Posts Tagged ‘from’

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells : Nature Biotechnology : Nature Publishing Group

November 14, 2015

Heterogeneity in #singlecell RNAseq…hidden subpopulations by @OliverStegle lab http://www.nature.com/nbt/journal/v33/n2/full/nbt.3102.html scLVM corrects for cell cycle phase

Buettner, Florian, Kedar N. Natarajan, F. Paolo Casale, Valentina
Proserpio, Antonio Scialdone, Fabian J. Theis, Sarah A. Teichmann,
John C. Marioni, and Oliver Stegle. "Computational analysis of
cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals
hidden subpopulations of cells." Nature biotechnology 33, no. 2
(2015): 155-160.

Single-cell ChIP-seq

October 23, 2015

#Singlecell ChIPseq reveals…subpopulations defined by chromatin statehttp://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3383.html Sparse data: on order of 1K uniq. reads/cell

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3383.html

Panorama of ancient metazoan macromolecular complexes : Nature : Nature Publishing Group

September 26, 2015

Panorama of ancient metazoan #macromolecular complexes
http://www.nature.com/nature/journal/v525/n7569/abs/nature14877.html Finding many more #complexes from integrating many co-elutions

http://www.nature.com/nature/journal/v525/n7569/full/nature14877.html#affil-auth

Commonly Taught Bioinformatics Topics, Derived from Syllabi of 19 Universities.

September 24, 2015

A Helpful Reference

https://apps.lis.illinois.edu/wiki/download/attachments/4369699/curriculum+analysis.doc?version=4

IBM Research: Preserving Validity in Adaptive Data Analysis

September 23, 2015

Preserving Validity in Adaptive Data Analysis http://ibmresearchnews.blogspot.com/2015/08/preserving-validity-in-adaptive-data_6.html Using differential #privacy for correct #stats even w/ test-set reuse

QT:{{"
“A common next step would be to use the least-squares linear regression to check whether a simple linear combination of the three strongly correlated foods can predict the grade. It turns out that a little combination goes a long way: we discover that a linear combination of the three selected foods can explain a significant fraction of variance in the grade (plotted below). The regression analysis also reports that the p-value of this result is 0.00009 meaning that the probability of this happening purely by chance is less than 1 in 10,000.

Recall that no relationship exists in the true data distribution, so this discovery is clearly false. This spurious effect is known to experts as Freedman’s paradox. It arises since the variables (foods) used in the regression were chosen using the data itself.


We found that challenges of adaptivity can be addressed using techniques developed for privacy-preserving data analysis. These techniques rely on the notion of differential privacy that guarantees that the data analysis is not too sensitive to the data of any single individual. We rigorously demonstrated that ensuring differential privacy of an analysis also guarantees that the findings will be statistically valid. We then also developed additional approaches to the problem based on a new way to measure how much information an analysis reveals about a dataset.

The Thresholdout Algorithm

Using our new approach we designed an algorithm, called Thresholdout, that allows an analyst to reuse the holdout set of data for validating a large number of results, even when those results are produced by an adaptive analysis.

"}}

Punctuated equilibrium in the large-scale evolution of programming languages | Journal of The Royal Society Interface

September 22, 2015

Punctuated equilibrium in the large-scale #evolution of #programming languages http://rsif.royalsocietypublishing.org/content/12/107/20150249 Clustering groups these into trees

Punctuated equilibrium in the large-scale evolution of programming languages
Sergi Valverde, Ricard V. Solé

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

September 22, 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.

"}}

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

September 14, 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

September 6, 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

September 2, 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?