Stephen R. Quake

The paper uses single-cell RNA sequencing to identify and characterize neuropeptide and peptide hormone genes in pulmonary neuroendocrine cells from mice and humans, revealing their diverse signaling roles and potential endocrine functions.

This paper uses a mouse lemur transcriptomic atlas to identify new genes, splice junctions, and disease-related features, highlighting their relevance to primate biology and human disease.

The paper examines age-related changes in gene expression noise across multiple cell types and tissues using single-cell transcriptomics, identifying thousands of genes with significant noise changes.

The paper analyzes single-cell transcriptome and chromatin accessibility data to uncover transcription factor networks governing pancreatic endocrine cell lineage specification.

This study identifies Acj6 as a transcription factor that controls dendrite targeting in Drosophila PNs by regulating combinatorial expression of cell-surface proteins.

Nearly 500,000 cells from 24 human tissues, many from one donor, characterize over 400 cell types and enable within-donor study of T-cell clones, B-cell mutation rates and splicing.

This paper identifies activated interstitial macrophages as a key target of SARS-CoV-2 infection in human lung tissue, showing their role in viral takeover, inflammation, and fibrosis.

The paper characterizes the microbial community of Auka vents, revealing high diversity, novel metabolic traits, and evidence of long-distance species transfer and thermophilic evolution.

The paper shows reducing USP16 improves neural precursor cell function and memory in an Alzheimer's model by affecting Cdkn2a and BMP signaling.

The paper creates a single-cell transcriptomic atlas of the adult fruit fly, identifying over 250 cell types and analyzing gene signatures and sexual dimorphism across tissues.

The paper creates a comprehensive cell atlas of mouse lemurs using single-cell RNA sequencing, identifying over 750 cell types and comparing their molecular profiles to humans, mice, and macaques.

The paper shows that coronary endothelial cells in mouse and human hearts initially show lineage-specific transcriptional differences but later become influenced by location, with adult cells becoming more homogeneous.

The paper introduces SpliZ, a statistical method to detect cell-type-specific splicing regulation in single-cell RNA-seq data, finding 9.1% of genes show such regulation in human tissues.

The paper characterizes cell types in the fly kidney using snRNA-seq and identifies new clusters, markers, and signaling networks, linking them to mammalian and planarian kidney structures.

The paper shows that reciprocal repulsions between Teneurin-3 and Latrophilin-2 guide the assembly of parallel hippocampal networks during development.

The paper studies neurodegeneration in the colonial chordate Botryllus schlosseri, finding conserved mechanisms between tunicates and humans.

The paper uses single-cell transcriptomics and in-situ imaging to study lung mesenchymal cell diversity during development and hyperoxia, finding delayed diversity and emergence of Acta1+ cells under hyperoxic conditions.

The paper develops methods to identify cell type contributions in cell-free RNA from blood, showing it reflects diverse cell types in health and disease.

The paper uses SAMap to compare single-cell atlases across species, identifying homologous cell types and revealing ancient cell families in animal evolution.

The paper profiles the transcriptional development and injury sensitivity of lung endothelial subtypes during postnatal growth, revealing distinct transcriptomic changes and differential responses to hyperoxia.

The paper generates single-cell transcriptomes of Drosophila olfactory receptor neurons across development and adulthood, revealing stable receptor expression and cell-type-specific transcriptomic features.

The paper analyzes single-cell transcriptomes of Drosophila olfactory projection neurons across developmental stages to identify transcriptomic changes and cellular diversity patterns.

The paper identifies a conserved cell type set in cerebellar nuclei across species and shows how it was duplicated to form new regions, with a shift in dominance in humans.

The paper identifies age-specific circadian gene expression patterns in Botryllus schlosseri and links them to aging phenotypes and pathways.

The paper creates a comprehensive molecular cell atlas of the human lung using single-cell RNA sequencing, identifying 58 cell populations including 14 new types and revealing evolutionary changes in lung cell types.

Northstar automatically classifies known and novel cell types from tumor samples with high accuracy and robustness.

The paper uses single-cell RNA sequencing to map gene expression changes in the human endometrium across the menstrual cycle, identifying distinct cell types and their transcriptional signatures.

This paper introduces Smart-seq-total, a single-cell RNA-seq method that captures both poly(A)+ and poly(A)- transcripts, enabling comprehensive analysis of the RNAome and revealing new roles of non-coding RNA in cellular processes.

This study uses single-cell transcriptomics to reveal diverse immune cell roles in the developing mouse lung, showing dynamic changes in macrophage subtypes and their functions during lung development.