scRNA-seq

RankMap: Rank-based reference mapping for fast and robust cell type annotation in spatial and single-cell transcriptomics

RankMap improves cell type annotation in spatial and single-cell transcriptomics by using rank-based representations and multinomial regression, achieving competitive accuracy and faster runtime.

Conserved cell state dynamics reveal targetable resistance patterns in ovarian high-grade serous carcinoma

The paper identifies conserved cell states in ovarian high-grade serous carcinoma that correlate with poor prognosis and presents actionable targets for improving platinum response.

sox17 mutagenesis reveals microglia can be impacted by genetic maternal effects

The paper identifies a genetic maternal effect on microglia development through sox17 mutation in zebrafish, showing that maternal genotype impacts microglia and yolk sac precursor cells.

Spatial Single-Cell Mapping of Transcriptional Differences Across Genetic Backgrounds in Mouse Brains

The paper introduces ATLAS, a method to map transcriptional differences across genetic backgrounds in mouse brains, revealing significant cell type distribution changes between sexes and genetic models.

Elevated mitochondrial metabolism in Down syndrome iPSCs reduces commitment to neuroectoderm

This study shows that increased mitochondrial metabolism in Down syndrome iPSCs impairs neuroectoderm commitment by reducing ciliation, and this effect can be reversed by inhibiting mitochondrial calcium uptake.

IFNγ and proinflammatory cytokines cooperatively license astrocytes to support antigen-dependent CD4+ T cell restimulation

The paper shows that IFNγ and proinflammatory cytokines activate astrocytes to express antigen-presenting machinery, supporting CD4+ T cell restimulation in vitro and in vivo.

Whole-body single-cell atlas of an adult vertebrate in homeostasis and regeneration

Region-stratified scRNA-seq of 607,370 cells plus 500-gene MERFISH maps adult Danionella cerebrum cell types body-wide, revealing fibroblast Hox and limb-identity programs and telencephalon regeneration dynamics.

Multi-omics analysis reveals chromatin and transcriptomic remodeling in hippocampal CA1 following adolescent social isolation

Two weeks of post-weaning isolation in male mice altered expression of 106 CA1 genes, enriched for myelination, while chromatin accessibility shifted only at nominal significance and tracked expression weakly.

Single-Cell Transcriptomic Analysis of the Immune Response to CHIKVInfection

This study uses scRNA-seq to analyze the immune response to CHIKV infection, finding increased monocytes and dendritic cells, and a strong interferon response driven by monocytes.

Model-based inference of gene expression noise from single-cell RNA-sequencing data

This paper introduces a maximum-likelihood framework to estimate gene expression noise from scRNA-seq data, accounting for technical noise and cell type heterogeneity, and demonstrates its reproducibility using yeast data.

Ablation of a maternal Cryptosporidium mRNA-binding protein results in sterile sporozoites

The paper identifies an RNA-binding protein essential for female gamete development and sporozoite infectivity in Cryptosporidium by analyzing single-cell data and conducting conditional ablation experiments.

XChrom: a cross-cell chromatin accessibility prediction model integrating genomic sequence and cellular context

XChrom predicts chromatin accessibility across cells and genomic regions using genomic sequence and cell identity, outperforming existing methods and enabling cross-species analysis.

Impact of Rare and Common Genetic Variation on Cell Type-Specific Gene Expression

Single-cell eQTL mapping in 5.4 million PBMCs from 1,925 individuals with matched WGS finds common-variant eQTLs for 83% and rare-variant signals for 47% of 21,404 genes.

Tandem repeat variation shapes immune cell type-specific gene expression

The paper identifies immune cell type-specific gene expression regulated by tandem repeats using multi-omics data from large cohorts.

Longitudinal single-cell RNA sequencing of a neuroendocrine transdifferentiation model reveals transcriptional reprogramming in treatment-induced neuroendocrine prostate cancer

This study uses longitudinal scRNA-seq to track neuroendocrine transdifferentiation in a prostate cancer model, identifying transcriptional changes and key regulators during treatment-induced NEPC progression.

Perinatal Elimination of Genetically Aberrant Neurons from Human Cerebral Cortex

The paper investigates somatic copy number variants (CNVs) in human neurons across development, finding that perinatal elimination of neurons with aberrant genomes reduces CNV prevalence and targets dosage-sensitive genes.

Increasing Cancer Stemness Drives Prostate Cancer Progression, Plasticity, Therapy Resistance and Poor Patient Survival

This study quantifies cancer stemness in prostate cancer across progression stages, showing its association with therapy resistance, poor survival, and lineage plasticity.

Distinct muscle stem cell fates correlated with hyperplasia and hypertrophy during skeletal muscle growth in rainbow trout

Disrupted glial-mediated synaptic refinement in Fragile X syndrome

This study identifies impaired glial-mediated synaptic refinement in FXS model mice, showing enhanced astrocyte-microglia signaling and synaptic over-engulfment as key features.

Single-cell analysis of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-treated murine skin demonstrates that sebaceous gland differentiation precedes Ahr-dependent seboatrophy with elevated expression of infundibular Blimp1

This study shows TCDD induces Cyp1a1 in murine skin, enhancing sebaceous gland differentiation and lipid production before causing Ahr-dependent seboatrophy.

Single-Cell Sequencing in Pediatric Acute Leukemia: A Systematic Review of Biologic Insights and Translational Potential

This review evaluates single-cell sequencing findings in pediatric acute leukemia, highlighting insights into clonal evolution, chemoresistance, and immune dynamics, while noting limitations in study design and bias.

A multi-omics resource of B cell activation reveals genetic mechanisms for immune-mediated diseases

This study profiles B cell activation states using multi-omics data to identify genetic mechanisms underlying immune-mediated diseases.

RiboTRAP-seq identifies spatially distinct functions for the anterior and posterior intestine in immune and metabolic regulation in C. elegans

NOTCH-driven oscillations control cell fate decisions during intestinal homeostasis

The paper shows that NOTCH-driven Hes1 oscillations with different periods control cell fate decisions in intestinal stem cells, influencing secretory and absorptive lineage commitment.

Systematic evaluation of integration methods and parameters on single-cell RNA-sequencing biological insights: a case study on cattle embryos.

The paper evaluates integration methods and parameters on cattle embryos to assess their impact on biological insights, finding that parameter choices affect cell type classification and functional interpretation.

A DNA Typewriter records the cell lineage history of a mouse, from zygote to late organogenesis

A prime-editing recorder in one mouse embryo yields a dated, zygote-rooted lineage tree of 1.28M cells at E13.5, enabling clonal dominance, sibling-fate and cell-type coupling analyses.

Characterizing and Mitigating Protocol-Dependent Gene Expression Bias in 3' and 5' Single-Cell RNA Sequencing

This study identifies and mitigates protocol-dependent gene expression bias between 3' and 5' scRNA-seq by focusing on a small set of biased genes rather than applying broad normalization.

Estimating the completeness of large-scale single-cell sequencing projects

This paper estimates the completeness of large-scale single-cell sequencing projects using ecological richness metrics applied to cellular diversity data.

Myeloid cell reprogramming drives enhanced defense against Streptococcus pneumoniae lung infection following exposure to commensal Prevotella

The paper shows that exposure to Prevotella melaninogenica reprograms myeloid cells to enhance defense against Streptococcus pneumoniae lung infection.

Diverse infections transcriptionally reprogram the intestinal epithelium and epithelial-immune cell interactions

The paper creates a single-cell and spatial transcriptomics atlas of the ileum during diverse infections, revealing novel cell states and immune responses.