Archive for the 'SciLit' Category

expression patterns in brain

November 18, 2015

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: Origins of Affinity and Selectivity: Biophysical Journal

November 15, 2015

#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 Biomolecular Systems – The Journal of Physical Chemistry B (ACS Publications)

November 15, 2015

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

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.

Inference of human population history from individual whole-genome sequences : Nature : Nature Publishing Group

November 1, 2015

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

BMC Bioinformatics | Full text | QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments

November 1, 2015

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

LoRDEC: accurate and efficient long read error correction

October 27, 2015

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

proovread: large-scale high accuracy PacBio correction through iterative short read consensus

October 27, 2015

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

analogies between josephson junction linkage and huygens coupled pendulums

October 24, 2015

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

Huygens’s Clocks Revisited » American Scientist

October 24, 2015

http://www.americanscientist.org/issues/pub/huygenss-clocks-revisited