Assembly-based inference of Bcell receptor repertoires from..RNAseq w/
V’DJer https://academic.OUP.com/bioinformatics/article/32/24/3729/2525640/Assembly-based-inference-of-B-cell-receptor Less diversity assoc w/ long survival
Calling genotypes from public RNA-sequencing data enables
identification of genetic variants that affect gene-expression levels
Patrick Deelen†,
Daria V Zhernakova†,
Mark de Haan,
Marijke van der Sijde,
Marc Jan Bonder,
Juha Karjalainen,
K Joeri van der Velde,
Kristin M Abbott,
Jingyuan Fu,
Cisca Wijmenga,
Richard J Sinke,
Morris A Swertz† and
Lude Franke†
Genotypes from…#RNAseq…enables identification of…variants, related to ASE & eQTLs
https://GenomeMedicine.biomedcentral.com/articles/10.1186/s13073-015-0152-4 Validation w/ #Geuvadis
Genotypes from…#RNAseq…enables identification of…variants, related to ASE & eQTLs
https://GenomeMedicine.biomedcentral.com/articles/10.1186/s13073-015-0152-4 Validation w/ #Geuvadis
What Dead Pigs Can’t Teach Us About @CSI_CBS
http://www.nytimes.com/2016/06/14/science/forensic-science-body-farm.html Wonder what this tells us about RIN? #RNAseq
#SingleCell #RNASeq Reveals Dynamic, Random Monoallelic Gene Expression, occurring in ~20% of genes in mice cells
http://science.sciencemag.org/content/343/6167/193.abstract
Heterogeneity in #singlecell RNAseq…hidden subpopulations by @OliverStegle lab http://www.nature.com/nbt/journal/v33/n2/full/nbt.3102.html scLVM corrects for cell cycle phase
Buettner, Florian, Kedar N. Natarajan, F. Paolo Casale, Valentina
Proserpio, Antonio Scialdone, Fabian J. Theis, Sarah A. Teichmann,
John C. Marioni, and Oliver Stegle. "Computational analysis of
cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals
hidden subpopulations of cells." Nature biotechnology 33, no. 2
(2015): 155-160.
Landscape of lncRNAs in the human #transcriptome
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3192.html Derived from RNAseq read assembly; not much overlap w/ @GencodeGenes
Matthew K Iyer,
Yashar S Niknafs,
Rohit Malik,
Udit Singhal,
Anirban Sahu,
Yasuyuki Hosono,
Terrence R Barrette,
John R Prensner,
Joseph R Evans,
Shuang Zhao,
Anton Poliakov,
Xuhong Cao,
Saravana M Dhanasekaran,
Yi-Mi Wu,
Dan R Robinson,
David G Beer,
Felix Y Feng,
Hariharan K Iyer
& Arul M Chinnaiyan
Nature Genetics (2015) doi:10.1038/ng.3192Received 20 June 2014 Accepted 18 December 2014
Comprehensive assessment of #RNAseq… by #SEQC http://www.nature.com/nbt/journal/v32/n9/full/nbt.2957.html Spikeins as negative controls, so all diff expression results in FPs.
Multiplatform assessment of #transcriptome profiling [w.] RNAseq http://www.nature.com/nbt/journal/v32/n9/full/nbt.2972.html Nice plots showing great effect of poly-A selection
#Singlecell #RNAseq highlights intratumoral heterogeneity http://www.sciencemag.org/content/344/6190/1396.abs Subtype classifiers variably expressed across indiv. cells
Patel AP(1), Tirosh I(2), Trombetta JJ(2), Shalek AK(2), Gillespie SM(3),
Wakimoto H(4), Cahill DP(4), Nahed BV(4), Curry WT(4), Martuza RL(4), Louis
DN(5), Rozenblatt-Rosen O(2), Suvà ML(6), Regev A(7), Bernstein BE(8).
Published Online June 12 2014
Science 20 June 2014:
Vol. 344 no. 6190 pp. 1396-1401
DOI: 10.1126/science.1254257