Comprehensive analysis of DNA methylation data with RnBeads

Y Assenov, F Müller, P Lutsik, J Walter, T Lengauer… - Nature …, 2014 - nature.com
RnBeads is a software tool for large-scale analysis and interpretation of DNA methylation
data, providing a user-friendly analysis workflow that yields detailed hypertext reports …

Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation

J Paulsen, TM Liyakat Ali, M Nekrasov, E Delbarre… - Nature …, 2019 - nature.com
Genomic information is selectively used to direct spatial and temporal gene expression
during differentiation. Interactions between topologically associating domains (TADs) and …

Ancestral perinatal obesogen exposure results in a transgenerational thrifty phenotype in mice

R Chamorro-Garcia, C Diaz-Castillo… - Nature …, 2017 - nature.com
Ancestral environmental exposures to non-mutagenic agents can exert effects in unexposed
descendants. This transgenerational inheritance has significant implications for …

The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet

H Liu, C Chen, Z Gao, J Min, Y Gu, J Jian, X Jiang… - …, 2017 - academic.oup.com
The blunt snout bream Megalobrama amblycephala is the economically most important
cyprinid fish species. As an herbivore, it can be grown by eco-friendly and resource …

Substantial loss of conserved and gain of novel microRNA families in flatworms

B Fromm, MM Worren, C Hahn, E Hovig… - Molecular biology …, 2013 - academic.oup.com
Recent studies on microRNA (miRNA) evolution focused mainly on the comparison of
miRNA complements between animal clades. However, evolution of miRNAs within such …

Uracil accumulation and mutagenesis dominated by cytosine deamination in CpG dinucleotides in mice lacking UNG and SMUG1

L Alsøe, A Sarno, S Carracedo, D Domanska… - Scientific reports, 2017 - nature.com
Both a DNA lesion and an intermediate for antibody maturation, uracil is primarily processed
by base excision repair (BER), either initiated by uracil-DNA glycosylase (UNG) or by single …

ATRX binds to atypical chromatin domains at the 3′ exons of zinc finger genes to preserve H3K9me3 enrichment

D Valle-García, ZA Qadeer, DS McHugh… - Epigenetics, 2016 - Taylor & Francis
ABSTRACT ATRX is a SWI/SNF chromatin remodeler proposed to govern genomic stability
through the regulation of repetitive sequences, such as rDNA, retrotransposons, and …

EBNA2 binds to genomic intervals associated with multiple sclerosis and overlaps with vitamin D receptor occupancy

VAG Ricigliano, AE Handel, GK Sandve, V Annibali… - PLoS …, 2015 - journals.plos.org
Epstein-Barr virus (EBV) is a non-heritable factor that associates with multiple sclerosis
(MS). However its causal relationship with the disease is still unclear. The virus establishes …

glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data

AP Hutchins, R Jauch, M Dyla, D Miranda-Saavedra - Cell Regeneration, 2014 - Springer
Genomic datasets and the tools to analyze them have proliferated at an astonishing rate.
However, such tools are often poorly integrated with each other: each program typically …

Local euchromatin enrichment in lamina-associated domains anticipates their repositioning in the adipogenic lineage

J Madsen-Østerbye, M Abdelhalim, MO Baudement… - Genome Biology, 2022 - Springer
Background Interactions of chromatin with the nuclear lamina via lamina-associated
domains (LADs) confer structural stability to the genome. The dynamics of positioning of …