Stephen R. Quake

Translation fidelity mechanisms and their changes in aging

This study measures proteome-wide translation errors in yeast and mouse, finding that fidelity varies by organism and tissue, increases with age in post-mitotic cells, and is regulated by tRNA pool remodeling.

Heterophilic interactions between cell-surface proteins Teneurin-m and Capricious drive dendrite segregation in the Drosophila olfactory circuit

Single-cell splice isoform usage reveals distinct axes of cellular identity and senescence

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.

Hypothalamic Cell Type Evolution across Vertebrates

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

Site-dependent transcriptomic signatures of endometriosis are conserved across hormonal states

The paper identifies core lesion cells in endometriosis that retain uterine transcriptomic identity across hormonal states and uses them to classify disease status and lesion subtype.

The molecular triggers of human labour: a longitudinal plasma proteomics study

This study identifies five proteins whose sequential changes in plasma precede spontaneous labour onset, implicating the IL-33/ST2 axis in labour timing and identifying LMOD1 as a novel marker.

Informational blueprints reveal condition-dependent gene regulatory architectures

The paper introduces an algorithm to identify condition-dependent transcription factor binding sites by compressing promoter sequences into hyperletters, validated on E. coli data.

A Cross-Species Generative Cell Atlas Across 1.5 Billion Years of Evolution: The TranscriptFormer Single-cell Model

The paper introduces TranscriptFormer, a generative model trained on 112 million cells across 12 species, demonstrating cross-species cell type classification and disease state prediction.

Engulfment by brain macrophages in a short-lived vertebrate

This study identifies brain macrophages in the African turquoise killifish that engulf brain extracellular material, showing age-related decline in engulfment capacity.

Survival Benefits Outweigh Germline Competition Costs in Kin Chimeras

The study quantifies survival benefits and germline competition costs of chimerism in Botryllus schlosseri, finding survival advantages outweigh competition costs.

Cell-free RNA reveals host and microbial correlates of broadly neutralizing antibody development against HIV

The paper uses cfDNA/cfRNA sequencing to identify molecular correlates of bNAb development in HIV patients, finding an MHC class I activation signature and microbial changes associated with bNAb production.

Tabula Sapiens reveals the non-coding RNA landscape across 22 human organs and tissues

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.

Pareto Optimality Reveals an Atlas of Cellular Archetypes

The paper applies Pareto optimality to single-cell RNA sequencing data to identify cellular archetypes and their functions, finding that this principle explains transcriptomic variation across cell types.

Spatial and molecular insights into microglial roles in cerebellar aging

The paper investigates age-related changes in cerebellar microglia using single-nuclei RNA sequencing and MERFISH, finding enhanced neuroprotective immune activation and proximity to granule cells in aged mice.

Craters on the melanoma surface facilitate tumor-immune interactions and demonstrate pathologic response to checkpoint blockade in humans

The paper identifies crater-shaped structures in melanoma that enhance immune response to checkpoint blockade therapy in humans and zebrafish.

Beyond polyA: scalable single-cell total RNA-seq unifies coding and non-coding transcriptomics

This paper introduces a method to capture non-coding RNAs in single-cell RNA-seq, revealing new insights into gene regulation in immune cells, infected hepatocytes, and brain development.

Illuminating the uncharacterized regulatory genome of E. coli with massively parallel reporters

The paper identifies regulatory elements and transcription factors in E. coli genes across diverse environments using experimental and computational methods.

Simultaneous analysis of single-cell gene expression and morphology provides new insight into how microglia change with age

The paper analyzes single-cell gene expression and morphology in microglia to show how aging changes their spatial transcript organization and functional roles.

Linking molecular pathways and islet cell dysfunction in human type 1 diabetes

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.

Spatially-structured inflammatory response in the presence of a uniform stimulus

The paper studies spatially structured inflammatory gene expression in zebrafish tailfin using LPS, finding that uniform stimuli generate non-uniform responses through tissue-induced spatial correlations.

Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues

Tabula Sapiens 2.0 expands the human cell atlas with new data, analyzing transcription factor expression, senescence, and sex-specific features across cell types.

Multiomics characterization of cell type repertoires for urine liquid biopsies

This study characterizes transcriptomic and metabolomic profiles in human urine, identifying distinct cell type repertoires and metabolic signals compared to plasma.

Coordinated wound responses in a regenerative animal-algal photosymbiotic metaorganism

This study shows that injury in the acoel Convolutriloba longifissura triggers coordinated responses between the host and its symbiotic algae, mediated by the runt transcription factor.

Machine learning models of human tissue microbiomes for tissue-of-origin prediction

This study builds machine learning models to predict human tissue of origin from microbiome data and shows contaminants can contribute to model performance.

Activity-Dependent Alternative Splicing of Adhesion-GPCR Latrophilin-3 Controls Synapse Formation

This study shows that activity-dependent alternative splicing of Latrophilin-3 controls synapse formation through dual pathways involving GS/cAMP signaling and phase-separated protein scaffolds.

Aging Fly Cell Atlas Identifies Exhaustive Aging Features at Cellular Resolution

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

Spatial and single-cell transcriptomics reveal neuron-astrocyte interplay in long-term memory

The paper uses spatial and single-cell transcriptomics to identify memory-specific transcriptional signatures in neurons and astrocytes of the basolateral amygdala, revealing their role in long-term memory formation.

Neuroendocrinology of the lung revealed by single cell RNA sequencing

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.

Mouse lemur transcriptomic atlas informs primate genes, mutations, physiology, and disease

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.

Aging causes changes in transcriptional noise across a diverse set of cell types

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.