Stephen R. Quake

This study links transcriptomic heterogeneity in pancreatic islet cells to their physiological function using a combined electrophysiological and single-cell RNA sequencing approach, identifying genes and pathways associated with diabetes-related dysfunction.

This study investigates pig pancreatic islet development, identifying similarities with human islet ontogeny and uncovering signaling pathways relevant to beta-cell maturation.

The paper creates a comprehensive mouse tissue atlas of small non-coding RNAs, revealing tissue-specific and sex-specific expression patterns and linking ncRNAs to cell types in the brain.

This study shows that cell-free mRNA reflects BM transcriptional activity and functional changes in response to growth factors and hematopoietic reconstitution.

The paper examines how transcriptomic types of mouse prefrontal cortex projection neurons relate to axonal projections and encoding properties across cognitive tasks, finding redundant but quantitatively biased task signal encoding.

The paper profiles cell-surface proteomes in Drosophila olfactory neurons across development, identifying new regulators of neural circuit assembly.

The paper creates a cell type atlas of the adult murine striatum using single-cell RNA-seq and identifies discrete and continuous cell identities within spiny projection neurons.

The paper identifies IgnaviCas9, a hyperthermophilic Cas9 from an unculturable Ignavibacterium, which functions at higher temperatures than existing Cas9 variants and is applied in RNA-seq library preparation.

The paper characterizes serotonin neuron subtypes in the dorsal and medial raphe nuclei using single-cell RNA sequencing and maps their axonal projections to understand their functional diversity.

This study compares molecular and morphological signatures in two developmental pathways of tunicates, finding distinct molecular programs but shared stem cell profiles.

The paper identifies persistent transcriptional changes in diverse cells of the medial prefrontal cortex associated with remote memory, including neurons, astrocytes, and microglia.

The paper introduces the self-assembling manifold algorithm to improve gene relevance quantification and dimensionality reduction in single-cell RNA sequencing data, showing it outperforms existing methods in identifying stem cell populations and across multiple datasets.

PhaMers identifies 103 novel phage sequences from Yellowstone hot spring metagenomes using tetranucleotide frequency analysis and compares results with VirSorter.

This paper introduces a genome alignment-based model for viral classification using information theory and gene match scores, resulting in clusters that correlate with existing viral classifications.

The paper analyzes aging dynamics across 17 organs and plasma proteomics in mice, revealing consistent gene expression trajectories with organ-specific timing and amplitude.

This study shows that overexpressing c-Jun in CAR-T cells reduces exhaustion and improves antitumor activity in vivo.

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

The paper identifies transcription factors that coordinate olfactory receptor expression and wiring specificity in Drosophila ORNs using single-cell RNA-sequencing and genetic analysis.

This study uses single-cell RNA sequencing to show that brain endothelial cells respond to circulatory cues of aging, with aged plasma inducing aging transcriptomes and young plasma reversing them.

This study uses scRNA-seq to analyze microglia and myeloid cells across brain regions and developmental stages, revealing heterogeneity in postnatal microglia and their roles in disease.

The paper identifies EpCAM+/CDH6+/TROP-2- cells as liver progenitors using single-cell RNA sequencing in human fetal and adult liver tissue.

This study demonstrates that hypothermic storage of intact mouse kidneys in organ transplant preservative maintains transcriptome quality for single cell RNAseq analysis.

This study shows aged blood reduces hippocampal neurogenesis and activates microglia via VCAM1 at the BBB, and blocking VCAM1 reverses these effects.

The paper identifies hematopoietic stem cells and related lineages in Botryllus schlosseri, suggesting their evolutionary origin in a common ancestor of tunicates and vertebrates.

The paper uses single-cell RNA-seq to study stress response heterogeneity in yeast, finding regulatory variation and decoupled transcription-factor activation.

This paper develops a noninvasive prenatal diagnosis method using ddPCR to detect single-gene disorders from maternal plasma, successfully identifying affected pregnancies as early as week 11.

This study uses single-cell RNA sequencing to classify Drosophila olfactory projection neuron subtypes and identifies key transcription factors and molecular codes involved in their specification.

This study uses cell-free RNA from blood samples to create a molecular clock for fetal development, predicting gestational age and preterm delivery risk.

This study uses single-cell RNA-seq to analyze human pancreatic cells across age, identifying transcriptional instability and age-related mutational signatures linked to oxidative stress.

The paper analyzes 5-hydroxymethylcytosine in cell-free DNA to predict tumor types and stages with high accuracy.