Epigenetic modifications of histones in cancer

Z Zhao, A Shilatifard - Genome biology, 2019 - Springer
The epigenetic modifications of histones are versatile marks that are intimately connected to
development and disease pathogenesis including human cancers. In this review, we will …

Sequencing depth and coverage: key considerations in genomic analyses

D Sims, I Sudbery, NE Ilott, A Heger… - Nature Reviews …, 2014 - nature.com
Sequencing technologies have placed a wide range of genomic analyses within the
capabilities of many laboratories. However, sequencing costs often set limits to the amount …

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

MA Quail, M Smith, P Coupland, TD Otto, SR Harris… - BMC genomics, 2012 - Springer
Background Next generation sequencing (NGS) technology has revolutionized genomic and
genetic research. The pace of change in this area is rapid with three major new sequencing …

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 …

Profiling genome-wide DNA methylation

WS Yong, FM Hsu, PY Chen - Epigenetics & chromatin, 2016 - Springer
DNA methylation is an epigenetic modification that plays an important role in regulating
gene expression and therefore a broad range of biological processes and diseases. DNA …

DNA methylation methods: Global DNA methylation and methylomic analyses

S Li, TO Tollefsbol - Methods, 2021 - Elsevier
DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has
significant involvement for numerous biological processes in health and disease. The …

Epigenetic modifications and human disease

A Portela, M Esteller - Nature biotechnology, 2010 - nature.com
Epigenetics is one of the most rapidly expanding fields in biology. The recent
characterization of a human DNA methylome at single nucleotide resolution, the discovery of …

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

SC Mack, H Witt, RM Piro, L Gu, S Zuyderduyn… - Nature, 2014 - nature.com
Ependymomas are common childhood brain tumours that occur throughout the nervous
system, but are most common in the paediatric hindbrain. Current standard therapy …

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

B Langmead, C Trapnell, M Pop, SL Salzberg - Genome biology, 2009 - Springer
Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence
reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie …

DNA methylation profiling in the clinic: applications and challenges

H Heyn, M Esteller - Nature Reviews Genetics, 2012 - nature.com
Abstract Knowledge of epigenetic alterations in disease is rapidly increasing owing to the
development of genome-wide techniques for their identification. The ever-growing number …