Dinger
The extent of functionality in the human genome
http://www.thehugojournal.com/content/7/1/2/