Epigenetic modifications of histones in cancer
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 …
development and disease pathogenesis including human cancers. In this review, we will …
Organizational principles of 3D genome architecture
Studies of 3D chromatin organization have suggested that chromosomes are hierarchically
organized into large compartments composed of smaller domains called topologically …
organized into large compartments composed of smaller domains called topologically …
Performance measures in evaluating machine learning based bioinformatics predictors for classifications
Y Jiao, P Du - Quantitative Biology, 2016 - Springer
Background Many existing bioinformatics predictors are based on machine learning
technology. When applying these predictors in practical studies, their predictive …
technology. When applying these predictors in practical studies, their predictive …
Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations
A three-dimensional chromatin state underpins the structural and functional basis of the
genome by bringing regulatory elements and genes into close spatial proximity to ensure …
genome by bringing regulatory elements and genes into close spatial proximity to ensure …
Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2
Fit-Hi-C is a programming application to compute statistical confidence estimates for Hi-C
contact maps to identify significant chromatin contacts. By fitting a monotonically non …
contact maps to identify significant chromatin contacts. By fitting a monotonically non …
Dissecting super-enhancer hierarchy based on chromatin interactions
Recent studies have highlighted super-enhancers (SEs) as important regulatory elements
for gene expression, but their intrinsic properties remain incompletely characterized …
for gene expression, but their intrinsic properties remain incompletely characterized …
Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation
Developmental genes in metazoan genomes are surrounded by dense clusters of
conserved noncoding elements (CNEs). CNEs exhibit unexplained extreme levels of …
conserved noncoding elements (CNEs). CNEs exhibit unexplained extreme levels of …
Epigenomic landscape and 3D genome structure in pediatric high-grade glioma
Pediatric high-grade gliomas (pHGGs), including glioblastoma multiforme (GBM) and diffuse
intrinsic pontine glioma (DIPG), are morbid brain tumors. Even with treatment survival is …
intrinsic pontine glioma (DIPG), are morbid brain tumors. Even with treatment survival is …
Comparative 3D genome architecture in vertebrates
Background The three-dimensional (3D) architecture of the genome has a highly ordered
and hierarchical nature, which influences the regulation of essential nuclear processes at …
and hierarchical nature, which influences the regulation of essential nuclear processes at …
Constructing 3D interaction maps from 1D epigenomes
The human genome is tightly packaged into chromatin whose functional output depends on
both one-dimensional (1D) local chromatin states and three-dimensional (3D) genome …
both one-dimensional (1D) local chromatin states and three-dimensional (3D) genome …