Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics

GS Gulati, JP D'Silva, Y Liu, L Wang… - … Reviews Molecular Cell …, 2024 - nature.com
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene
expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has …

Single-cell analysis in rheumatic and allergic diseases: insights for clinical practice

M Nishide, H Shimagami, A Kumanogoh - Nature Reviews Immunology, 2024 - nature.com
Since the advent of single-cell RNA sequencing (scRNA-seq) methodology, single-cell
analysis has become a powerful tool for exploration of cellular networks and dysregulated …

Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data

F Drost, Y An, I Bonafonte-Pardàs, LM Dratva… - Nature …, 2024 - nature.com
Recent advances in single-cell immune profiling have enabled the simultaneous
measurement of transcriptome and T cell receptor (TCR) sequences, offering great potential …

Considerations for building and using integrated single-cell atlases

K Hrovatin, L Sikkema, VA Shitov, G Heimberg… - Nature …, 2024 - nature.com
The rapid adoption of single-cell technologies has created an opportunity to build single-cell
'atlases' integrating diverse datasets across many laboratories. Such atlases can serve as a …

Single-cell integration reveals metaplasia in inflammatory gut diseases

AJ Oliver, N Huang, R Bartolome-Casado, R Li… - Nature, 2024 - nature.com
The gastrointestinal tract is a multi-organ system crucial for efficient nutrient uptake and
barrier immunity. Advances in genomics and a surge in gastrointestinal diseases, has …

Delineating the effective use of self-supervised learning in single-cell genomics

T Richter, M Bahrami, Y **a, DS Fischer… - Nature Machine …, 2024 - nature.com
Self-supervised learning (SSL) has emerged as a powerful method for extracting meaningful
representations from vast, unlabelled datasets, transforming computer vision and natural …

Establishing a human bone marrow single cell reference atlas to study ageing and diseases

NYS Lee, M Li, KS Ang, J Chen - Frontiers in Immunology, 2023 - frontiersin.org
Introduction Ageing in the human bone marrow is associated with immune function decline
that results in the elderly being vulnerable to illnesses. A comprehensive healthy bone …

Estimating the impact of single-cell RNA sequencing of human tissues on drug target validation

E Dann, E Teeple, R Elmentaite, KB Meyer, G Gaglia… - MedRxiv, 2024 - medrxiv.org
Early characterization of drug targets associated with disease can greatly reduce clinical
failures attributed to lack of safety or efficacy. As single-cell RNA sequencing (scRNA-seq) of …

Computational single cell oncology: state of the art

E Paas-Oliveros, E Hernández-Lemus… - Frontiers in …, 2023 - frontiersin.org
Single cell computational analysis has emerged as a powerful tool in the field of oncology,
enabling researchers to decipher the complex cellular heterogeneity that characterizes …

Rapid Identification of Cell Types and Phenotypic States Using a One-Polymer Multichannel Nanosensor Fabricated via Flash Nanoprecipitation

M Jiang, J Yang, L Liu, AN Chattopadhyay… - … Applied Materials & …, 2024 - ACS Publications
Cell state transitions are fundamental in biology, determining how cells respond to
environmental stimuli and adapt to diseases and treatments. Cell surface-based sensing of …