linkstream2 microblog

Citi #Bike Rides 9/17/2013. Great #visualization of daily #network dynamics. Neat if applicable to cellular networks
http://vimeo.com/89305412

Developmental dynamics… of random monoallelic gene expression. #RNAseq on 100s of instances without causative SNPs

An analysis of differentiated cell lines.

http://www.cell.com/developmental-cell/abstract/S1534-5807(14)00057-4

Interesting study looking at the effect of gene duplication on TF binding
"…when a TF is shared among many binding sites, either due to multiple identical copies of a gene regulated by that TF or due to unrelated genes that also independently bind the TF, the correlation in occupancy between the binding sites will lead to a complex dosage response to that TF." http://www.cell.com/abstract/S0092-8674(14)00221-9

http://genome.cshlp.org/content/early/2014/03/11/gr.164822.113.abstract

“We further demonstrate that the observed signatures of positive selection correlate better with the presence of regulatory sequences, as predicted by the ENCODE Project Consortium, than with the positions of amino acid substitutions. Our results suggest that adaptation was frequent in human evolution and provide support for the hypothesis of King and Wilson that adaptive divergence is primarily driven by regulatory changes.”

Similar to conclusion positive-section section in FunSeq paper

Finding lost treasures in #exome sequencing data. Mining off-target, often noncoding, reads from 1000G, TCGA, ESP, &c
http://www.ncbi.nlm.nih.gov/pubmed/23972387

Cofounder Of 23andMe’s Next Project: Mining Your #QuantifiedSelf. @lindaavey’s @WeAreCurious creates a forum for this
http://www.fastcoexist.com/3027630/the-cofounder-of-23andmes-next-project-mining-your-quantified-self

paper from RECOMB 2014 might be interesting to you, which uses
hitting time in random walk to identify cancer drivers.

http://link.springer.com/chapter/10.1007%2F978-3-319-05269-4_23

HIT.nDRIVE: Multi-Driver Gene Prioritization based on Hitting Time

Raunak Shrestha, Ermin Hodzic, Jake Yeung, Kendric Wang, Thomas
Sauerwald, Phuong Dao, Shawn Anderson, Himisha Beltran, Mark A. Rubin,
Colin Collins, Gholamreza Haffari and S. Cenk Sahinalp.

“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#