Artificial intelligence-based multi-omics analysis fuels cancer precision medicine

X He, X Liu, F Zuo, H Shi, J **g - Seminars in Cancer Biology, 2023 - Elsevier
With biotechnological advancements, innovative omics technologies are constantly
emerging that have enabled researchers to access multi-layer information from the genome …

Epigenetic regulation of T cell exhaustion

JA Belk, B Daniel, AT Satpathy - Nature immunology, 2022 - nature.com
Chronic antigen stimulation during viral infections and cancer can lead to T cell exhaustion,
which is characterized by reduced effector function and proliferation, and the expression of …

[HTML][HTML] Direct observation of a condensate effect on super-enhancer controlled gene bursting

M Du, SH Stitzinger, JH Spille, WK Cho, C Lee, M Hijaz… - Cell, 2024 - cell.com
Enhancers are distal DNA elements believed to loop and contact promoters to control gene
expression. Recently, we found diffraction-sized transcriptional condensates at genes …

The spatial organization of transcriptional control

A Hafner, A Boettiger - Nature Reviews Genetics, 2023 - nature.com
In animals, the sequences for controlling gene expression do not concentrate just at the
transcription start site of genes, but are frequently thousands to millions of base pairs distal …

Understanding 3D genome organization by multidisciplinary methods

I Jerkovic, G Cavalli - Nature reviews Molecular cell biology, 2021 - nature.com
Understanding how chromatin is folded in the nucleus is fundamental to understanding its
function. Although 3D genome organization has been historically difficult to study owing to a …

Mechanisms of enhancer action: the known and the unknown

A Panigrahi, BW O'Malley - Genome biology, 2021 - Springer
Differential gene expression mechanisms ensure cellular differentiation and plasticity to
shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential …

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies

A Rhie, BP Walenz, S Koren, AM Phillippy - Genome biology, 2020 - Springer
Recent long-read assemblies often exceed the quality and completeness of available
reference genomes, making validation challenging. Here we present Merqury, a novel tool …

Pharmacogenomics: driving personalized medicine

W Sadee, D Wang, K Hartmann, AE Toland - Pharmacological reviews, 2023 - Elsevier
Personalized medicine tailors therapies, disease prevention, and health maintenance to the
individual, with pharmacogenomics serving as a key tool to improve outcomes and prevent …

Long-range enhancer–promoter contacts in gene expression control

S Schoenfelder, P Fraser - Nature Reviews Genetics, 2019 - nature.com
Spatiotemporal gene expression programmes are orchestrated by transcriptional
enhancers, which are key regulatory DNA elements that engage in physical contacts with …

Computational methods for analysing multiscale 3D genome organization

Y Zhang, L Boninsegna, M Yang, T Misteli… - Nature Reviews …, 2024 - nature.com
Recent progress in whole-genome map** and imaging technologies has enabled the
characterization of the spatial organization and folding of the genome in the nucleus. In …