scRNA-seq

A single-nuclei multiomics resource across four brain regions prioritises human neural cell types influencing brain-related traits

The paper integrates multiomic data from human brain nuclei with GWAS statistics to prioritize neural cell types associated with brain-related traits.

Robustness measures for cell type classification in single-cell RNA-seq datasets of kidney organoids

The paper introduces robustness measures to evaluate cell-type classification reliability in single-cell RNA-seq datasets of kidney organoids and finds high robustness in most cell types except immature ones.

APOA1 links a late fetal epithelial program to colonic maturation and injury responses

This study identifies APOA1 as a marker of a late fetal colonic epithelial state that reappears after injury, linking it to colonic maturation and injury responses through interactions with WNT5A and regulation by HOXB7.

PerturbBridge: Conditional Latent Schr\"{o}dinger Bridge for Single-Cell Perturbation Prediction

PerturbBridge predicts single-cell perturbation responses by modeling population-level distribution shifts using a conditional latent Schrödinger Bridge framework, achieving state-of-the-art differential-expression recovery.

OmicsResonance: An LLM-assisted cloud ecosystem for interactiveand reproducible single-cell transcriptomic analysis

OmicsResonance provides a code-free web platform for scRNA-seq analysis, integrating LLM-assisted tools and interactive features to enable reproducible and transparent single-cell research.

Robust Inference of Phage Host Infection Dynamics from Sparse Single-Cell Transcriptomic Profiles in Pseudomonas aeruginosa

The paper uses scRNA-seq to study phage-host interactions in Pseudomonas aeruginosa and identifies non-random infection patterns using machine learning.

EISCA and EISTA: Full-Spectrum Pipelines for Single-Cell and Spatial Transcriptomics Analysis

EISCA and EISTA are pipelines for single-cell and spatial transcriptomics analysis that provide standardized, modular workflows for data processing and downstream analysis.

Somatic mutations and single-nucleus transcriptomics reveal uniquely human properties of neuronal aging

The paper compares somatic mutation rates and transcriptomic changes in neurons across six mammalian species, finding higher mutation accumulation and distinct age-related dysregulation in human neurons.

Cellular basis of accelerated whole-tooth regeneration

The paper studies tooth regeneration in cichlid fishes, identifying accelerated replacement and cellular interactions involved in the process.

Galectin and Myc enable cochlear progenitor expansion in vitro and in vivo

Single-cell profiling of mouse greater epithelial ridge (GER) organoids points to galectin-1 and Myc as drivers of cochlear progenitor expansion. Myc overexpression also yields organoids from post-hearing-onset cochlear epithelium.

ISP Platform powered by Geneformer: Framework for Cross-Species, State-feedback, and Multi-Gene In Silico Perturbation Screens with Application to iPS Cell State Transitions

CardioChrom Reconstructs the Human Cardiac Virtual Epigenome from Single-Nucleus Transcriptomes

CardioChrom reconstructs chromatin accessibility and histone modifications from single-nucleus RNA data in human heart failure, improving prediction accuracy and identifying regulatory changes in endothelial cells.

MoTRUST: adaptive semantic protection for mosaic single-cell integration and molecular recovery

MoTRUST integrates mosaic single-cell multi-omics data and recovers missing molecular information, achieving top performance in integration and recovery tasks.

singIST: an R/Bioconductor library and Quarto dashboard for automated single-cell comparative transcriptomics analysis ofdisease models and humans

singIST compares disease model scRNA-seq data to human references to assess recapitulation at superpathway, cell type, and gene levels.

NicheScribe: consistent and generalizable annotation of stromal cells in the murine bone marrow niche

The paper develops NicheScribe, a method for consistently annotating stromal cells in the murine bone marrow niche using scRNA-seq data, enabling comparative analysis across different conditions.

Senescence-directed nanotherapy ameliorates fibrosis and overcomes immune exclusion in cancer

P-selectin-targeted fucoidan nanoparticles carrying Navitoclax or dBET6 deplete a senescent-like, lipid-associated macrophage subset, reverse mouse liver and lung fibrosis with less toxicity, and restore checkpoint therapy response in fibrotic tumors.

A repair-associated bronchial epithelial differentiation trajectory through KRT14+ basal and hillock-like cells drives airway inflammation and remodelling in childhood-onset asthma

The paper identifies a novel asthma-associated epithelial differentiation trajectory involving KRT14+ basal cells and hillock-like cells that contributes to airway inflammation and remodelling in childhood-onset asthma.

Single-Cell and Spatial Analysis Reveals Retention of FCRL4⁺ Memory B Cells in Pediatric Tonsillar Hypertrophy

The paper identifies FCRL4+ memory B cells retained in hypertrophic pediatric tonsils through single-cell and spatial analysis, showing their interaction with Tr1 cells to sustain follicular hypertrophy.

Single-cell analysis identifies TOP2α as a critical regulator of G2/M entry and differentiation-dependent productive HPV replication

The paper identifies TOP2α as a critical regulator of HPV genome amplification during differentiation by analyzing single-cell RNA-seq data from HPV-infected keratinocytes.

Decoding subtype development and function in human pluripotent stem cell-derived midbrain dopaminergic neurons

This study develops a method to derive and maintain specific subtypes of human midbrain dopaminergic neurons in vitro, revealing their functional and molecular characteristics and potential vulnerability in disease.

Hepatic cholinergic T cell signaling mediates an adaptive response to alcohol-induced liver stress

This study identifies cholinergic T cell signaling and cholesterol metabolism in CD4 T cells as adaptive responses to alcohol-induced liver stress, suggesting new therapeutic targets for ALD.

PeakATail: precision-first poly(A)-site calling and calibrated alternative polyadenylation analysis in single-cell RNA-seq

PeakATail identifies poly(A)-sites in single-cell RNA-seq with precision, controlling error rates and validating results against curated data.

TREM2 Orchestrates Myeloid Cell Programming and Immune Dysregulation in Pulmonary Hypertension

This study identifies TREM2 as a regulator of myeloid cell function and immune dysregulation in pulmonary hypertension, showing its role in disease progression and potential as a therapeutic target.

CMAC: A deep learning framework for absolute cardiomyocyte transcriptional age estimation

CMAC estimates absolute transcriptional age of cardiomyocytes using deep learning, achieving high accuracy across multiple datasets and platforms.

Long-read RNA sequencing identifies non-coding isoform switching as a regulator of cell fate

The paper uses long-read RNA sequencing to identify non-coding isoform switching that regulates cell fate during reprogramming.

Ultra-fast and scalable high-resolution full-length single-cell RNA sequencing using CHART-seq

CHART-seq enables ultra-fast, scalable full-length single-cell RNA sequencing with improved gene detection and isoform annotation compared to existing methods.

Extracting interpretable single-cell metabolic states with graph-guided representation learning

The paper introduces MeRN, a graph-guided variational autoencoder for learning single-cell metabolic states from transcriptomes, and identifies metabolic drivers in various biological contexts.

Discovery of rare antigen-specific TCRs via replicate profiling

The paper develops a high-throughput TCR discovery assay to identify antigen-specific T cells, finding over 90 SARS-CoV-2-specific TCR clonotypes in one donor and nearly 1,000 in five donors.

A CRISPR-Based Humanized Model Reveals Cooperative Role of STAG2 Loss in Familial GATA2-Deficient MDS Progression

This paper uses a CRISPR-based humanized model to show that STAG2 loss cooperates with GATA2 deficiency to drive MDS progression through increased HSC self-renewal and myeloid bias.

FlowMap: Geometry Dynamics Consistent Embedding of RNA Velocity for Interpretable Cellular Trajectories

FlowMap jointly models cellular states and dynamics in a geometric framework, recovering interpretable trajectories and developmental patterns from single-cell RNA sequencing data.