Archive for the 'SciLit' Category

Single cell Genome + Transcriptome Sequencing

July 28, 2015

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

Statistics requantitates the central dogma

July 26, 2015

@ewanbirney @jkpritch @alexisjbattle @dermitzakis My use of “expected” is coming from 1st reading the perspective
http://www.sciencemag.org/content/347/6226/1066.summary

Effect of VKORC1 Haplotypes on Transcriptional Regulation and Warfarin Dose

July 21, 2015

http://www.nejm.org/doi/full/10.1056/NEJMoa044503

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. – PubMed – NCBI

July 21, 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.

pQTLs

July 21, 2015

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

Real-Time DNA Sequencing Using Detection of Pyrophosphate Release — ScienceDirect

July 21, 2015

http://www.sciencedirect.com/science/article/pii/S0003269796904327?via%3Dihub

Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms

July 21, 2015

clusters from single molecules
http://nar.oxfordjournals.org/content/28/20/e87.abstract

Designed protein pores as components for biosensors — ScienceDirect

July 21, 2015

http://www.sciencedirect.com/science/article/pii/S1074552197903215

Mechanism, Prevalence, and More Severe Neuropathy Phenotype of the Charcot-Marie-Tooth Type 1A Triplication: The American Journal of Human Genetics

July 21, 2015

http://www.cell.com/ajhg/abstract/S0002-9297(14)00055-X

Lessons from modENCODE

July 11, 2015

http://www.annualreviews.org/doi/abs/10.1146/annurev-genom-090413-025448