linkstream2 microblog

[[* M-F 8a-9:30p; Sa spec. w no tablecloth ; 74&lex *]]

bad inner 4G & no wifi

http://www.cucinavivolo.com/

Long-span PET mapping reveals characteristic patterns of #SVs in… cancer [v norm] genomes, but no MEIs or small events
http://genome.cshlp.org/content/early/2011/04/05/gr.113555.110.abstract

The described study used long paired-end-tags (PET) to analyze and compare SVs in cancer and normal genomes. It determined the prevalence of different types of SVs in normal and cancer sample. Overall, the results are interesting and convincing on a qualitative level; however, for the reasons outlined below, more precise and quantitative delineation of the observed effects is highly desirable.

1) Small sample size of normal genomes (only 2 normal genomes)

2) Validation rate was low (< 77%) for everything except deletions, and for singletons it was even lower. .

3) Long PET is not good for finding smaller events (few kbps). Thus, this analysis missed smaller scale SVs and cancer rearrangements.

4) While there is a discussion about breakpoints and associated repeats, it is not very informative as breakpoint locations were not determined to basepair resolution.

5) No MEI were considered — particularly, no cancer MEI were considered in the analysis, while recently it was found that somatic retrotransposition occurs in cancer (Lee et al., PMID: 22745252)..

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes –

Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo AS, Woo XY, Zhang Z, Zhao H, Ukil L, Chen JP, Zhu F, So JB, Salto-Tellez M, Poh WT, Zawack KF, Nagarajan N, Gao S, Li G, Kumar V, Lim HP, Sia YY, Chan CS, Leong ST, Neo SC, Choi PS, Thoreau H, Tan PB, Shahab A, Ruan X, Bergh J, Hall P, Cacheux-Rataboul V, Wei CL, Yeoh KG, Sung WK, Bourque G, Liu ET, Ruan Y.

Genome Res. 2011 May;21(5):665-75. doi: 10.1101/gr.113555.110. Epub 2011 Apr 5.

How a #Gawker Editor Picks the ‘Viral’ Content Readers Can’t Resist: Human intuition trumps data #mining
http://m.us.wsj.com/articles/SB10001424052702304579404579231772007379090

Neetzan Zimmerman is the human intuition between Gawker’s successful shares Sort of like buZz feed….

How a Gawker Editor Picks the ‘Viral’ Content Readers Can’t Resist Sharing

http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg3655.html

on the various sources of errors in NGS and the role of replicates in reducing errors:

came across this paper: http://genomebiology.com/content/11/2/R14, which uses GO for RNA-seq data analysis
looks interesting – GoSeq !

“This amazing iPhone app 3D models your face and let’s you try glasses on your own face! ”

https://itunes.apple.com/us/app/glasses.com-for-iphone/id738159996

Sort of like buZz feed….
http://m.us.wsj.com/articles/SB10001424052702304579404579231772007379090

QT:{{”
We found that ~15% of human codons are dual-use codons (“duons”) that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias.
“}}

http://www.sciencemag.org/content/342/6164/1325.summary
http://www.sciencemag.org/content/342/6164/1367.abstract

http://www.ncbi.nlm.nih.gov/pubmed/23176822
Am J Hum Genet. 2012 Dec 7;91(6):1033-40. doi:
10.1016/j.ajhg.2012.10.018. Epub 2012 Nov 21.
Differential relationship of DNA replication timing to different forms of human mutation and variation.
Koren A, Polak P, Nemesh J, Michaelson JJ, Sebat J, Sunyaev SR, McCarroll SA.

Datasexual, the latest incarnation of metrosexual. Other related terms: narb (=narrative bits), data hygiene, QSer
http://spectrum.ieee.org/at-work/test-and-measurement/meet-the-datasexual
Meet the Datasexual