Using clusterProfiler to characterize multiomics data

S Xu, E Hu, Y Cai, Z Xie, X Luo, L Zhan, W Tang… - Nature protocols, 2024 - nature.com
With the advent of multiomics, software capable of multidimensional enrichment analysis
has become increasingly crucial for uncovering gene set variations in biological processes …

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 …

Transformers in single-cell omics: a review and new perspectives

A Szałata, K Hrovatin, S Becker, A Tejada-Lapuerta… - Nature …, 2024 - nature.com
Recent efforts to construct reference maps of cellular phenotypes have expanded the
volume and diversity of single-cell omics data, providing an unprecedented resource for …

Guidelines for minimal information on cellular senescence experimentation in vivo

M Ogrodnik, JC Acosta, PD Adams, FA di Fagagna… - Cell, 2024 - cell.com
Cellular senescence is a cell fate triggered in response to stress and is characterized by
stable cell-cycle arrest and a hypersecretory state. It has diverse biological roles, ranging …

Construction of a 3D whole organism spatial atlas by joint modelling of multiple slices with deep neural networks

G Wang, J Zhao, Y Yan, Y Wang, AR Wu… - Nature Machine …, 2023 - nature.com
Spatial transcriptomics (ST) technologies are revolutionizing the way to explore the spatial
architecture of tissues. Currently, ST data analysis is often restricted to a single two …

Strategies for the development of metalloimmunotherapies

X Sun, X Zhou, X Shi, OA Abed, X An, YL Lei… - Nature Biomedical …, 2024 - nature.com
Metal ions play crucial roles in the regulation of immune pathways. In fact, metallodrugs
have a long record of accomplishment as effective treatments for a wide range of diseases …

SpatialData: an open and universal data framework for spatial omics

L Marconato, G Palla, KA Yamauchi, I Virshup… - Nature …, 2024 - nature.com
Spatially resolved omics technologies are transforming our understanding of biological
tissues. However, the handling of uni-and multimodal spatial omics datasets remains a …

Cell–cell communication: new insights and clinical implications

J Su, Y Song, Z Zhu, X Huang, J Fan, J Qiao… - Signal Transduction and …, 2024 - nature.com
Multicellular organisms are composed of diverse cell types that must coordinate their
behaviors through communication. Cell–cell communication (CCC) is essential for growth …

Benchmarking spatial clustering methods with spatially resolved transcriptomics data

Z Yuan, F Zhao, S Lin, Y Zhao, J Yao, Y Cui… - Nature …, 2024 - nature.com
Spatial clustering, which shares an analogy with single-cell clustering, has expanded the
scope of tissue physiology studies from cell-centroid to structure-centroid with spatially …

Regulation and targeting of SREBP-1 in hepatocellular carcinoma

F Su, A Koeberle - Cancer and Metastasis Reviews, 2024 - Springer
Hepatocellular carcinoma (HCC) is an increasing burden on global public health and is
associated with enhanced lipogenesis, fatty acid uptake, and lipid metabolic …