Candidate gene–environment interaction research: Reflections and recommendations

DM Dick, A Agrawal, MC Keller… - Perspectives on …, 2015 - journals.sagepub.com
Studying how genetic predispositions come together with environmental factors to contribute
to complex behavioral outcomes has great potential for advancing the understanding of the …

Chromosome conformation capture technologies and their impact in understanding genome function

S Sati, G Cavalli - Chromosoma, 2017 - Springer
It has been more than a decade since the first chromosome conformation capture (3C) assay
was described. The assay was originally devised to measure the frequency with which two …

H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation

N Kubo, PB Chen, R Hu, Z Ye, H Sasaki, B Ren - Molecular Cell, 2024 - cell.com
Histone H3 lysine 4 mono-methylation (H3K4me1) marks poised or active enhancers.
KMT2C (MLL3) and KMT2D (MLL4) catalyze H3K4me1, but their histone methyltransferase …

WashU epigenome browser update 2022

D Li, D Purushotham, JK Harrison, S Hsu… - Nucleic acids …, 2022 - academic.oup.com
Abstract WashU Epigenome Browser (https://epigenomegateway. wustl. edu/browser/) is a
web-based genomic data exploration tool that provides visualization, integration, and …

HiGlass: web-based visual exploration and analysis of genome interaction maps

P Kerpedjiev, N Abdennur, F Lekschas, C McCallum… - Genome biology, 2018 - Springer
We present HiGlass, an open source visualization tool built on web technologies that
provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps …

Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom

NC Durand, JT Robinson, MS Shamim, I Machol… - Cell systems, 2016 - cell.com
Hi-C experiments study how genomes fold in 3D, generating contact maps containing
features as small as 20 bp and as large as 200 Mb. Here we introduce Juicebox, a tool for …

Activation of proto-oncogenes by disruption of chromosome neighborhoods

D Hnisz, AS Weintraub, DS Day, AL Valton, RO Bak… - Science, 2016 - science.org
Oncogenes are activated through well-known chromosomal alterations such as gene fusion,
translocation, and focal amplification. In light of recent evidence that the control of key genes …

Ensembl 2016

A Yates, W Akanni, MR Amode, D Barrell… - Nucleic acids …, 2016 - academic.oup.com
Abstract The Ensembl project (http://www. ensembl. org) is a system for genome annotation,
analysis, storage and dissemination designed to facilitate the access of genomic annotation …

The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

Y Wang, F Song, B Zhang, L Zhang, J Xu, D Kuang… - Genome biology, 2018 - Springer
Here, we introduce the 3D Genome Browser, http://3dgenome. org, which allows users to
conveniently explore both their own and over 300 publicly available chromatin interaction …

3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis

Y Ke, Y Xu, X Chen, S Feng, Z Liu, Y Sun, X Yao, F Li… - Cell, 2017 - cell.com
High-order chromatin structure plays important roles in gene expression regulation.
Knowledge of the dynamics of 3D chromatin structures during mammalian embryo …