PETModule…enhancer-target-gene prediction
http://www.nature.com/articles/srep30043 Compares activity
correlations against a Hi-C/ChIA-PET gold std.
Archive for the 'SciLit' Category
PETModule: a motif module based approach for enhancer target gene prediction : Scientific Reports
September 17, 2016Cancer undefeated. – PubMed – NCBI
September 11, 2016http://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."}}
Treatment of Acute Lymphoblastic Leukemia — 30 Years’ Experience at St. Jude Children’s Research Hospital — NEJM
September 11, 2016http://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.
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Result of Pinkel ’79 study
Synthetic microbe lives with fewer than 500 genes
September 10, 2016Synthetic 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.”
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Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay: Cell
August 18, 2016Identification 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 and cumulative genome editing | Science
August 17, 2016Whole-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 transcription factor binding in liver and cervix cells unveils many likely drivers of GWAS signals. – PubMed – NCBI
August 7, 2016Allele-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
Spatial confinement is a major determinant of the folding landscape of human chromosomes
July 28, 2016Gamze 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
GERV: a statis,tical method for generative evaluation of regulatory variants for transcription factor binding
July 23, 2016GERV: stats method for generative evaluation of regulatory variants
for TF binding http://bioinformatics.oxfordjournals.org/content/early/2015/11/05/bioinformatics.btv565 Predicts effect of #allelic SNPs
GERV: a statistical method for generative evaluation of regulatory ariants for transcription factor binding
> Haoyang Zeng
> Tatsunori Hashimoto
> Daniel D. Kang
> David K. Gifford
linkstream2 microblog 