## Archive for the 'SciLit' Category

### Chromatin states define tumour-specific T cell dysfunction and reprogramming | Nature

November 19, 2017### PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF | Bioinformatics | Oxford Academic

November 19, 2017### Quantifying the local resolution of cryo-EM density maps | Nature Methods

November 14, 2017Quantifying the local resolution of #cryoEM density maps

https://www.Nature.com/articles/nmeth.2727 “Theory…based on the following idea: a L Angstrom feature exists at a pt…if a 3D local sinusoid of wavelength L is statistically detectable above noise at that point.”

QT:{{”

We propose a mathematical theory and an efficient algorithm for measuring local resolution that address all of the above limitations. The theory (Online Methods) is based on the following idea: a λ-Å feature exists at a point in the volume if a three-dimensional (3D) local sinusoid of wavelength λ is statistically detectable above noise at that point. A likelihood-ratio hypothesis test of the local sinusoid versus noise can detect this feature at a given P value (typically P = 0.05). We define the local resolution at a point as the smallest λ at which the local sinusoid is detectable, and we account for multiple testing with an FDR procedure.

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### Alignment-free sequence comparison: benefits, applications, and tools

November 12, 2017Might be useful for noncoding comparisons

Alignment-free seq. comparison: benefits, apps & tools

https://GenomeBiology.biomedcentral.com/articles/10.1186/s13059-017-1319-7 Great tidbits, viz: Shannon asked von Neumann what to call his info measure – “Why don’t you call it entropy…no one understands entropy…so in any discussion, you’ll be in a position of advantage.”

QT:{{”

“Reportedly, Claude Shannon, who was a mathematician working at Bell Labs, asked John von Neumann what he should call his newly developed measure of information content; “Why don’t you call it entropy,” said von Neumann, “[…] no one understands entropy very well so in any discussion you will be in a position of advantage […]” []. The concept of Shannon entropy came from the observation that some English words, such as “the” or “a”, are very frequent and thus unsurprising” ….

“The calculation of a distance between sequences using complexity (compression) is relatively straightforward (Fig. ). This procedure takes the sequences being compared (x = ATGTGTG and y = CATGTG) and concatenates them to create one longer sequence (xy = ATGTGTGCATGTG). If x and y are exactly the same, then the complexity (compressed length) of xy will be very close to the complexity of the individual x or y. However, if x and y are dissimilar, then the complexity of xy (length of compressed xy) will tend to the cumulative complexities of x and y.”

…

“Intriguingly, BLOSUM matrices, which are the most commonly used substitution matrix series for protein sequence alignments, were found to have been miscalculated years ago and yet produced significantly better alignments than their corrected modern version (RBLOSUM) []; this paradox remains a mystery.”

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### Fast search of thousands of short-read sequencing experiments : Nature Biotechnology : Nature Research

November 5, 2017### SEQSpark: A Complete Analysis Tool for Large-Scale Rare Variant Association Studies Using Whole-Genome and Exome Sequence Data: The American Journal of Human Genetics

November 5, 2017http://www.cell.com/ajhg/fulltext/S0002-9297(17)30235-5