Robert C. Jones

The paper presents a single-cell long-read isoform atlas across 26 human tissues, revealing novel isoforms and their role in cellular identity and senescence.

This study identifies conserved and clade-specific hypothalamic cell types across vertebrates using single-cell transcriptomics, revealing conserved transcription factors and rewired regulatory linkages.

The paper expands Tabula Sapiens to include non-coding RNA data from 22 human tissues, revealing cell type-specific expression and subcellular localization patterns of non-coding RNAs.

The paper benchmarks large language models for cell-type and gene set annotation using AnnDictionary, finding high accuracy in cell-type annotation and strong functional gene set recovery.

This study investigates islet cell dysfunction in type 1 diabetes by integrating electrophysiological, transcriptomic, and machine learning analyses of human islet cells from T1D donors.

The paper presents an aging Drosophila cell atlas, identifies cell type-specific aging patterns, and shows ribosomal gene expression as a conserved aging predictor.

Portal integrates large-scale single-cell datasets efficiently and accurately by preserving biological variation across samples, platforms, and species.

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.

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.

This study uses single-cell RNA-sequencing to analyze cell type-specific responses to young or aged blood in heterochronic parabiosis, identifying mitochondrial function as a key factor in rejuvenation.

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 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.

This paper introduces a microfluidic platform for standardized, sensitive ChIP-Seq on low-input samples, enabling high-throughput and reproducible epigenetic profiling.

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.

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

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.

This study benchmarks 13 scRNA-seq protocols to evaluate their effectiveness in characterizing cell types and states for cell atlas projects.

The paper develops a tool to analyze spatial gene expression correlations in tissue sections, applied to human fetal pancreas development.