75 & Mad.
Open New Year’s Day
[[* 6a-10p *]]
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January 1, 2014Via Quadronno in NYC | Known for our Unforgettable Cappucinos and Paninis
December 31, 2013[[* 8a-11p (mf), 9a-11p, 10a-9p (ss) *]]
(could be 10-10 for su)
Nice outer area for wine + good 4G there
Cucina Vivolo
December 31, 2013[[* M-F 8a-9:30p; Sa spec. w no tablecloth ; 74&lex *]]
bad inner 4G & no wifi
Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes – Genome Res.
December 27, 2013Long-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.
Why Everyone Will Totally Read This Column – WSJ.com
December 24, 2013How 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
The role of replicates for error mitigation in next-generation sequencing
December 16, 2013http://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:
Use of ontologies in RNAseq data analysis
December 16, 2013came across this paper: http://genomebiology.com/content/11/2/R14, which uses GO for RNA-seq data analysis
looks interesting – GoSeq !
glasses.com for iPhone on the App Store on iTunes
December 16, 2013“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
Why Everyone Will Totally Read This Column – WSJ.com
December 16, 2013Sort of like buZz feed….
http://m.us.wsj.com/articles/SB10001424052702304579404579231772007379090
Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution
December 15, 2013QT:{{”
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.
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http://www.sciencemag.org/content/342/6164/1325.summary
http://www.sciencemag.org/content/342/6164/1367.abstract
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