linkstream2 microblog

BRAF #Pseudogene Functions as a Competitive Endogenous RNA; [Shows it] induces Lymphoma [after alteration, in mice]
http://www.cell.com/cell/abstract/S0092-8674(15)00244-5

Cell. 2015 Apr 9;161(2):319-32. doi: 10.1016/j.cell.2015.02.043. Epub 2015 Apr 2.

Karreth FA1, Reschke M1, Ruocco A1, Ng C1, Chapuy B2, Léopold V1, Sjoberg M3, Keane TM3, Verma A4, Ala U1, Tay Y1, Wu D5, Seitzer N1, Velasco-Herrera Mdel C3, Bothmer A1, Fung J1, Langellotto F6, Rodig SJ7, Elemento O4, Shipp MA2, Adams DJ3, Chiarle R8, Pandolfi PP9.

Abstract
Research over the past decade has suggested important roles for pseudogenes in physiology and disease. In vitro experiments
demonstrated that pseudogenes contribute….

Changes in [DHS] #regulatory element activity…[over 3 primates] associated w/ altered…expression & pos. selection
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002789

DHS across 3 primates finds species specific sites associated with differential expression & positive selection

Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee BK, Iyer VR, Parker SC, Margulies EH, Wray GA, Furey TS, Crawford GE*. Extensive evolutionary changes in regulatory element activity during human origins are
associated with altered gene expression and positive selection. PLoS Genet. 2012 Jun; 8(6):e1002789. doi: 10.1371/journal.pgen.1002789. Epub 2012 Jun 28. PubMed PMID: 22761590; PubMed Central PMCID: PMC3386175

SUMMARY (from csds):

The study is focused on analyzing genotype-phenotype correlation by looking at the evolution of DHS sites across three primate genomes: human, chimp and macaque. By comparing the data they were able to identify common DHS sites across the three species (sites that show similar DHS levels) and also species-specific sites. All the assays were supported by ChiP experiments. The study identified >2000 regulatory elements that were gained/lost since the divergence of
human and chimp. Looking at DNase and RNAseq data the authors show that the enrichment of regulatory elements next to genes with species-specific expression, suggests that the gain or loss of DHS sites impacts transcript abundance. The human DHS sites were enhanced for chromatin marks predictive of enhancers, while common regions were preferentially associated with promoters and insulators. By looking at species specificity, they found that species-specific DHS gains are cell type specific while both species specific DHS gains and losses are subject to positive selection. The common DHS sites are conserved and are suggested to have roles involving transcription and general housekeeping.

https://veracrypt.codeplex.com/

The pi moment of the century just occurred on the E Coast, USA: 3.14.15 9:26:53 (March 14, 2015 9:26:53 am ET)! via @bornalibran #PiDay2015

Main one:
http://www.evercontact.com/
auto-updating your gmail contacts by analyzing email signatures:

The other softwares related are:
1) Contactually
(https://www.contactually.com/for-individuals/tour/contact-management/) 2) Signusapp https://signusapp.wordpress.com/

http://osxdaily.com/2015/01/27/os-x-10-10-2-yosemite-released-mac-bug-fixes/

What Makes Art Popular?…Luck & #Opinion of Others
http://www.fastcocreate.com/3027193/what-makes-art-popular-science-says-its-luck-and-the-opinion-of-others Author buys 15k copies of his book to create a bestseller

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of #Chromatin Looping
http://www.cell.com/cell/abstract/S0092-8674(14)01497-4 HiC data for 9 celltypes

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Suhas S.P. Rao
,Miriam H. Huntley
Neva C. Durand
Elena K. Stamenova
Ivan D. Bochkov
James T. Robinson
Adrian L. Sanborn
Ido Machol
Arina D. Omer
Eric S. Lander
Erez Lieberman Aiden

DOI: http://dx.doi.org/10.1016/j.cell.2014.11.021

http://www.cell.com/cell/abstract/S0092-8674(14)01497-4

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Suhas S.P. Rao
,Miriam H. Huntley
Neva C. Durand
Elena K. Stamenova
Ivan D. Bochkov
James T. Robinson
Adrian L. Sanborn
Ido Machol
Arina D. Omer
Eric S. Lander
Erez Lieberman Aiden

DOI: http://dx.doi.org/10.1016/j.cell.2014.11.021

http://www.cell.com/cell/abstract/S0092-8674(14)01497-4

High-throughput functional testing of ENCODE segmentation
predictionsGenome Res. October 2014 24: 1595-1602; Published in Advance July 17, 2014,

that can be used for training predicted enhancers

http://genome.cshlp.org/content/24/10/1595.full.pdf