The most incompressible metal Os at… >750 GPa
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14681.html Surprisingly, core rather than valence electrons affected by pressure
Archive for the 'SciLit' Category
The most incompressible metal osmium at static pressures above 750 gigapascals : Nature : Nature Publishing Group
August 31, 2015Endosymbiotic origin and differential loss of eukaryotic genes : Nature : Nature Publishing Group
August 28, 2015Endosymbiotic origin & differential loss of eukaryotic
geneshttp://www.nature.com/nature/journal/v524/n7566/full/nature14963.html For Euks, horizontal transfer is episodic (v continuous)
DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data
August 28, 2015DeconRNASeq…framework for #deconvolution of heterogeneous tissue samples http://bioinformatics.oxfordjournals.org/content/29/8/1083.long “App note” w/ very concise code snippet
30 lines of R?
The genetics of Mexico recapitulates Native American substructure and affects biomedical traits
August 28, 2015[Population] genetics of Mexico by @cdbustamante lab
http://www.sciencemag.org/content/344/6189/1280.abstract Has groups as divergent from each other as Europeans v Asians
QT:{{”
We found striking genetic stratification among indigenous populations within Mexico at varying degrees of geographic isolation. Some groups were as differentiated as Europeans are from East Asians.
Pre-Columbian genetic substructure is recapitulated in the indigenous ancestry of admixed mestizo individuals across the country.
The genetics of indigenous Mexicans exhibit substantial geographical structure, some as divergent from each other as are existing populations of Europeans and Asians.
“}}
lof paper in Nat Gen
August 28, 2015Analysis of #LOF variants & 20 risk factor phenotypes in 8.6K individuals identifies loci [both well known & new]
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3270.html
NATURE GENETICS | LETTER
Analysis of loss-of-function variants and 20 risk factor phenotypes in 8,554 individuals identifies loci influencing chronic disease
Alexander H Li,
Alanna C Morrison,
Christie Kovar,
L Adrienne Cupples,
Jennifer A Brody,
Linda M Polfus,
Bing Yu,
Ginger Metcalf,
Donna Muzny,
Narayanan Veeraraghavan,
Xiaoming Liu,
Thomas Lumley,
Thomas H Mosley,
Richard A Gibbs
& Eric Boerwinkle
Single-cell chromatin accessibility reveals principles of regulatory variation : Nature : Nature Publishing Group
August 28, 2015#SingleCell chromatin accessibility
http://www.nature.com/nature/journal/v523/n7561/full/nature14590.html >1.6k ATAC-seq expts; many on @ENCODE_NIH cell lines H1, GM12878 & K562
Lanosterol reverses protein aggregation in cataracts : Nature : Nature Publishing Group
August 17, 2015Lanosterol reverses protein aggregation in cataracts
http://www.nature.com/nature/journal/v523/n7562/full/nature14650.html A finding from rare-disease #exome sequencing cc @solvemendelian
QT:{{”
…Lanosterol is an
amphipathic molecule enriched in the lens. It is synthesized by lanosterol synthase (LSS) in a key cyclization reaction of a cholesterol synthesis pathway. Here we identify two distinct homozygousLSS missense mutations (W581R and G588S) in two families with extensive congenital cataracts. Both of these mutations affect highly conserved amino acid residues and impair key catalytic functions of LSS. Engineered expression of wild-type, but not mutant, LSSprevents intracellular protein aggregation of various
cataract-causing mutant crystallins.
“}}
Multiple hypothesis testing in genomics – Goeman – 2014 – Statistics in Medicine – Wiley Online Library
August 17, 2015Multiple hypothesis testing in genomics
http://onlinelibrary.wiley.com/doi/10.1002/sim.6082/full Nice overview, comparing familywise error & FDR control + FDP estimation
http://www.few.vu.nl/~mavdwiel/HDDA/tutorial_multtest.pdf
QT:{{”
This paper presents an overview of the current state-of-the-art in multiple testing in genomics data from a user’s perspective. We describe methods for familywise error control, false discovery rate control and false discovery proportion estimation and confidence, both conceptually and practically, and explain when to use which type of error rate. We elaborate the assumptions underlying the methods, and discuss pitfalls in the interpretation of results. In our discussion we take into account the exploratory nature of genomics experiments, looking at selection of genes before or after testing, and at the role of validation experiments.
“}}
Glypican-1 identifies cancer exosomes and detects early pancreatic cancer : Nature : Nature Publishing Group
August 16, 2015[Protein] Glypican-1 [uniquely] identifies [circulating] cancer #exosomes & detects…cancer
http://www.nature.com/nature/journal/v523/n7559/full/nature14581.html Maybe also for @exRNA
QT:{{”
Exosomes are lipid-bilayer-enclosed extracellular vesicles that contain proteins and nucleic acids. They are secreted by all cells and circulate in the blood. Specific detection and isolation of
…we identify a cell surface
proteoglycan, glypican-1 (GPC1), specifically enriched on
cancer-cell-derived exosomes. GPC1+ circulating exosomes (crExos) were monitored …”}}
http://www.nature.com/nature/journal/v523/n7559/full/nature14581.html
A naturally occurring variant of the human prion protein completely prevents prion disease : Nature : Nature Publishing Group
August 14, 2015Natural variant of the…#prion protein [G127V] completely
prevents…disease
http://www.nature.com/nature/journal/v522/n7557/full/nature14510.html Under pos. selection for kuru afflicted
QT:{{”
A novel PrP variant, G127V, was under positive evolutionary selection during the epidemic of kuru—an acquired prion disease epidemic of the Fore population in Papua New Guinea—and appeared to provide strong protection against disease in the heterozygous state2. Here we have investigated the protective role of this variant and its interaction with the common, worldwide M129V PrP polymorphism. V127 was seen exclusively on a M129 PRNP allele. We demonstrate that transgenic mice expressing both variant and wild-type human PrP are completely resistant to both kuru…”
“}}
linkstream2 microblog 