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 …

Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system

PSL Schäfer, D Dimitrov, EJ Villablanca… - Nature …, 2024 - nature.com
The immune system comprises diverse specialized cell types that cooperate to defend the
host against a wide range of pathogenic threats. Recent advancements in single-cell and …

Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities

S Müller-Dott, E Tsirvouli, M Vazquez… - Nucleic Acids …, 2023 - academic.oup.com
Gene regulation plays a critical role in the cellular processes that underlie human health and
disease. The regulatory relationship between transcription factors (TFs), key regulators of …

Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data

Q Yuan, Z Duren - Nature Biotechnology, 2024 - nature.com
Existing methods for gene regulatory network (GRN) inference rely on gene expression data
alone or on lower resolution bulk data. Despite the recent integration of chromatin …

Microfluidic impedance cytometry enabled one‐step sample preparation for efficient single‐cell mass spectrometry

J Zhu, S Pan, H Chai, P Zhao, Y Feng, Z Cheng… - Small, 2024 - Wiley Online Library
Single‐cell mass spectrometry (MS) is significant in biochemical analysis and holds great
potential in biomedical applications. Efficient sample preparation like sorting (ie, separating …

Single-cell analysis of chromatin accessibility in the adult mouse brain

S Zu, YE Li, K Wang, EJ Armand, S Mamde, ML Amaral… - Nature, 2023 - nature.com
Recent advances in single-cell technologies have led to the discovery of thousands of brain
cell types; however, our understanding of the gene regulatory programs in these cell types is …

Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data

D Kim, A Tran, HJ Kim, Y Lin, JYH Yang… - NPJ Systems Biology and …, 2023 - nature.com
Inferring gene regulatory networks (GRNs) is a fundamental challenge in biology that aims
to unravel the complex relationships between genes and their regulators. Deciphering these …

Cancer drug-tolerant persister cells: from biological questions to clinical opportunities

M Russo, M Chen, E Mariella, H Peng… - Nature Reviews …, 2024 - nature.com
The emergence of drug resistance is the most substantial challenge to the effectiveness of
anticancer therapies. Orthogonal approaches have revealed that a subset of cells, known as …

Predicting proximal tubule failed repair drivers through regularized regression analysis of single cell multiomic sequencing

N Ledru, PC Wilson, Y Muto, Y Yoshimura, H Wu… - Nature …, 2024 - nature.com
Renal proximal tubule epithelial cells have considerable intrinsic repair capacity following
injury. However, a fraction of injured proximal tubule cells fails to undergo normal repair and …

Gene expression networks regulated by human personality

C Del Val, E Díaz de la Guardia-Bolívar, I Zwir… - Molecular …, 2024 - nature.com
Genome-wide association studies of human personality have been carried out, but
transcription of the whole genome has not been studied in relation to personality in humans …