Gene regulatory network inference in the era of single-cell multi-omics
P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
Chromatin accessibility profiling by ATAC-seq
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a
simple and scalable way to detect the unique chromatin landscape associated with a cell …
simple and scalable way to detect the unique chromatin landscape associated with a cell …
[HTML][HTML] Single-cell multiomics: technologies and data analysis methods
Advances in single-cell isolation and barcoding technologies offer unprecedented
opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk …
opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk …
Chromatin accessibility and the regulatory epigenome
SL Klemm, Z Shipony, WJ Greenleaf - Nature Reviews Genetics, 2019 - nature.com
Physical access to DNA is a highly dynamic property of chromatin that plays an essential
role in establishing and maintaining cellular identity. The organization of accessible …
role in establishing and maintaining cellular identity. The organization of accessible …
Generating specificity in genome regulation through transcription factor sensitivity to chromatin
Cell type-specific gene expression relies on transcription factors (TFs) binding DNA
sequence motifs embedded in chromatin. Understanding how motifs are accessed in …
sequence motifs embedded in chromatin. Understanding how motifs are accessed in …
[HTML][HTML] Natural products for drug discovery in the 21st century: innovations for novel drug discovery
NE Thomford, DA Senthebane, A Rowe… - International journal of …, 2018 - mdpi.com
The therapeutic properties of plants have been recognised since time immemorial. Many
pathological conditions have been treated using plant-derived medicines. These medicines …
pathological conditions have been treated using plant-derived medicines. These medicines …
The chromatin accessibility landscape of primary human cancers
INTRODUCTION Cancer is one of the leading causes of death worldwide. Although the 2%
of the human genome that encodes proteins has been extensively studied, much remains to …
of the human genome that encodes proteins has been extensively studied, much remains to …
Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements
Epigenomic maps identify gene regulatory elements by their chromatin state. However,
prevailing short-read sequencing methods cannot effectively distinguish alleles, evaluate …
prevailing short-read sequencing methods cannot effectively distinguish alleles, evaluate …
Genomics in the long-read sequencing era
EL van Dijk, D Naquin, K Gorrichon, Y Jaszczyszyn… - Trends in Genetics, 2023 - cell.com
Long-read sequencing (LRS) technologies have provided extremely powerful tools to
explore genomes. While in the early years these methods suffered technical limitations, they …
explore genomes. While in the early years these methods suffered technical limitations, they …
A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells
Cellular lineage histories and their molecular states encode fundamental principles of tissue
development and homeostasis. Current lineage-recording mouse models have insufficient …
development and homeostasis. Current lineage-recording mouse models have insufficient …