[HTML][HTML] Strategies for analyzing bisulfite sequencing data

K Wreczycka, A Gosdschan, D Yusuf, B Grüning… - Journal of …, 2017‏ - Elsevier
DNA methylation is one of the main epigenetic modifications in the eukaryotic genome; it
has been shown to play a role in cell-type specific regulation of gene expression, and …

Statistical methods for detecting differentially methylated loci and regions

MD Robinson, A Kahraman, CW Law, H Lindsay… - Frontiers in …, 2014‏ - frontiersin.org
DNA methylation, the reversible addition of methyl groups at CpG dinucleotides, represents
an important regulatory layer associated with gene expression. Changed methylation status …

Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species

D Anastasiadi, A Esteve-Codina, F Piferrer - Epigenetics & chromatin, 2018‏ - Springer
Background DNA methylation is one of the main epigenetic mechanisms for the regulation of
gene expression in eukaryotes. In the standard model, methylation in gene promoters has …

A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data

H Feng, KN Conneely, H Wu - Nucleic acids research, 2014‏ - academic.oup.com
DNA methylation is an important epigenetic modification that has essential roles in cellular
processes including gene regulation, development and disease and is widely dysregulated …

De novo identification of differentially methylated regions in the human genome

TJ Peters, MJ Buckley, AL Statham, R Pidsley… - Epigenetics & …, 2015‏ - Springer
Background The identification and characterisation of differentially methylated regions
(DMRs) between phenotypes in the human genome is of prime interest in epigenetics. We …

DNMT3A mutations promote anthracycline resistance in acute myeloid leukemia via impaired nucleosome remodeling

OA Guryanova, K Shank, B Spitzer, L Luciani… - Nature medicine, 2016‏ - nature.com
Although the majority of patients with acute myeloid leukemia (AML) initially respond to
chemotherapy, many of them subsequently relapse, and the mechanistic basis for AML …

Aging human hematopoietic stem cells manifest profound epigenetic reprogramming of enhancers that may predispose to leukemia

ER Adelman, HT Huang, A Roisman, A Olsson… - Cancer …, 2019‏ - aacrjournals.org
Aging is associated with functional decline of hematopoietic stem cells (HSC) as well as an
increased risk of myeloid malignancies. We performed an integrative characterization of …

[HTML][HTML] Mutational cooperativity linked to combinatorial epigenetic gain of function in acute myeloid leukemia

AH Shih, Y Jiang, C Meydan, K Shank, S Pandey… - Cancer cell, 2015‏ - cell.com
Specific combinations of acute myeloid leukemia (AML) disease alleles, including FLT3 and
TET2 mutations, confer distinct biologic features and adverse outcome. We generated mice …

The loss of TET2 promotes CD8+ T cell memory differentiation

SA Carty, M Gohil, LB Banks, RM Cotton… - The Journal of …, 2018‏ - journals.aai.org
T cell differentiation requires appropriate regulation of DNA methylation. In this article, we
demonstrate that the methylcytosine dioxygenase ten-eleven translocation (TET) 2 regulates …

Migration‐related phenotypic divergence is associated with epigenetic modifications in rainbow trout

MR Baerwald, MH Meek, MR Stephens… - Molecular …, 2016‏ - Wiley Online Library
Migration is essential for the reproduction and survival of many animals, yet little is
understood about its underlying molecular mechanisms. We used the salmonid …