Posts Tagged ‘entex’

GTEx sex differential expression paper

September 5, 2018

https://www.nature.com/articles/nature24265
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0352-z

+
TCGA sex differences
https://www.cell.com/cancer-cell/abstract/S1535-6108(16)30111-8

Leveraging molecular QTL to understand the genetic architecture of diseases and complex traits | bioRxiv

July 11, 2018

https://www.biorxiv.org/content/early/2017/10/15/203380

Leveraging molecular QTL to understand the genetic architecture of diseases and complex traits

Farhad Hormozdiari, Steven Gazal, Bryce van de Geijn, Hilary Finucane, Chelsea J.-T. Ju, Po-Ru Loh, Armin Schoech, Yakir Reshef, Xuanyao Liu, Luke O’Connor, Alexander Gusev, Eleazar Eskin, Alkes Price
doi: https://doi.org/10.1101/203380

differential Hi-C analysis

July 10, 2018

https://genome.cshlp.org/content/28/3/412.long

It is kind of a similar idea about finding the differential chromatin interactions

mammalian tissue expression database

June 1, 2018

curated tissue expression database for mammalians: human, mouse, rat, pig

web: https://tissues.jensenlab.org/
paper: https://academic.oup.com/database/article/doi/10.1093/database/bay003/4851151 a relevant figure:
https://academic.oup.com/view-large/figure/112879298/bay003f2.tif

systematic comparison of dnase-seq & atac-seq

April 21, 2018

Reproducible inference of TF footprints in #ATACseq & DNase-seq…via protocol-specific bias modeling
https://www.BiorXiv.org/content/early/2018/03/19/284364 Systematic comparison of the 2 assay HT @gamzeandgursoy

Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression | eLife

April 21, 2018

Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression https://eLifeSciences.org/articles/25125 More noncoding than coding #allelic activity. Also, finding windows of allelic activity for chromatin

Daniel Andergassen,
Christoph P Dotter,
Daniel Wenzel,
Verena Sigl,
Philipp C Bammer,
Markus Muckenhuber,
Daniela Mayer,
Tomasz M Kulinski,
Hans-Christian Theussl,
Josef M Penninger,
Christoph Bock,
Denise P Barlow ,
Florian M Pauler ,
Quanah J Hudson

Research Center for Molecular Medicine of the Austrian Academy of Sciences, Austria;
Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Austria;
Institute of Molecular Pathology, Austria

illumina platinum genomes paper

January 10, 2017

Set of 5.4M phased…variants…from seq. a 3-gen. 17-member [CEPH] pedigree, centered on #NA12878
http://genome.cshlp.org/content/early/2016/11/25/gr.210500.116 $ILMN Pt genomes

A reference data set of 5.4 million phased human
variants validated by genetic inheritance from
sequencing a three-generation 17-member pedigree

Michael A. Eberle,1 Epameinondas Fritzilas,2 Peter Krusche,2 Morten Källberg,2 Benjamin L. Moore,2 Mitchell A. Bekritsky,2 Zamin Iqbal,3 Han-Yu Chuang,1 Sean J. Humphray,2 Aaron L. Halpern,1 Semyon Kruglyak,1 Elliott H. Margulies,1 Gil McVean,3,4 and David R. Bentley2

http://genome.cshlp.org/content/early/2016/11/25/gr.210500.116

Scientists are assembling a new picture of humanity

December 4, 2016

Assembling a new picture of humanity by @CarlZimmer
https://www.statnews.com/2016/10/07/dna-genome-sequencing-new-maps/ 1 graph to represent everyone, counterpoint to #personalgenomes

Allele-specific transcription factor binding in liver and cervix cells unveils many likely drivers of GWAS signals. – PubMed – NCBI

August 7, 2016

Allele-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