Posts Tagged ‘from’

Before I Go: A Stanford neurosurgeon’s parting wisdom about life and time – The Washington Post

Tuesday, September 22nd, 2015

Before I Go: A Stanford neurosurgeon’s parting wisdom https://www.washingtonpost.com/news/inspired-life/wp/2015/03/12/before-i-go-a-stanford-neurosurgeons-parting-wisdom-about-life-and-time/ Eloquent writing on the passing of time, in one’s final hours

QT:{{"
there are two strategies to cutting the time short, like the tortoise and the hare. The hare moves as fast as possible, hands a blur, instruments clattering, falling to the floor; the skin slips open like a curtain, the skull flap is on the tray before the bone dust settles. But the opening might need to be expanded a centimeter here or there because it’s not optimally placed. The tortoise proceeds deliberately, with no wasted movements, measuring twice, cutting once. No step of the operation needs revisiting; everything proceeds in orderly fashion. If the hare makes too many minor missteps and has to keep adjusting, the tortoise wins. If the tortoise spends too much time planning each step, the hare wins.

The funny thing about time in the OR, whether you frenetically race or steadily proceed, is that you have no sense of it passing. If boredom is, as Heidegger argued, the awareness of time passing, this is the opposite: The intense focus makes the arms of the clock seem arbitrarily placed. Two hours can feel like a minute.

But the years did, as promised, fly by. Six years passed in a flash, but then, heading into chief residency, I developed a classic constellation of symptoms — weight loss, fevers, night sweats, unremitting back pain, cough — indicating a diagnosis quickly confirmed: metastatic lung cancer. The gears of time ground down.

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Why Human Disease-Associated Residues Appear as the Wild-Type in Other Species: Genome-Scale Structural Evidence for the Compensation Hypothesis

Monday, September 14th, 2015

Why human disease-associated residues appear as WT in other species http://mbe.oxfordjournals.org/content/31/7/1787.abstract Compensation by their 3D structural neighbors

Useful NIH Funding Data on Bioinformatics Education

Sunday, September 6th, 2015

BD2K funded programs so far…
https://datascience.nih.gov/bd2k/funded-programs/enhancing-training/institutional-grants

NIGMS Comp Bio & Bioinfo funded predoctoral programs
http://www.nigms.nih.gov/Training/InstPredoc/Pages/PredocInst-Bioinformatics.aspx

THE NLM funded Biomedical Informatics training programs
https://www.nlm.nih.gov/ep/GrantTrainInstitute.html#5

Cell-of-origin chromatin organization shapes the mutational landscape of cancer : Nature : Nature Publishing Group

Wednesday, September 2nd, 2015

#Chromatin…shapes the mutational landscape of cancer
http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Low DNase correlates w/ high SNVs in melanoma. True generally?

GPS4CAM

Saturday, August 29th, 2015

http://gps4cam.com/

Isp-fellows another privacy tool

Friday, August 28th, 2015

Browse More Privately With the Privacy Badger

Jason B. Jones looks at a new plug-in from the Electronic Frontier Foundation that blocks companies from tracking your behavior across multiple sites.

http://chronicle.com/blogs/profhacker/browse-more-privately-with-the-privacy-badger/60825

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

Friday, August 28th, 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?

lof paper in Nat Gen

Friday, August 28th, 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

Single-cell chromatin accessibility reveals principles of regulatory variation : Nature : Nature Publishing Group

Friday, August 28th, 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

Multiple hypothesis testing in genomics – Goeman – 2014 – Statistics in Medicine – Wiley Online Library

Monday, August 17th, 2015

Multiple 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.
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