[HTML][HTML] From reads to insight: a hitchhiker's guide to ATAC-seq data analysis
Abstract Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely
used in studying chromatin biology, but a comprehensive review of the analysis tools has …
used in studying chromatin biology, but a comprehensive review of the analysis tools has …
[HTML][HTML] Pig genome functional annotation enhances the biological interpretation of complex traits and human disease
The functional annotation of livestock genomes is crucial for understanding the molecular
mechanisms that underpin complex traits of economic importance, adaptive evolution and …
mechanisms that underpin complex traits of economic importance, adaptive evolution and …
Genomic enhancers in cardiac development and disease
CG Anene-Nzelu, MCJ Lee, WLW Tan… - Nature Reviews …, 2022 - nature.com
Abstract The Human Genome Project marked a major milestone in the scientific community
as it unravelled the~ 3 billion bases that are central to crucial aspects of human life. Despite …
as it unravelled the~ 3 billion bases that are central to crucial aspects of human life. Despite …
[HTML][HTML] Dissecting cell identity via network inference and in silico gene perturbation
Cell identity is governed by the complex regulation of gene expression, represented as gene-
regulatory networks. Here we use gene-regulatory networks inferred from single-cell multi …
regulatory networks. Here we use gene-regulatory networks inferred from single-cell multi …
[HTML][HTML] HNF4A defines tissue-specific circadian rhythms by beaconing BMAL1:: CLOCK chromatin binding and shaping the rhythmic chromatin landscape
Transcription modulated by the circadian clock is diverse across cell types, underlying
circadian control of peripheral metabolism and its observed perturbation in human diseases …
circadian control of peripheral metabolism and its observed perturbation in human diseases …
[HTML][HTML] A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues
Background Although considerable progress has been made towards annotating the
noncoding portion of the human and mouse genomes, regulatory elements in other species …
noncoding portion of the human and mouse genomes, regulatory elements in other species …
[HTML][HTML] ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation
Background Chromatin dysregulation is associated with developmental disorders and
cancer. Numerous methods for measuring genome-wide chromatin accessibility have been …
cancer. Numerous methods for measuring genome-wide chromatin accessibility have been …
[HTML][HTML] Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs
Background The genetic mechanisms that underlie phenotypic differentiation in breeding
animals have important implications in evolutionary biology and agriculture. However, the …
animals have important implications in evolutionary biology and agriculture. However, the …
Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma
Enhancer reprogramming has been proposed as a key source of transcriptional
dysregulation during tumorigenesis, but the molecular mechanisms underlying this process …
dysregulation during tumorigenesis, but the molecular mechanisms underlying this process …
[HTML][HTML] Effects of nucleases on cell-free extrachromosomal circular DNA
Cell-free extrachromosomal circular DNA (eccDNA) as a distinct topological form from linear
DNA has recently gained increasing research interest, with possible clinical applications as …
DNA has recently gained increasing research interest, with possible clinical applications as …