Genome-wide approaches to studying chromatin modifications

DE Schones, K Zhao - Nature Reviews Genetics, 2008 - nature.com
Over two metres of DNA is packaged into each nucleus in the human body in a manner that
still allows for gene regulation. This remarkable feat is accomplished by the wrapping of …

Computational intelligence approaches for classification of medical data: State-of-the-art, future challenges and research directions

A Kalantari, A Kamsin, S Shamshirband, A Gani… - Neurocomputing, 2018 - Elsevier
The explosive growth of data in volume, velocity and diversity that are produced by medical
applications has contributed to abundance of big data. Current solutions for efficient data …

iDNA-Methyl: Identifying DNA methylation sites via pseudo trinucleotide composition

Z Liu, X Xiao, WR Qiu, KC Chou - Analytical biochemistry, 2015 - Elsevier
Predominantly occurring on cytosine, DNA methylation is a process by which cells can
modify their DNAs to change the expression of gene products. It plays very important roles in …

Cancer DNA methylation: molecular mechanisms and clinical implications

MT McCabe, JC Brandes, PM Vertino - Clinical Cancer Research, 2009 - AACR
DNA methylation plays a crucial role in the regulation of gene expression and chromatin
organization within normal eukaryotic cells. In cancer, however, global patterns of DNA …

[HTML][HTML] Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements

W Zhang, TD Spector, P Deloukas, JT Bell… - Genome biology, 2015 - Springer
Background Recent assays for individual-specific genome-wide DNA methylation profiles
have enabled epigenome-wide association studies to identify specific CpG sites associated …

[HTML][HTML] Predicting DNA methylation state of CpG dinucleotide using genome topological features and deep networks

Y Wang, T Liu, D Xu, H Shi, C Zhang, YY Mo… - Scientific reports, 2016 - nature.com
The hypo-or hyper-methylation of the human genome is one of the epigenetic features of
leukemia. However, experimental approaches have only determined the methylation state of …

Prediction of genome-wide DNA methylation in repetitive elements

Y Zheng, BT Joyce, L Liu, Z Zhang… - Nucleic acids …, 2017 - academic.oup.com
DNA methylation in repetitive elements (RE) suppresses their mobility and maintains
genomic stability, and decreases in it are frequently observed in tumor and/or surrogate …

[HTML][HTML] CpG island mapping by epigenome prediction

C Bock, J Walter, M Paulsen… - PLoS computational …, 2007 - journals.plos.org
CpG islands were originally identified by epigenetic and functional properties, namely,
absence of DNA methylation and frequent promoter association. However, this concept was …

[HTML][HTML] Epigenetic Reprogramming in Mice and Humans: From Fertilization to Primordial Germ Cell Development

A Singh, DA Rappolee, DM Ruden - Cells, 2023 - mdpi.com
In this review, advances in the understanding of epigenetic reprogramming from fertilization
to the development of primordial germline cells in a mouse and human embryo are …

Computational epigenetics

C Bock, T Lengauer - Bioinformatics, 2008 - academic.oup.com
Epigenetic research aims to understand heritable gene regulation that is not directly
encoded in the DNA sequence. Epigenetic mechanisms such as DNA methylation and …