Scalable querying of human cell atlases via a foundational model reveals commonalities across fibrosis-associated macrophages

G Heimberg, T Kuo, D DePianto, T Heigl, N Diamant… - bioRxiv, 2023 - biorxiv.org
Single-cell RNA-seq (scRNA-seq) studies have profiled over 100 million human cells across
diseases, developmental stages, and perturbations to date. A singular view of this vast and …

Integration of spatial and single-cell data across modalities with weak linkage

S Chen, B Zhu, S Huang, JW Hickey, KZ Lin, M Snyder… - bioRxiv, 2023 - biorxiv.org
Abstract single-cell sequencing methods have enabled the profiling of multiple types of
molecular readouts at cellular resolution, and recent developments in spatial barcoding, in …

Computational methods for the integrative analysis of single-cell data

M Forcato, O Romano, S Bicciato - Briefings in bioinformatics, 2021 - academic.oup.com
Recent advances in single-cell technologies are providing exciting opportunities for
dissecting tissue heterogeneity and investigating cell identity, fate and function. This is a …

[HTML][HTML] Functional inference of gene regulation using single-cell multi-omics

VK Kartha, FM Duarte, Y Hu, S Ma, JG Chew… - Cell genomics, 2022 - cell.com
Cells require coordinated control over gene expression when responding to environmental
stimuli. Here we apply scATAC-seq and single-cell RNA sequencing (scRNA-seq) in resting …

Progress in single-cell multimodal sequencing and multi-omics data integration

X Wang, X Wu, N Hong, W Jin - Biophysical Reviews, 2024 - Springer
With the rapid advance of single-cell sequencing technology, cell heterogeneity in various
biological processes was dissected at different omics levels. However, single-cell mono …

Cells and gene expression programs in the adult human heart

M Litviňuková, C Talavera-López, H Maatz, D Reichart… - BioRxiv, 2020 - biorxiv.org
Cardiovascular disease is the leading cause of death worldwide. Advanced insights into
disease mechanisms and strategies to improve therapeutic opportunities require deeper …

Challenges and emerging directions in single-cell analysis

GC Yuan, L Cai, M Elowitz, T Enver, G Fan, G Guo… - Genome biology, 2017 - Springer
Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular
information at the individual cell level. Development of single-cell technologies and …

MultiCellDS: a standard and a community for sharing multicellular data

SH Friedman, ARA Anderson, DM Bortz, AG Fletcher… - bioRxiv, 2016 - biorxiv.org
Cell biology is increasingly focused on cellular heterogeneity and multicellular systems. To
make the fullest use of experimental, clinical, and computational efforts, we need …

From monkey single-cell atlases into a broader biomedical perspective

X Zou, X Dai, AFA Mentis, MA Esteban, L Liu… - Life …, 2022 - academic.oup.com
The cell is the fundamental constituent unit of a mammal which, in turn, depends on the
cooperative work of various cells to compose intricate life activities. Cells harbor diverse …

Single-cell atlases: shared and tissue-specific cell types across human organs

R Elmentaite, C Domínguez Conde, L Yang… - Nature Reviews …, 2022 - nature.com
The development of single-cell and spatial transcriptomics methods was instrumental in the
conception of the Human Cell Atlas initiative, which aims to generate an integrated map of …