TCGA sex differences
Interesting paper by alumnus Renqiang Min on “Video Generation from Text,” using a generative #MachineLearning model.
http://www.AAAI.org/GuideBook2018/16152-72279-GB.pdf (Press report by @SilverJacket: New algorithm can create movies from just a few snippets of text
Video Generation from Text Yitong Li†∗, Martin Renqiang Min‡ , Dinghan Shen† , David Carlson† , Lawrence Carin† †
A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex
, Shu Zhang
Received: 13 November 2017 Revised: 22 November 2017 Accepted: 29 November 2017 https://www.nature.com/articles/s41525-017-0040-5.pdf
3D clusters of somatic mutations…reveal numerous rare mutations as functional targets
https://GenomeMedicine.BiomedCentral.com/articles/10.1186/s13073-016-0393-x Introduces 3DHotSpots, which is one of a number of recent approaches (incl. CLUMPS, Hotspot3D, Mutation3D & HotMAPS) for finding groupings of somatic SNVs via structure
Zhou, J. and Troyanskaya, O.G. (2015). Predicting effects of noncoding variants with deep learning–based sequence model. Nature Methods, 12, 931–934.
Predicting (& prioritizing) effects of noncoding variants w. [DeepSEA] #DeepLearning…model
https://www.Nature.com/nmeth/journal/v12/n10/full/nmeth.3547.html Trained w #ENCODE data
.@denovodb: a compendium of [initially ~33K] human de novo variants w. phenotype, freely downloadable as a TSV table
As of July 2016, denovo-db contained 40 different studies and 32,991 de novo variants from 23,098 trios. Database features include basic variant information (chromosome location, change, type); detailed annotation at the transcript and protein levels; severity scores; frequency; validation status; and, most importantly, the phenotype of the individual with the variant.
Genes, environment & bad luck
http://science.ScienceMag.org/content/355/6331/1266 To what degree are #cancer mutations due to replication error (3rd factor), not 1st 2?
discusses R v D correlation
Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention Cristian Tomasetti1,2,*, Lu Li2, Bert Vogelstein3,*
Science 24 Mar 2017:
Vol. 355, Issue 6331, pp. 1330-1334