linkstream2 microblog

Here is the news about dropbox business.
http://allthingsd.com/20131113/dropbox-adds-enterprise-tools-without-splitting-them-out-from-personal-use
http://www.theverge.com/2013/11/13/5100176/dropbox-completely-rebuilds-its-business-product

Here is the news about dropbox business.
http://www.theverge.com/2013/11/13/5100176/dropbox-completely-rebuilds-its-business-product
http://allthingsd.com/20131113/dropbox-adds-enterprise-tools-without-splitting-them-out-from-personal-use

Bubble Popper !

By allowing peers to test some of the hypotheses stated in a theoretical paper (or stating that some statement(s) in the paper need additional justification)…

http://www.nature.com/ng/journal/v45/n12/full/ng.2845.html

Summary for:

“Epigenomic Alterations in Localized and Advanced Prostate Cancer” Lin PC, Giannopoulou E, Park K, Mosquera JM, Sboner A, Tewari AK, Garraway LA, Beltran H, Rubin MA*, Elemento O*. 2013. Epigenomic alterations in localized and advanced prostate cancer. Neoplasia

http://www.ncbi.nlm.nih.gov/pubmed/23555183

In this paper, the authors take advantage of new advances in reduced representation bisulfite sequencing, a method for measuring DNA methylation patterns genome-wide, with high coverage and
single-nucleotide resolution, to study methylation patterns in prostate cancer. Working with a prostate cancer cohort already studied with DNA-Seq and RNA-Seq analyses, the authors identified
differentially methylated regions (DMRs), comparing the methylation of prostate cancer samples to benign prostate samples. The analysis found an increase in DNA methylation in prostate cancer samples, and that the methylation was more diverse and heterogeneous compared to the patterns of benign samples. Furthermore, it was found that genes near hypermethylated DMRs tended to have decreased expression, while genes near hypomethylated DMRs tended to have increased expression. Additional analyses revealed that breakpoints associated with prostate-cancer-specific deletions, duplications, and translocations tended to be highly methylated in benign prostate tissue. Finally, a study of CpG islands at different stages of prostate cancer (benign vs. PCa vs. CRPC (castration-resistant prostate cancer)) revealed that certain islands become increasingly methylated with disease severity. The authors used this data as the basis for two classification models: one to discriminate between benign prostate tissue and PCa tissue, and another to discriminate between PCa tissue and CRPC tissue. Both models demonstrated high sensitivity and specificity, indicating that CpG islands with high discriminatory power could serve as a diagnostic basis for predicting disease aggressiveness. Finally, additional analyses revealed that breakpoints associated with
prostate-cancer-specific deletions, duplications, and translocations tended to be highly methylated in benign prostate tissue.

http://www.genomesunzipped.org/2013/10/genomics-england-and-the-100000-genomes.php

The RGASP papers are now out, back-to-back:
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2722.html http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2714.html A tour de force.
.@markgerstein Both #rnaseq #RGASP papers list the “RGASP Consortium” as an author. But this comprises different people in the 2 papers!

Some notes from a senior author:

* Due to space constraints unfortunately most of the results are in the supplemental data.

* If it is helpful for testing updates to programs, or to compare the results against future methods not yet considered, the analysis code from each study is on GitHub: https://github.com/RGASP-Consortium.

* The papers are not open access, unfortunately.

Interesting title
http://liorpachter.wordpress.com/2013/11/07/zero-cell-rna-seq

http://genome.cshlp.org/content/early/2013/11/05/gr.164806.113.abstract Interesting association of viral integration, relevant to bkpts

http://rt.com/news/genome-british-project-data-376

http://database.oxfordjournals.org/content/2013/bat069.abstract.html