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
Archive for the 'SciLit' Category
Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay: Cell
August 18, 2016Whole 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
Journal Club
July 23, 2016Basset: #DeepLearning the regulatory code w/…NNs by @noncodarnia lab http://genome.cshlp.org/content/early/2016/05/03/gr.200535.115 Has score for all possible SNVs in the genome
“Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks”
Identification of type 2 diabetes subgroups through topological analysis of patient similarity | Science Translational Medicine
July 16, 2016Patient records
http://stm.sciencemag.org/content/7/311/311ra174
Construction of a genetic linkage map in man using restriction fragment length polymorphisms. – PubMed – NCBI
July 15, 2016A deep learning framework for modeling structural features of RNA-binding protein targets
July 12, 2016#Deeplearning framework for modeling…RBP sites
http://nar.oxfordjournals.org/content/44/4/e32 Uses topic models & determines key primary & tert. struct. features
The Ascent of Mammals – Scientific American
July 4, 2016The Ascent of #Mammals
http://www.scientificamerican.com/article/the-ascent-of-mammals/ Overview of their slow growth & coexistence w. dinosaurs, not just advent after KT asteroid
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