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 …
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
Abstract Single-cell RNA-Seq (scRNA-Seq) enables the systematic molecular
characterization of heterogeneous tissues at an unprecedented resolution and scale …
characterization of heterogeneous tissues at an unprecedented resolution and scale …
Geometric sketching compactly summarizes the single-cell transcriptomic landscape
Large-scale single-cell RNA sequencing (scRNA-seq) studies that profile hundreds of
thousands of cells are becoming increasingly common, overwhelming existing analysis …
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
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 …
recent advances in single-cell transcriptomics and computational approaches, it is now …
[HTML][HTML] Comprehensive integration of single-cell data
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 …
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
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 …
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 …
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
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 …
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 …
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
Background Pro-inflammatory fibroblasts are critical for pathogenesis in rheumatoid arthritis,
inflammatory bowel disease, interstitial lung disease, and Sjögren's syndrome and represent …
inflammatory bowel disease, interstitial lung disease, and Sjögren's syndrome and represent …