QT:{{”
Various forms of stress-induced mutagenesis are tightly regulated and comprise a universal adaptive response to environmental stress in cellular life forms. Stress-induced mutagenesis can be construed as a quasi-Lamarckian phenomenon because the induced genomic changes, although random, are triggered by environmental factors and are beneficial to the organism.
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Archive for the 'SciLit' Category
Is evolution Darwinian or/and Lamarckian?
August 2, 2015BMC Genomics | Full text | Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential
July 31, 2015[440 @GencodeGenes] #Pseudogenes transcribed in breast…carcinoma show subtype-specific expression & ceRNA potential http://www.biomedcentral.com/1471-2164/16/113
Single cell Genome + Transcriptome Sequencing
July 28, 2015G&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
Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. – PubMed – NCBI
July 21, 2015http://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, 2015Impact 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
Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms
July 21, 2015clusters from single molecules
http://nar.oxfordjournals.org/content/28/20/e87.abstract
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