Widespread [25% genes] seasonal…expression reveals [circ]annual differences in…immunity, relevant for vaccination http://www.nature.com/ncomms/2015/150512/ncomms8000/full/ncomms8000.html
In addition to circadian rhythms, batch effects, now consider seasonal effects on gene expression
DNA sequence…#compression
http://bib.oxfordjournals.org/content/16/1/1.full Nice review comparing approaches on 2 axes: classic v Nextgen & reference-based v -free
Not much on LD-based approaches
Zexuan Zhu
Yongpeng Zhang
Zhen Ji
Shan He
Xiao Yang
Brief Bioinform (2015) 16 (1): 1-15.doi: 10.1093/bib/bbt087
First published online: December 3, 2013
Poster of -Seq expts from @Illumina
http://www.illumina.com/content/dam/illumina-marketing/documents/applications/ngs-library-prep/ForAllYouSeqMethods.pdf Nextgen update to @Roche’s famous biochem. #pathway chart
http://biochemical-pathways.com/#/map/1
Originally Boehringer Mannheim chart of pathways
Cell Lineage Analysis in Human Brain Using Endogenous Retroelements http://www.sciencedirect.com/science/article/pii/S0896627314011374 Somatic events from #neuron #singlecell WGS
[440 @GencodeGenes] #Pseudogenes transcribed in breast…carcinoma show subtype-specific expression & ceRNA potential http://www.biomedcentral.com/1471-2164/16/113
G&T-seq: parallel…#singlecell genomes & transcriptomes by @CGATist
lab & others http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3370.html low cov. matched data on 130+ cells
https://twitter.com/CGATist/status/604271101678587904
G&T-seq: parallel sequencing of single-cell genomes and transcriptomes
Iain C Macaulay,
Wilfried Haerty,
Parveen Kumar,
Yang I Li,
Tim Xiaoming Hu,
Mabel J Teng,
Mubeen Goolam,
Nathalie Saurat,
Paul Coupland,
Lesley M Shirley,
Miriam Smith,
Niels Van der Aa,
Ruby Banerjee,
Peter D Ellis,
Michael A Quail,
Harold P Swerdlow,
Magdalena Zernicka-Goetz,
Frederick J Livesey,
Chris P Ponting
& Thierry Voet
Nature Methods 12, 519–522 (2015) doi:10.1038/nmeth.3370Received 18 November 2014 Accepted 27 March 2015 Published online 27 April 2015
http://Oqtans.org: RNAseq…in the cloud by @gxr http://bioinformatics.oxfordjournals.org/content/30/9/1300.long Distributing a tool in many ways: AMI, GIT, Galaxy workflow, &c
Nice illustration how to distribute a tool in many forms —
AMI, GIT, Galaxy workflow + more.
* Sreedharan et al. Oqtans: the RNA-seq workbench in the cloud for
complete and reproducible quantitative transcriptome analysis.
The authors describe an open source transcriptome analysis software
package, Oqtans. The package contains a variety of existing analysis
tools (from short-read alignment, transcript quantification and
expression analysis) assembled into a comprehensive workflow. The
package can be either run locally or as a virtual machine in the cloud
using the AWS. One innovative feature is the availability of comparing
the efficiency of the integrated tools on the same data set. Oqtans is
a highly modular software package that can be easily extended. It also
offers the possibility to create customized workflows based on the
integrated tools available.
Impact of regulatory variation from RNA to protein
http://www.sciencemag.org/content/347/6222/664.abstract pQTLs for prot levels less related to #eQTLs & rQTLs than expected
How genetics affect phenotypic variation
http://www.sciencemag.org/content/347/6222/664.abstract