http://www.nature.com/ng/journal/v49/n5/full/ng.3818.html
Ref component analysis..of transcriptomes, by @Robson_Paul &co http://www.Nature.com/ng/journal/v49/n5/full/ng.3818.html Clustering similarity of samples to tissue references
Archive for the 'SciLit' Category
Evolution of Bow-Tie Architectures in Biology
April 28, 2017Evolution of BowTie Architectures http://journals.PLOS.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004055 3-layer, in-mid-out systems can have small a waist when their goal is compressible
Aging increases cell-to-cell transcriptional variability upon immune stimulation | Science
April 21, 2017#Aging increases cell-to-cell transcriptional variability upon immune stimulation, but just for 225 up-reg. genes http://science.ScienceMag.org/content/355/6332/1433
Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression: Cell
April 16, 2017"Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression"
(http://www.sciencedirect.com/science/article/pii/S0092867417301289)
#Neanderthal-Introgressed Sequences [&]…Gene Expression http://www.Cell.com/cell/abstract/S0092-8674(17)30128-9?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867417301289%3Fshowall%3Dtrue ASE for Hn SNPs shows lower #brain expression vs reference
The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery. – PubMed – NCBI
April 16, 2017#IHEC: A Blueprint for…Collab. & Discovery
http://www.Cell.com/cell/abstract/S0092-8674(16)31528-8?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867416315288%3Fshowall%3Dtrue Summary bullets on heterogeneity, disease, rel. to SNPs, comp. tools
NAR Breakthrough Article: denovo-db: a compendium of human de novo variants
April 3, 2017.@denovodb: a compendium of [initially ~33K] human de novo variants w. phenotype, freely downloadable as a TSV table
https://academic.OUP.com/nar/article-lookup/doi/10.1093/nar/gkw865
QT:{{”
As of July 2016, denovo-db contained 40 different studies and 32,991 de novo variants from 23,098 trios. Database features include basic variant information (chromosome location, change, type); detailed annotation at the transcript and protein levels; severity scores; frequency; validation status; and, most importantly, the phenotype of the individual with the variant.
“}}
denovo-db.gs.washington.edu/denovo-db/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210614/
Network analytics in the age of big data | Science
April 2, 2017#Network analytics in the age of #BigData
http://science.ScienceMag.org/content/353/6295/123.full Emphasizes analyzing connectivity of graph structures (eg motifs) v nodes
QT:{{”
To mine the wiring patterns of networked data and uncover the functional organization, it is not enough to consider only simple descriptors, such as the number of interactions that each entity (node) has with other entities (called node degree), because two networks can be identical in such simple descriptors, but have a very different connectivity structure (see the figure). Instead, Benson et al. use higher-order descriptors called graphlets (e.g., a triangle) that are based on small subnetworks obtained on a subset of nodes in the data that contain all interactions that appear in the data (3). They identify network regions rich in instances of a particular graphlet type, with few of the instances of the particular graphlet crossing the boundaries of the regions. If the graphlet type is specified in advance, the method can uncover the nodes interconnected by it, which enabled Benson et al. to group together 20 neurons in the nematode worm neuronal network that are known to control a particular type of movement. In this way, the method unifies the local wiring patterning with higher-order structural modularity imposed by it, uncovering higher-order functional regions in networked data. “}}
whole genome assembly from Hi-C data
April 2, 2017De novo assembly of the A aegypti genome using #HiC, by @erezaterez et al http://science.ScienceMag.org/content/early/2017/03/22/science.aal3327.full Works on human too, w. promise for #SVs
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
Olga Dudchenko1,2,3,4,
Sanjit S. Batra1,2,3,*,
Arina D. Omer1,2,3,*,
Sarah K. Nyquist1,3,
Marie Hoeger1,3,
Neva C. Durand1,2,3,
Muhammad S. Shamim1,2,3,
Ido Machol1,2,3,
Eric S. Lander5,6,7,
Aviva Presser Aiden1,2,8,9,
Erez Lieberman Aiden1,2,3,4,5,†
Science 23 Mar 2017:
eaal3327
DOI: 10.1126/science.aal3327
on whole genome assembly from Hi-C reads. There is also some info on chromosomal rearrangement from Hi-C.
Mechanisms underlying structural variant formation in genomic disorders : Nature Reviews Genetics : Nature Publishing Group
April 1, 2017Mechanisms underlying #SV formation in…disorders
http://www.Nature.com/nrg/journal/v17/n4/abs/nrg.2015.25.html Highlights importance of repeats in creating genomic plasticity
Nat Rev Genet. 2016 Apr;17(4):224-38. doi: 10.1038/nrg.2015.25. Epub 2016 Feb 29.
Mechanisms underlying structural variant formation in genomic disorders. Carvalho CM, Lupski JR
Phys. Rev. E 92, 032810 (2015) – Thermodynamic characterization of networks using graph polynomials
March 31, 2017Thermodynamic characterization of #networks using graph polynomials https://journals.APS.org/pre/abstract/10.1103/PhysRevE.92.032810 Application to the stockmarket & biological data
linkstream2 microblog 