linkstream2 microblog

Treefinder Retraction Note [interestingly, done editorially due to change in software-license terms] http://www.biomedcentral.com/1471-2148/15/243 HT @bornalibran

Canonical genetic signatures [across 132 structures] of the adult human #brain [in 6 individuals]
http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4171.html HT @ozgunharmanci

QT:{{”
We applied a correlation-based metric called differential stability to assess reproducibility of gene expression patterning across 132 structures in six individual brains, revealing mesoscale genetic organization. The genes with the highest differential stability are highly biologically relevant, with enrichment for brain-related annotations, disease associations, drug targets and literature citations.
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#Thermodynamics of Antimicrobial Lipopeptide Binding to Membranes http://www.cell.com/biophysj/abstract/S0006-3495(14)00928-X Non-human selectivity studied w. coarse-grained MD

A Multiscale Coarse-Graining Method for Biomolecul[es] http://pubs.acs.org/doi/abs/10.1021/jp044629q Simplified force field from fitting to all-atom #simulations

Sergei Izvekov and Gregory A. Voth *
J. Phys. Chem. B, 2005, 109 (7), pp 2469–2473
DOI: 10.1021/jp044629q

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.

http://www.nature.com/nature/journal/v475/n7357/full/nature10231.html

http://www.biomedcentral.com/1471-2105/16/224

http://bioinformatics.oxfordjournals.org/content/early/2014/08/27/bioinformatics.btu538.long

http://bioinformatics.oxfordjournals.org/content/early/2014/07/10/bioinformatics.btu392

QT:{{”
In 1665, Christiaan Huygens [Huygens, 1673] noted “When we suspended two clocks so constructed from two hooks imbedded in the same wooden beam, the motions of each pendulum on opposite swings were so much in agreement that they never receded the least bit from each other and the sound of each was always heard simultaneously. Further, if this agreement was disturbed by some interference, it reestablished itself in a short time. For a long time I was amazed at this unexpected result, but after a careful examination finally found that the cause of this is due to the motion of the beam, even though this is hardly perceptible. The cause is that the oscillations of the pendula, in proportion to their weight, communicate some motion to the clocks. This motion, impressed onto the beam, necessarily has the effect of making the pendula come to a state of exactly contrary swings if it happened that they moved otherwise at first, and from this finally the motion of the beam completely ceases.” The study of coupled
oscillators has since become an active branch of mathematics, with applications in physics, biology, and chemistry. In physics, one encounters coupled oscillators in arrays of Josephson junctions [Chung et al., 1989, Blackburn et al., 1994], in modelling molecules [Sage, 1994], and in coupled lasers [Dente et al., 1990]. Coupled oscillators are also prevalent in biological systems. Most organisms appear to be coupled to various periodicities extant in our surroundings, such as the rotation of the earth about the sun, the alternation of night and day, or the tides. Not only do organisms exhibit periodicities due to their environment, but they also exhibit innate periodic behavior. Breathing, pumping blood, chewing, and galloping are examples of rhythmic patterns of motion…
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http://web.cse.ohio-state.edu/pnl/theses/campbell/Ch1.pdf