The technological landscape and applications of single-cell multi-omics

A Baysoy, Z Bai, R Satija, R Fan - Nature Reviews Molecular Cell …, 2023 - nature.com
Single-cell multi-omics technologies and methods characterize cell states and activities by
simultaneously integrating various single-modality omics methods that profile the …

Decoding the tumor microenvironment with spatial technologies

LA Walsh, DF Quail - Nature immunology, 2023 - nature.com
Visualization of the cellular heterogeneity and spatial architecture of the tumor
microenvironment (TME) is becoming increasingly important to understand mechanisms of …

Systematic comparison of sequencing-based spatial transcriptomic methods

Y You, Y Fu, L Li, Z Zhang, S Jia, S Lu, W Ren, Y Liu… - Nature …, 2024 - nature.com
Recent developments of sequencing-based spatial transcriptomics (sST) have catalyzed
important advancements by facilitating transcriptome-scale spatial gene expression …

The status of the human gene catalogue

P Amaral, S Carbonell-Sala, FM De La Vega, T Faial… - Nature, 2023 - nature.com
Scientists have been trying to identify every gene in the human genome since the initial draft
was published in 2001. In the years since, much progress has been made in identifying …

[HTML][HTML] Empowering biomedical discovery with AI agents

S Gao, A Fang, Y Huang, V Giunchiglia, A Noori… - Cell, 2024 - cell.com
We envision" AI scientists" as systems capable of skeptical learning and reasoning that
empower biomedical research through collaborative agents that integrate AI models and …

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 …

Spatial map** of cellular senescence: emerging challenges and opportunities

AU Gurkar, AA Gerencser, AL Mora, AC Nelson… - Nature aging, 2023 - nature.com
Cellular senescence is a well-established driver of aging and age-related diseases. There
are many challenges to map** senescent cells in tissues such as the absence of specific …

Spatial metatranscriptomics resolves host–bacteria–fungi interactomes

S Saarenpää, O Shalev, H Ashkenazy, V Carlos… - Nature …, 2024 - nature.com
The interactions of microorganisms among themselves and with their multicellular host take
place at the microscale, forming complex networks and spatial patterns. Existing technology …

Custom microfluidic chip design enables cost-effective three-dimensional spatiotemporal transcriptomics with a wide field of view

J Zhu, K Pang, B Hu, R He, N Wang, Z Jiang, P Ji… - Nature Genetics, 2024 - nature.com
Spatial transcriptomic techniques offer unprecedented insights into the molecular
organization of complex tissues. However, integrating cost-effectiveness, high throughput, a …

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 …