Photogs Who Risk Jail to Capture Crumbling #ColdWar Relics
http://www.wired.com/2014/06/the-cold-war-relics-three-photographers-are-documenting-before-they-disappear #Urbex #placehackers as archivists for massive US effort
might be fun to see the light at new subway, which certainly has handicap access
station is on 4,5, R + others & is slated to open soon (fall ’14)?
http://www.wired.com/2014/06/new-york-subway-2/
http://en.wikipedia.org/wiki/Fulton_Center
http://www.nytimes.com/2014/06/24/nyregion/mta-says-transit-plans-are-facing-new-delays.html
#Exome sequencing & #genetic basis of complex traits
http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html Key pt: amt of rare variants exceeds that from neutral model
Kiezun A, Garimella K, Do R, Stitziel NO, Neale BM, McLaren PJ, Gupta N, Sklar P, Sullivan PF, Moran JL, Hultman CM, Lichtenstein P, Magnusson P, Lehner T, Shugart YY, Price AL, de Bakker PI, Purcell SM, Sunyaev SR. Exome sequencing and the genetic basis of complex traits. Nature Genetics (2012) 44: 623-630
SUMMARY
This article serves as part review, and part research article, focusing on using exome sequencing to detect associations between variants and complex traits.
An important fact they point out, with a wide range of implications for studying disease, is that the number of rare variants exceeds the number predicted by the neutral model. Figure 1 illustrates nicely this excess of rare variants.
I agree with their statement that the majority of these mutations are not “neutral”. They attribute this excess to population expansion or purifying selection, but a plausible explanation that explains this excess, which is found in all organisms regardless of demographic history, is linked selection.
The authors compare statistics derived before and after filtering exome sequencing data of 438 individuals (HIV and Scizophrenia data-sets), illustrating the importance of filtering in obtaining high quality calls. WGS (CGI data on 37 individuals) was used as a benchmark for the number of called SNP counts of different categories (silent, missense, nonsense).
They then proceed to analyze the affect of population stratification on significance values by combining different ratios of individuals from the European-American HIV cohort and the Swedish schizophrenia cohort. (Theory predicts that older populations should have more rare variants because recombination has had more time to break up linkage blocks, and because newer populations have most likely gone through homogenizing bottlenecks.) They find that calculating p-values using a permutation test provides fewer type I errors (false positives), and that this technique can competently deal with population
stratification when conducting association studies.
Billionaire Mathematician’s Life
http://www.nytimes.com/2014/07/08/science/a-billionaire-mathematicians-life-of-ferocious-curiosity.html “I wasn’t the fastest guy…but I like to ponder[;] turns out to be…pretty good.”
A Billionaire Mathematician’s Life of Ferocious Curiosity
http://www.nytimes.com/2014/07/08/science/a-billionaire-mathematicians-life-of-ferocious-curiosity.html
QT:{{
“I wasn’t the fastest guy in the world,” Dr. Simons said of his youthful math enthusiasms. “I wouldn’t have done well in an Olympiad or a math contest. But I like to ponder. And pondering things, just sort of thinking about it and thinking about it, turns out to be a pretty good approach.”
}}
#Scottish nationalism: How did it come to this?
http://www.economist.com/news/britain/21606865-confluence-historical-forces-north-sea-oil-and-absent-minded-politicians-has-put-britains Overview of sides in 9/18 referendum HT @benedictpringle
I took lots of notes at ISMB 2014. I saved “public” versions of these as a storified tweet-stream, viz:
https://storify.com/markgerstein/tweet-related-to-ismb-2014-i0imsb14-i0afpsig-ismb
I also tagged lots of sites & papers that I discovered at the meeting, viz:
http://linkstream2.gerstein.info/tag/i0ismb14
http://linkstream2.gerstein.info/tag/i0afpsig
http://www.iscb.org/ismb2014 [Main meeting]
http://biofunctionprediction.org/node/7 [AFP SIG]
Below is key ref.
## From Brenner talk at ISMB:
Argues that domain trunc prot have a dom. neg pheno.
(ex binding domain for reg & tf or sox10)
NMD fixes this; truncated case now looks like hemizyg.
## Related twitter dialogue:
Brenner: expl. how premature truncation is often a dominant neg. (ex SOX10), providing a rationalization for the purpose of NMD #ISMB #LBR01
@rtraborn · Jul 13
Why would cells generate mRNA that are then immediately degraded by NMD? Brenner suggests that this process has a regulatory function #ISMB
@raarjr · Jul 13
Brenner: 50 nt rule accurately predicts NMD, and is prevalent in auto regulation.so what’s our ruler? #ismb
## REF
http://www.ncbi.nlm.nih.gov/pubmed/9862469
Mol Gen Genet. 1998 Nov;260(2-3):176-84.
mRNA surveillance mitigates genetic dominance in Caenorhabditis elegans.
Cali BM, Anderson P.
Linial: ClanTox (www.clantox.cs.huji.ac.il) to classify short peptides as toxins. #ismb #kn1
TOLIPS relevant to brain, neuropeptides
Linial mentions NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes
http://bioinformatics.oxfordjournals.org/content/early/2014/03/05/bioinformatics.btt725.abstract #ismb #kn1