Posts Tagged ‘i0enc15’

GERV: a statis,tical method for generative evaluation of regulatory variants for transcription factor binding

July 23, 2016

GERV: 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

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dataviz sites from ENCODE mtg

June 21, 2016

https://d3js.org/
http://amp.pharm.mssm.edu/clustergrammer/

http://bibviz.com/
http://www.visualcinnamon.com/portfolio/top-2000-songs

Top 10 baby names in the US since 1880 – Visual Cinnamon

June 21, 2016

Great viz

http://www.visualcinnamon.com/babynamesus

RNA splicing is a primary link between genetic variation and disease | Science

June 21, 2016

http://science.sciencemag.org/content/352/6285/600.long

Yang I. Li1,
Bryce van de Geijn2,
Anil Raj1,
David A. Knowles3,4,
Allegra A. Petti5,
David Golan1,
Yoav Gilad2,*,
Jonathan K. Pritchard1,6,7,*

GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding

June 21, 2016

http://bioinformatics.oxfordjournals.org/content/early/2015/11/05/bioinformatics.btv565

GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding

Haoyang Zeng
Tatsunori Hashimoto
Daniel D. Kang
David K. Gifford

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP) : Nature Methods : Nature Publishing Group

June 18, 2016

http://www.nature.com/nmeth/journal/v13/n6/abs/nmeth.3810.html

My notes from ENCODE Consortium Meeting

March 23, 2015

links: https://linkstream2.gerstein.info/tag/i0enc15

http://lectures.gersteinlab.org/summary/thoughts-on-ENCODE-annotations–final-i0enc15/

ReplicationDomain – Online database resource for DNA replication timing, transcription and other epigenetic data types – Main Page

March 23, 2015

http://replicationdomain.org/

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus : Nature : Nature Publishing Group

March 23, 2015

From noncoding variant to phenotype…at…#cholesterol locus http://www.nature.com/nature/journal/v466/n7307/full/nature09266.html
Gold standard ex of #SNP functional effect: LDL changes

Kiran Musunuru,
Alanna Strong,
Maria Frank-Kamenetsky,
et al.

Nature 466, 714–719 (05 August 2010) doi:10.1038/nature09266

Changes LDL level

Genome sequence-independent identification of RNA editing sites : Nature Methods : Nature Publishing Group

March 21, 2015

Genome sequence-independent identification of #RNA editing
siteshttp://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3314.html GIREMI uses LD to separate edit sites from #SNPs

Qing Zhang
& Xinshu Xiao

Nature Methods (2015) doi:10.1038/nmeth.3314Received