linkstream2 microblog

“Flexible isoform-level differential expression analysis with Ballgown” http://biorxiv.org/content/early/2014/03/30/003665

Deletion of introns and other intergenic regions

Total Synthesis of a Functional Designer Eukaryotic Chromosome

http://www.sciencemag.org/content/early/2014/03/26/science.1249252

http://syntheticyeast.org/

http://www.sciencedirect.com/science/article/pii/S0092867414002013#

Looks like 88 freely available liver cancer genome datasets
http://gigadb.org/dataset/100034

QT:{{”
Such findings highlight the hidden privacy costs of widespread information dissemination and the complex interactions among multiple data sources in modern information economies (11), underscoring the role of public records as breeder documents (12) of more sensitive data.
“}}

http://www.pnas.org/content/106/27/10975.full

http://www.gigasciencejournal.com/content/1/1/4

QT:{{”
The atlas is used to compare regulatory programs between different cells at unprecedented depth, to identify disease-associated regulatory single nucleotide polymorphisms, and to classify
cell-type-specific and ubiquitous enhancers.
“}}

A promoter-level mammalian expression atlas
http://www.nature.com/nature/journal/v507/n7493/full/nature13182.html

An atlas of active enhancers across human cell types and tissues http://www.nature.com/nature/journal/v507/n7493/full/nature12787.html

het/hom ratio = ~1.5
in the sequencing of many Asian individuals (Table 1)

http://www.nature.com/ng/journal/v43/n8/fig_tab/ng.872_T1.html

From
Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals
Nature Genetics 43, 745-752 (2011) doi:10.1038/ng.872

From the following article:
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium
Nature 409, 860-921(15 February 2001)
doi:10.1038/35057062

Alu age distribution

http://www.nature.com/nature/journal/v409/n6822/fig_tab/409860a0_F18.html

System-wide analyses have underestimated #protein abundances… Corrected protein conc. better correlated w/ #mRNA
https://peerj.com/articles/270

…once a non linear bias in mass spec. data is corrected, the concentration of the factor expressed at the median level is present at 70,000 molecules per cell. ….

Li, J, Bickel, P.J. and Biggin M.D. (2014) System Wide Analyses have Underestimated Protein Abundances and the Importance of Transcription in Mammals. PeerJ DOI10.7717/peerj.270