DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data

August 28, 2015

DeconRNASeq…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, 2015

Analysis 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


Eye Shape May Help Distinguish Predator From Prey

August 28, 2015

#Eye Shape May Help Distinguish Predator From Prey
http://www.nytimes.com/2015/08/08/science/eye-shape-may-help-distinguish-predator-from-prey.html Vertical v horzonital slits, resp., for depth v field-of-view

QT:{{”
“Why do the eyes of some animals, including goats, have
horizontal-shaped pupils, while others, such as rattlesnakes and domestic cats, have vertical slits?

It is a question that has longed intrigued researchers, and a study of 214 species published Friday suggests the answer may be strongly linked to giving animals a survival edge: vertical pupils and circular pupils help certain predators hunt, while horizontal pupils help other species spot predators from afar.”
“}}


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


We’ll see you, anon

August 28, 2015

We’ll see you, anon
http://www.economist.com/news/science-and-technology/21660966-can-big-databases-be-kept-both-anonymous-and-useful-well-see-you-anon “A dilemma. People want perfect #privacy & all the benefits of openness.” Math to the rescue?

Good for an intro. on privacy & attacks

QT:{{”

This is a true dilemma. People want both perfect privacy and all the benefits of openness. But they cannot have both.

“While some level of anonymisation will remain part of any resolution of the dilemma, mathematics may change the overall equation. One approach that would shift the balance to the good is homomorphic encryption, whereby queries on an encrypted data set are themselves encrypted. The result of any inquiry is the same as the one that would have been obtained using a standard query on the unencrypted database, but the questioner never sets eyes on the data. Or there is secure multiparty computation, in which a database is divided among several repositories. Queries are thus divvied up so that no one need have access to the whole database.

These approaches are, on paper, absolute in their protections. But putting them to work on messy, real-world data is proving tricky. Another set of techniques called differential privacy seems further ahead. The idea behind it is to ensure results derived from a database would look the same whether a given individual’s data were in it or not. It works by adding a bit of noise to the data in a way that does not similarly fuzz out the statistical results.


America’s Census Bureau has used differential privacy in the past for gathering commuters’ data. Google is employing it at the moment as part of a project in which a browser plug-in gathers lots of data about a user’s software, all the while guaranteeing anonymity. Cynthia Dwork, a differential-privacy pioneer at Microsoft Research, suggests a more high-profile proving ground would be data sets—such as some of those involving automobile data or genomes—that have remained locked up because of privacy concerns.”
“}}


Science Isn’t Broken | FiveThirtyEight

August 22, 2015

Science Isn’t Broken by @cragcrest
http://fivethirtyeight.com/features/science-isnt-broken Great (but cynical) description of “p-hacking” & “researcher degrees of freedom”


Stop Universities From Hoarding Money – The New York Times

August 22, 2015

http://www.nytimes.com/2015/08/19/opinion/stop-universities-from-hoarding-money.html?_r=0


Article: Illumina CEO Jay Flatley Launches Helix to Stoke Consumer Use of Genomic Data

August 22, 2015

http://www.technologyreview.com/news/540711/inside-illuminas-plans-to-lure-consumers-with-an-app-store-for-genomes/


Modern Lessons from Ancient Food Webs » American Scientist

August 22, 2015

Modern Lessons from [reconstructing] Ancient Food Webs http://www.americanscientist.org/issues/feature/2015/3/modern-lessons-from-ancient-food-webs/1 Overall #network structure (eg degree dist.) fairly invariant


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