A…transcriptional map of primate (macaque) #brain development http://www.Nature.com/nature/journal/vaop/ncurrent/full/nature18637.html Gene expression changes more rapidly before birth
Nature (2016) doi:10.1038/nature18637
Archive for the 'SciLit' Category
A comprehensive transcriptional map of primate brain development
June 19, 2017An Expanded View of Complex Traits: From Polygenic to Omnigenic: Cell
June 19, 2017Thought-provoking calculations, perhaps suggesting that ever bigger association studies won’t yield useful results
https://twitter.com/joe_pickrell/status/875406448716632064
http://www.cell.com/cell/abstract/S0092-8674(17)30629-3
An Expanded View of Complex Traits: From Polygenic to Omnigenic
Evan A. Boyle
Yang I. Li
Jonathan K. Pritchard
DOI: http://dx.doi.org/10.1016/j.cell.2017.05.038
Journal Club Paper
June 18, 2017Zhou, 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
Proportionality: A Valid Alternative to Correlation for Relative Data
June 12, 2017A Valid Alternative to #Correlation for Rel. Data
http://journals.PLoS.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004075 Illustrates how r fails on simple expression expts HT @mason_lab
A Big Bang model of human colorectal tumor growth : Nature Genetics : Nature Research
June 7, 2017https://www.nature.com/ng/journal/v47/n3/full/ng.3214.html
Big Bang model of…tumor growth, v. slow #evolution under selection https://www.Nature.com/ng/journal/v47/n3/full/ng.3214.html #Cancer is born w/ key mutations all there
Andrea Sottoriva,
Haeyoun Kang,
Zhicheng Ma,
Trevor A Graham,
Matthew P Salomon,
Junsong Zhao,
Paul Marjoram,
Kimberly Siegmund,
Michael F Press,
Darryl Shibata
& Christina Curtis
Nature Genetics 47, 209–216 (2015) doi:10.1038/ng.3214
Common SNPs explain a large proportion of the heritability for human height : Nature Genetics : Nature Research
June 2, 2017Common SNPs explain a large proportion (45%) of heritability for…height (85%)
http://www.Nature.com/ng/journal/v42/n7/abs/ng.608.html Cf 2010 GWASes could only explain 5%
Jian Yang,
Beben Benyamin,
Brian P McEvoy,
Scott Gordon,
Anjali K Henders,
Dale R Nyholt,
Pamela A Madden,
Andrew C Heath,
Nicholas G Martin,
Grant W Montgomery,
Michael E Goddard
& Peter M Visscher
Nature Genetics 42, 565–569 (2010) doi:10.1038/ng.608
QT:{{”
…conveniently implemented with a mathematically equivalent model that uses the SNPs to calculate the genomic relationship between pairs of subjects). Using this approach, we estimated the proportion of phenotypic variance explained by the SNPs as 0.45 (s.e. = 0.08, Table 1), a nearly tenfold increase relative to the 5% explained by published and validated individual SNPs
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CATO score
May 28, 2017Seq. variants influencing…TF occupancy
http://www.Nature.com/ng/journal/v47/n12/full/ng.3432.html Uses allelic analysis to develop the CATO score, how variants alter binding
QT:{{”
This approach resulted in a simple scoring scheme, termed contextual analysis of transcription factor occupancy (CATO), that provides a recalibrated probability of affecting the binding of any transcription factor, as well as a quantitatively ranked list of transcription factor families whose binding might be altered.
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