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
Posts Tagged ‘from’
The Transcription Factor Titration Effect Dictates Level of Gene Expression
April 6, 2014Genome-wide signals of positive selection in human evolution
April 6, 2014http://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 the lost treasures in exome sequencing data
April 6, 2014Finding 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
FYI: The Cofounder Of 23andMe’s Next Project: Mining Your Quantified Self
April 6, 2014Cofounder 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 on cancer driver genes in RECOMB 2014
April 6, 2014paper 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.
After TopHat, Bowtie and Cufflinks — here’s Ballgown !
April 6, 2014“Flexible isoform-level differential expression analysis with Ballgown” http://biorxiv.org/content/early/2014/03/30/003665
This synthetic yeast genome may reignite controversy regarding function of non-coding region
March 31, 2014Deletion 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
Looping Back to Leap Forward: Transcription Enters a New Era
March 31, 2014Statistics and the hot hand
March 29, 2014The hot hand might be real after all: But streaking shooters only 1-2% more likely than #random to make next basket
http://www.bostonglobe.com/ideas/2014/02/09/the-hot-hand-might-real-after-all/N8V34bGLWhPqk0Sx9yoHWI/story.html
Predicting Social Security numbers from public data
March 27, 2014QT:{{”
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.
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