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To demonstrate the promise of personalized genome analysis, the genome of HuRef was sequenced using the Life SOLiD™ platform. Nimbus Informatics performed the analytical work for this project and has made the resulting data available here, running entirely on the Amazon Cloud.
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http://huref.nimbusinformatics.com
Posts Tagged ‘from’
huref on Solid
January 4, 2014single cell trascriptomes and WGCNA
January 2, 2014Nature. 2013 Aug 29;500(7464):593-7. doi: 10.1038/nature12364. Epub 2013 Jul 28.
Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.
Xue Z, Huang K, Cai C, Cai L, Jiang CY, Feng Y, Liu Z, Zeng Q, Cheng L, Sun YE, Liu JY, Horvath S, Fan G.
QT:{{”
…We report here a comprehensive analysis of transcriptome dynamics from oocyte to morula in both human and mouse embryos, using single-cell RNA sequencing…. By weighted gene co-expression network analysis, we find that each developmental stage can be delineated concisely by a small number of functional modules of co-expressed genes. This result indicates a sequential order of transcriptional changes in pathways of cell cycle, gene regulation, translation and metabolism, acting in a step-wise fashion from cleavage to morula. Cross-species comparisons with mouse pre-implantation embryos reveal that the majority of human stage-specific modules (7 out of 9) are notably preserved, but developmental specificity and timing differ between human and mouse. Furthermore, we identify conserved key members (or hub genes) of the human and mouse networks.
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Kruglyak paper on C. elegans
January 2, 2014A paper on C. elegans that’s very informative:
http://www.nature.com/ng/journal/v44/n3/full/ng.1050.html
Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity
Most notable of their findings is evidence of recent selective sweeps on chromosomes I, IV, V and (sort of) X. These sweeps have the potential to fix pseudogenes that might have been present at the time.
GenomeWeb young investigator feature
January 2, 2014Young Investigator for Ekta Khurana
http://www.genomeweb.com/genomeweb-feature-eighth-annual-young-investigators
3 Guys
January 1, 201475 & Mad.
Open New Year’s Day
[[* 6a-10p *]]
Via 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:
linkstream2 microblog 