Posts Tagged ‘from_jclub’

Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V’DJer | Bioinformatics | Oxford Academic

September 30, 2017

Assembly-based inference of Bcell receptor repertoires from..RNAseq w/
V’DJer https://academic.OUP.com/bioinformatics/article/32/24/3729/2525640/Assembly-based-inference-of-B-cell-receptor Less diversity assoc w/ long survival

Network propagation: a universal amplifier of genetic associations : Nature Reviews Genetics : Nature Research

September 11, 2017

#Network propagation [by Markov walks, heat flow, diffusion, &c]: a universal amplifier of genetic associations
http://www.Nature.com/nrg/journal/v18/n9/abs/nrg.2017.38.html

Lenore Cowen,
Trey Ideker,
Benjamin J. Raphael
& Roded Sharan

http://www.nature.com/nrg/journal/v18/n9/abs/nrg.2017.38.html?foxtrotcallback=true

Whole-genome landscapes of major melanoma subtypes : Nature : Nature Research

September 4, 2017

Hayward, Nicholas K., et al. "Whole-genome landscapes of major melanoma subtypes." Nature 545.7653 (2017): 175-180.

Whole-genome landscapes of…#melanoma subtypes http://www.Nature.com/nature/journal/vaop/ncurrent/full/nature22071.html Sun-exposed cutaneous w. many C>T SNVs v acral/mucosal w. many SVs

Evaluation Of Chromatin Accessibility In Prefrontal Cortex Of Schizophrenia Cases And Controls | bioRxiv

July 31, 2017

Eval of Chromatin Accessibility [via #ATACSeq] in DLPFC of SCZ Cases/Ctrls, by @JulienBryois et al.
http://www.BiorXiv.org/content/early/2017/05/25/141986 List of cQTLs

Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak — NEJM

July 22, 2017

WGS & Social-#Network Analysis of a TB Outbreak http://www.NEJM.org/doi/full/10.1056/NEJMoa1003176 Nice tech combo but not sure transmission & phylogeny are consistent

Zika virus evolution and spread in the Americas : Nature : Nature Research

June 25, 2017

http://www.nature.com/nature/journal/v546/n7658/full/nature22402.html

#Zika virus evolution & spread in the Americas, by @sabeti_lab http://www.Nature.com/nature/journal/v546/n7658/full/nature22402.html #Phylogeny reconstruction of 110 new + 64 known seqs.

A Big Bang model of human colorectal tumor growth : Nature Genetics : Nature Research

June 7, 2017

https://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, 2017

Common 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
“}}

Common SNPs explain a large proportion of the heritability for human height : Nature Genetics : Nature Research

June 1, 2017

http://www.nature.com/ng/journal/v42/n7/abs/ng.608.html

Common SNPs explain a large proportion of the heritability for human height

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
"}}

Common SNPs explain a large proportion (45%) of heritability for…height (80%) http://www.Nature.com/ng/journal/v42/n7/abs/ng.608.html Vs ’10 GWAS SNPs could only expl. 5%

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors : Nature Genetics : Nature Research

May 6, 2017

http://www.nature.com/ng/journal/v49/n5/full/ng.3818.html

Ref component analysis..of transcriptomes, by @Robson_Paul &co http://www.Nature.com/ng/journal/v49/n5/full/ng.3818.html Clustering similarity of samples to tissue references