S. R. Quake

Universal Cell Embeddings: A Foundation Model for Cell Biology

The paper introduces UCE, a foundation model that creates a universal cell embedding space from single-cell data across species, enabling new insights into cell organization and function.

Long-term B cell memory emerges at uniform relative rates in the human immune response

The paper analyzes single B cell data from human tissues to show lineage co-localization and uniform differentiation rates, providing a model for antibody memory formation.

Reference-Free Germline Immunoglobulin Allele Discovery from B CellReceptor Sequencing Data

This paper introduces grmlin, a reference-free method to detect germline immunoglobulin alleles from B cell receptor sequencing data, achieving better specificity than existing methods.

Global and cell type-specific immunological hallmarks of severe dengue progression

This study identifies DENV target cells and immunological changes in severe dengue progression using single-cell RNA-Seq and functional assays in children.

Single-cell profiling identifies ACE+ granuloma macrophages as a non-permissive niche for intracellular bacteria during persistent Salmonella infection

The paper identifies ACE+ granuloma macrophages as non-permissive for intracellular Salmonella persistence using single-cell transcriptomics in mice.

Survey of extracellular communication of systemic and organ-specific inflammatory responses through cell free messenger RNA profiling in mice

This study uses cf-mRNA profiling in mice to assess systemic and organ-specific inflammatory responses to LPS and JAK inhibitor treatment.

Hepatitis C Virus Infects and Perturbs Liver Stem Cells

This study identifies liver stem cells as targets of HCV infection, showing their transcriptional reprogramming and role in liver damage and cancer risk.

Heterogenous impairment of α-cell function in type 2 diabetes is linked to cell maturation state

This study identifies heterogeneous α-cell dysfunction in type 2 diabetes linked to impaired maturation and electrophysiological changes.

An inexpensive semi-automated sample processing pipeline for cell-free RNA

This paper describes a low-cost, semi-automated pipeline for extracting cell-free RNA that improves throughput, reduces time, cost, and waste compared to manual methods.

Temperature Effect on Polymerase Fidelity

This study examines how temperature affects DNA polymerase fidelity across psychrophilic, mesophilic, and thermophilic origins, finding that temperature increases error rates independently of sequence context.

Single-cell transcriptional atlas of the Chinese horseshoe bat (Rhinolophus sinicus) provides insight into the cellular mechanisms which enable bats to be viral reservoirs

This paper creates a single-cell transcriptomic atlas of the Chinese horseshoe bat to study its role as a viral reservoir, identifying cell types and receptor expression patterns related to viral entry.

A Single Cell Transcriptomic Atlas Characterizes Aging Tissues in the Mouse

This study creates a single cell transcriptomic atlas of aging mouse tissues, identifying age-related changes in cell types and organ composition across 23 tissues.

The transcriptional landscape of Venezuelan equine encephalitis virus (TC-83) infection

This study uses single-cell RNA sequencing to analyze the host and viral RNA dynamics during VEEV infection, identifying superproducer cells and candidate antiviral targets.

A single-parasite transcriptional atlas of Toxoplasma gondii reveals novel control of antigen expression

This study constructs a single-parasite transcriptional atlas of Toxoplasma gondii using scRNA-seq, revealing novel control mechanisms of antigen expression and developmental transitions.

Differential Impacts on Host Transcription by ROP and GRA Effectors from the Intracellular Parasite Toxoplasma gondii

This study analyzes the effects of ROP and GRA effector proteins from Toxoplasma gondii on host transcription using single-cell transcriptomics of uninfected-injected cells.

Heterogeneous T cell motility behaviors emerge from a coupling between speed and turning in vivo

The paper shows that T cell motility variability arises from a coupling between speed and turning, observed across species and preserved under perturbations.

NFIA regulates granule recruitment and exocytosis in the adult pancreas

This study identifies NFIA as a regulator of granule recruitment and exocytosis in pancreatic cells, showing its role in insulin and enzyme secretion and linking it to metabolic disorders.

Functional characterization and lineage analysis of broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics

The paper identifies two broadly neutralizing antibodies against dengue virus through single B cell transcriptomics and characterizes their epitopes and evolutionary pathways.

Aging-related inflammation driven by cellular senescence enhances NAD consumption via activation of CD38+ macrophages

This study identifies CD38+ macrophages as a driver of NAD decline during aging through inflammation linked to cellular senescence in metabolic tissues.

Transcriptional program of memory B cell activation, broadly binding anti-influenza antibodies, and bystander activation after vaccination revealed by single-cell transcriptomics

This study uses single-cell transcriptomics to analyze memory B cell activation, antibody production, and bystander activation after influenza vaccination, revealing transcriptional programs and clonal dynamics.

c-Jun Overexpressing CAR-T Cells are Exhaustion-Resistant and Mediate Enhanced Antitumor Activity

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

Cell-free DNA Reveals Potential Zoonotic Reservoirs in Non-Human Primates

The paper uses cell-free DNA sequencing to identify microbial taxa in non-human primates, revealing potential zoonotic pathogens and their association with host species.

Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA

This study identifies 5-hydroxymethylcytosine (5hmC) signatures in circulating cell-free DNA to detect early-stage pancreatic cancer with high accuracy.

Human IgE producing B cells have a unique transcriptional program and generate high affinity, allergen-specific antibodies

The paper isolates and characterizes IgE-producing B cells from allergic individuals using scRNA-seq, revealing unique transcriptional features, high-affinity antibodies, and convergent evolution in allergen specificity.

Single-cell transcriptional dynamics of flavivirus infection

This study introduces viscRNA-Seq to analyze virus-host interactions at the single-cell level, revealing host factors specific to dengue and Zika virus infections.

Matrix-corrected mass spectrometry enables sensitive detection of food allergens and reveals widespread soy contamination of processed foods

The paper develops a mass spectrometry method to detect food allergens and finds widespread soy contamination in processed foods, with many precautionary labels not accurately reflecting contamination risks.

Signatures of Selection in the Human Antibody Repertoire: Selective Sweeps, Competing Subclones, and Neutral Drift

The paper identifies molecular signatures of evolutionary processes in human antibody repertoires, showing how selective sweeps, competing subclones, and neutral drift shape antibody diversity.

T-cell receptor sequencing of early stage breast cancer tumors identifies altered clonal structure of the T-cell repertoire

The paper analyzes T-cell receptor sequencing data from early-stage breast cancer tumors and normal tissue to show differences in T-cell clonal structure between tumor and normal tissue.

Dynamics Of The Human Antibody Repertoire Following B-cell Depletion In Systemic Sclerosis

This study examines changes in the B-cell antibody repertoire in SSc-PAH patients before and after B-cell depletion, revealing anomalies in B-cell development and homeostasis that reverse temporarily.

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples

This paper introduces a microfluidic-based mini-metagenomic method to extract novel microbial genomes from complex environmental samples, revealing 29 new genomes with diverse metabolic pathways and SNP distributions.