linkstream2 microblog

Dynamics of genomic clones in breast #cancer PDX at #singlecell resolution http://www.nature.com/nature/journal/v518/n7539/full/nature13952.html Extensive trees of samples & some WGS

Peter Eirew,
Adi Steif,
Jaswinder Khattra,
Gavin Ha,
…
Jazmine Brimhall,
Arusha Oloumi,
Tomo Osako
et al.

Nature 518, 422–426 (19 February 2015) doi:10.1038/nature13952

#SingleCell #RNASeq Reveals Dynamic, Random Monoallelic Gene Expression, occurring in ~20% of genes in mice cells
http://science.sciencemag.org/content/343/6167/193.abstract

Folding by Chaperones Accelerates Evolutionary Dynamics
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003269 Multiscale models link NT mutations, PPIs & cell populations

Celltype & region–resolved mouse brain proteome
http://www.nature.com/neuro/journal/v18/n12/full/nn.4160.html proteins enriched there v liver & in specific regions (eg NCX v STR)

http://www.nature.com/neuro/journal/v18/n12/full/nn.4160.html

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.

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

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

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

#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?

#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