linkstream2 microblog

http://www.ncbi.nlm.nih.gov/pubmed/25554788

PETModule…enhancer-target-gene prediction
http://www.nature.com/articles/srep30043 Compares activity
correlations against a Hi-C/ChIA-PET gold std.

http://www.ncbi.nlm.nih.gov/pubmed/9164814
Bailar JC 3rd1, Gornik HL.NEJM

QT:{{"
Despite decades of basic and clinical research and trials of promising new therapies, cancer remains a major cause of morbidity and mortality. We assessed overall progress against cancer in the United States from 1970 through 1994 by analyzing changes in age-adjusted mortality rates."}}

http://www.nejm.org/doi/full/10.1056/NEJM199310283291801#t=article

QT:{{”
When treated with effective multiagent chemotherapy, about two thirds of children with newly diagnosed acute lymphoblastic leukemia survive for long periods of time1-4. Much of this success can be credited to more intensive early treatment, especially of patients at higher risk of relapse.
“}}

Result of Pinkel ’79 study

Synthetic microbe lives with fewer than 500 genes from @JCVenterInst http://www.ScienceMag.org/news/2016/03/synthetic-microbe-lives-less-500-genes 179 of the 479 genes have unknown functions

QT:{{”
“The microbe’s streamlined genetic structure excites evolutionary biologists and biotechnologists, who anticipate adding genes back to it one by one to study their effects. “It’s an important step to creating a living cell where the genome is fully defined,” says synthetic biologist Chris Voigt of the Massachusetts Institute of Technology in Cambridge. But Voigt and others note that this complete definition remains a ways off, because the function of 149 of Syn 3.0’s genes—roughly one-third—
remains unknown. Investigators’ first task is to probe the roles of those genes, which promise new insights into the basic biology of life.”
“}}

Universality of human #microbial dynamics
http://www.nature.com/nature/journal/v534/n7606/abs/nature18301.html Addressed via simulations & graphs comparing counts of species v organisms

Identification of…expr.-Modulating Variants using #MPRA, by @sabeti_lab http://www.cell.com/cell/fulltext/S0092-8674(16)30421-4 Some w. allelic skew related to PWM change

Whole-organism lineage tracing by combinatorial… genome editing, w. #CRISPR + seq. barcodes, by @JShendure lab
http://science.sciencemag.org/content/early/2016/05/25/science.aaf7907 http://science.sciencemag.org/content/early/2016/05/25/science.aaf7907

Allele-specific TF binding in liver & cervix cells [HepG2 & HeLa] unveils many likely drivers of GWAS [SNP] signals
http://www.sciencedirect.com/science/article/pii/S0888754316300271

Gamze Gursoy, Yun Xu, Amy Kenter and Jie Liang. “Spatial confinement is a major determinant of folding landscape of human genome”, Nucleic Acids Research, 2014, 42 (13), 8223-8230

Confinement is a major determinant of the #folding…of chromosomes http://NAR.oxfordjournals.org/content/42/13/8223.full Simulations of self-avoiding chain growth

http://nar.oxfordjournals.org/content/42/13/8223.full