Comprehensive analysis of single cell ATAC-seq data with SnapATAC
Identification of the cis-regulatory elements controlling cell-type specific gene expression
patterns is essential for understanding the origin of cellular diversity. Conventional assays to …
patterns is essential for understanding the origin of cellular diversity. Conventional assays to …
Establishment and evolution of heterochromatin
The eukaryotic genome is packaged into transcriptionally active euchromatin and silent
heterochromatin, with most studies focused on the former encompassing the majority of …
heterochromatin, with most studies focused on the former encompassing the majority of …
Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells
Chromatin architecture has been implicated in cell type-specific gene regulatory programs,
yet how chromatin remodels during development remains to be fully elucidated. Here, by …
yet how chromatin remodels during development remains to be fully elucidated. Here, by …
DNA methylation atlas of the mouse brain at single-cell resolution
Mammalian brain cells show remarkable diversity in gene expression, anatomy and
function, yet the regulatory DNA landscape underlying this extensive heterogeneity is poorly …
function, yet the regulatory DNA landscape underlying this extensive heterogeneity is poorly …
An atlas of gene regulatory elements in adult mouse cerebrum
The mammalian cerebrum performs high-level sensory perception, motor control and
cognitive functions through highly specialized cortical and subcortical structures. Recent …
cognitive functions through highly specialized cortical and subcortical structures. Recent …
Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations
When different types of functional genomics data are generated on single cells from different
samples of cells from the same heterogeneous population, the clustering of cells in the …
samples of cells from the same heterogeneous population, the clustering of cells in the …
[HTML][HTML] The changing mouse embryo transcriptome at whole tissue and single-cell resolution
P He, BA Williams, D Trout, GK Marinov, H Amrhein… - Nature, 2020 - nature.com
During mammalian embryogenesis, differential gene expression gradually builds the identity
and complexity of each tissue and organ system. Here we systematically quantified mouse …
and complexity of each tissue and organ system. Here we systematically quantified mouse …
Annotation of chromatin states in 66 complete mouse epigenomes during development
The morphologically and functionally distinct cell types of a multicellular organism are
maintained by their unique epigenomes and gene expression programs. Phase III of the …
maintained by their unique epigenomes and gene expression programs. Phase III of the …
Reassessment of weak parent-of-origin expression bias shows it rarely exists outside of known imprinted regions
CA Edwards, WMD Watkinson, SB Telerman… - Elife, 2023 - elifesciences.org
In mouse and human, genes subjected to genomic imprinting have been shown to function
in development, behavior, and post-natal adaptations. Failure to correctly imprint genes in …
in development, behavior, and post-natal adaptations. Failure to correctly imprint genes in …
Time course regulatory analysis based on paired expression and chromatin accessibility data
A time course experiment is a widely used design in the study of cellular processes such as
differentiation or response to stimuli. In this paper, we propose time course reg ulatory …
differentiation or response to stimuli. In this paper, we propose time course reg ulatory …