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 …

Moana: a robust and scalable cell type classification framework for single-cell RNA-Seq data

F Wagner, I Yanai - BioRxiv, 2018 - biorxiv.org
Abstract Single-cell RNA-Seq (scRNA-Seq) enables the systematic molecular
characterization of heterogeneous tissues at an unprecedented resolution and scale …

Geometric sketching compactly summarizes the single-cell transcriptomic landscape

B Hie, H Cho, B DeMeo, B Bryson, B Berger - Cell systems, 2019 - cell.com
Large-scale single-cell RNA sequencing (scRNA-seq) studies that profile hundreds of
thousands of cells are becoming increasingly common, overwhelming existing analysis …

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

R Browaeys, J Gilis, C Sang-Aram, P De Bleser… - BioRxiv, 2023 - biorxiv.org
Dysregulated cell-cell communication is a hallmark of many disease phenotypes. Due to
recent advances in single-cell transcriptomics and computational approaches, it is now …

[HTML][HTML] Comprehensive integration of single-cell data

T Stuart, A Butler, P Hoffman, C Hafemeister… - cell, 2019 - cell.com
Single-cell transcriptomics has transformed our ability to characterize cell states, but deep
biological understanding requires more than a taxonomic listing of clusters. As new methods …

Identifying disease-critical cell types and cellular processes across the human body by integration of single-cell profiles and human genetics

KA Jagadeesh, KK Dey, DT Montoro, R Mohan… - bioRxiv, 2021 - biorxiv.org
Genome-wide association studies (GWAS) provide a powerful means to identify loci and
genes contributing to disease, but in many cases the related cell types/states through which …

Using LLMs and Explainable ML to Analyze Biomarkers at Single-Cell Level for Improved Understanding of Diseases

J Elsborg, M Salvatore - Biomolecules, 2023 - mdpi.com
Single-cell RNA sequencing (scRNA-seq) technology has significantly advanced our
understanding of the diversity of cells and how this diversity is implicated in diseases. Yet …

An integrated cell atlas of the lung in health and disease

L Sikkema, C Ramírez-Suástegui, DC Strobl… - Nature medicine, 2023 - nature.com
Single-cell technologies have transformed our understanding of human tissues. Yet, studies
typically capture only a limited number of donors and disagree on cell type definitions …

CZ CELLxGENE Discover: A single-cell data platform for scalable exploration, analysis and modeling of aggregated data

CZI Single-Cell Biology, S Abdulla, B Aevermann… - BioRxiv, 2023 - biorxiv.org
Hundreds of millions of single cells have been analyzed to date using high throughput
transcriptomic methods, thanks to technological advances driving the increasingly rapid …

Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases

I Korsunsky, K Wei, M Pohin, EY Kim, F Barone… - Med, 2022 - cell.com
Background Pro-inflammatory fibroblasts are critical for pathogenesis in rheumatoid arthritis,
inflammatory bowel disease, interstitial lung disease, and Sjögren's syndrome and represent …