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 …

Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics

A Dorey, S Howorka - Nature chemistry, 2024 - nature.com
Sequencing of nucleic acids with nanopores has emerged as a powerful tool offering rapid
readout, high accuracy, low cost and portability. This label-free method for sequencing at the …

Hallmarks of cancer stemness

JJ Loh, S Ma - Cell Stem Cell, 2024 - cell.com
Cancer stemness is recognized as a key component of tumor development. Previously
coined" cancer stem cells"(CSCs) and believed to be a rare population with rigid …

Benchmarking algorithms for single-cell multi-omics prediction and integration

Y Hu, S Wan, Y Luo, Y Li, T Wu, W Deng, C Jiang… - Nature …, 2024 - nature.com
The development of single-cell multi-omics technology has greatly enhanced our
understanding of biology, and in parallel, numerous algorithms have been proposed to …

scPROTEIN: a versatile deep graph contrastive learning framework for single-cell proteomics embedding

W Li, F Yang, F Wang, Y Rong, L Liu, B Wu, H Zhang… - Nature …, 2024 - nature.com
Single-cell proteomics sequencing technology sheds light on protein–protein interactions,
posttranslational modifications and proteoform dynamics in the cell. However, the …

The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells

J Li, Z **ao, D Wang, L Jia, S Nie, X Zeng, W Hu - Molecular Cancer, 2023 - Springer
Recent advances in neoantigen research have accelerated the development of tumor
immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody …

From genotype to phenotype: Raman spectroscopy and machine learning for label-free single-cell analysis

Y Zhang, K Chang, B Ogunlade, L Herndon… - ACS …, 2024 - ACS Publications
Raman spectroscopy has made significant progress in biosensing and clinical research.
Here, we describe how surface-enhanced Raman spectroscopy (SERS) assisted with …

Identification of unique cell type responses in pancreatic islets to stress

MM Maestas, M Ishahak, P Augsornworawat… - Nature …, 2024 - nature.com
Diabetes involves the death or dysfunction of pancreatic β-cells. Analysis of bulk sequencing
from human samples and studies using in vitro and in vivo models suggest that endoplasmic …

Spatial multi-omics: novel tools to study the complexity of cardiovascular diseases

P Kiessling, C Kuppe - Genome Medicine, 2024 - Springer
Spatial multi-omic studies have emerged as a promising approach to comprehensively
analyze cells in tissues, enabling the joint analysis of multiple data modalities like …

Single Cell mass spectrometry: Towards quantification of small molecules in individual cells

Y Lan, Z Zou, Z Yang - TrAC Trends in Analytical Chemistry, 2024 - Elsevier
Studying cell heterogeneity can provide a deeper understanding of biological activities, but
appropriate studies cannot be performed using traditional bulk analysis methods. The …