Posts Tagged ‘entex’

Personalized and graph genomes reveal missing signal in epigenomic data

June 14, 2020

Personalized and graph genomes reveal missing signal in epigenomic data Cristian Groza, Tony Kwan, Nicole Soranzo, Tomi Pastinen & Guillaume Bourque Genome Biology volume 21, Article number: 124 (2020)

QT:{{ “Using permissive cutoffs, modified reference genomes are found to alter approximately 1% of peak calls while de novo assembled genomes alter up to 5% of peaks.” }}

Mapping and characterization of structural variation in 17,795 human genomes

May 28, 2020

https://www.nature.com/articles/s41586-020-2371-0
think allele frequencies are publicly available

Detecting sample swaps in diverse NGS data types using linkage disequilibrium | bioRxiv

April 29, 2020

https://www.biorxiv.org/content/10.1101/2020.03.15.992750v2

https://twitter.com/michaelhoffman/status/1255222686646747136 swap paper

Comparing tads across samples

April 6, 2020

newly published tool

TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription

Guangyu Wang, Qingshu Meng, Bo Xia, Shuo Zhang, Jie Lv, Dongyu Zhao, Yanqiang Li, Xin Wang, Lili Zhang, John P. Cooke, Qi Cao & Kaifu Chen

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01992-7

chip-seq normalization

February 8, 2020

https://www.biorxiv.org/content/10.1101/2020.01.31.929174v1

Paper of interest

February 1, 2020

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6516-1

The effects of common structural variants on 3D chromatin structure

Omar Shanta, Amina Noor, Human Genome Structural Variation Consortium (HGSVC) & Jonathan Sebat

BMC Genomics volume 21, Article number: 95 (2020)

Tobacco smoking and somatic mutations in human bronchial epithelium

February 1, 2020

https://www.nature.com/articles/s41586-020-1961-1

Tobacco smoking and somatic mutations in human bronchial epithelium

Kenichi Yoshida, Kate H. C. Gowers, Henry Lee-Six, Deepak P. Chandrasekharan, Tim Coorens, Elizabeth F. Maughan, Kathryn Beal, Andrew Menzies, Fraser R. Millar, Elizabeth Anderson, Sarah E. Clarke, Adam Pennycuick, Ricky M. Thakrar, Colin R. Butler, Nobuyuki Kakiuchi, Tomonori Hirano, Robert E. Hynds, Michael R. Stratton, Iñigo Martincorena, Sam M. Janes & Peter J. Campbell

Characterizing the Major Structural Variant Alleles of the Human Genome: Cell

November 10, 2019

https://www.cell.com/cell/fulltext/S0092-8674(18)31633-7

DNA methylation age of human tissues and cell types | Genome Biology | Full Text

October 26, 2019

Published: 10 December 2013
DNA methylation age of human tissues and cell types
Steve Horvath
Genome Biology volume 14, Article number: 3156 (2013)

https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-10-r115

GWAS ATLAS resource

August 24, 2019

A global overview of pleiotropy and genetic architecture in complex traits

Kyoko Watanabe, Sven Stringer, Oleksandr Frei, Maša Umićević Mirkov, Christiaan de Leeuw, Tinca J. C. Polderman, Sophie van der Sluis, Ole A. Andreassen, Benjamin M. Neale & Danielle Posthuma

https://www.nature.com/articles/s41588-019-0481-0