scRNA-seq

Age-based shifts in multicellular community organization and abundance in HPV-Negative Head and Neck Cancer

This study identifies age-related changes in cellular composition and organization in HPV-negative head and neck cancer using single-cell data, highlighting MDK as a key factor in stromal remodeling and immunosuppression.

Pycea: a scverse toolkit for single-cell lineage tracing analysis

Pycea provides a toolkit for analyzing single-cell lineage tracing data, integrating with Scanpy and offering visualization and statistical methods for lineage trees.

FateDriver: Weakly supervised dual-view graph learning for transition-specific prioritization of candidate regulators in cellular reprogramming

FateDriver prioritizes candidate regulators for specific cellular transitions using a weakly supervised dual-view graph neural network, outperforming existing methods in recovering known regulators.

Single-cell transcriptome-wide association analysis reveals epithelial cell-specific genetic susceptibility to colorectal cancer

The paper performs single-cell transcriptome-wide association analysis to identify cell-type-specific genetic susceptibility genes for colorectal cancer, finding 546 gene-cell-type associations and 347 candidate susceptibility genes.

EMBER: Contextualized gene representations enable compositional prediction across cellular perturbations

EMBER, a gene-centric foundation model, improves cross-context perturbation-response prediction and genetic-interaction ranking using contextualized gene embeddings.

Single-cell perturbation prediction near experimental reproducibility with GENESIS

GENESIS predicts single-cell perturbation responses from experimental conditions, outperforming existing models and approaching experimental reproducibility.

Development of a multi-organ single-cell atlas of systemic sclerosis reveals shared and tissue-specific pathogenic pathways.

This study creates a multi-organ single-cell atlas of systemic sclerosis to identify shared and tissue-specific transcriptional programs and potential therapeutic targets.

Integrative multi-omics re-analysis of public sequencing and metabolomics repositories defines the mucosal immune and metabolic landscape of Helicobacter pylori infection and supports CagW as a rational mRNA-LNP vaccine antigen

The paper re-analyses public multi-omics data to characterize the gastric mucosal immune and metabolic landscape of H. pylori infection and identifies CagW as a promising mRNA-LNP vaccine antigen.

Single-cell foundation models transfer across deep evolutionary distances

This paper evaluates the transferability of single-cell foundation models across deep evolutionary distances using developmental atlases of Dictyostelium discoideum and Caenorhabditis elegans.

DCAF: Unifying Data Validity, Evaluation Validity and Predictive Modeling for Single-cell Perturbation Simulation

DCAF improves single-cell perturbation simulation by addressing data, evaluation, and model validity, outperforming baselines in generalization and recapitulating regulatory heterogeneity in mouse brain.

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.

Dengue Virus Serotype 2 Infection Transcriptionally Reprograms Host Neutrophils to Establish an Immunosuppressive Microenvironment in Mice

This study shows that Dengue virus serotype 2 reprograms neutrophils in mice to create an immunosuppressive environment, with FGL2-expressing neutrophils playing a key role.

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.

Mechanistic gene-regulation-based trajectory inference with bowside

The paper introduces bowside, a neural model for trajectory inference and gene regulatory network reconstruction in single-cell RNA sequencing data, showing it recovers known regulatory motifs in hematopoiesis and reprogramming.

Single-nucleus transcriptomics links telencephalic cell signatures to ocean acidification effects on social behaviour in a coral reef fish

The paper uses single-nucleus transcriptomics to identify neural cell type responses to elevated CO2 in cleaner wrasse, revealing disruptions in myelination, glutamatergic signalling, and cell-cell communication.

Regionalisation of muscle nucleus heterogeneity in foetal skeletal muscle

The paper identifies transcriptionally distinct muscle nuclei in fetal chicken limb muscles, showing tip and central domain identities and signaling roles in muscle development.

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.

Integrative multi-omics decoding of the host response to Klebsiella pneumoniae infection reveals an itaconate-centred metabolic-immune axis and a spatially organised inflammatory programme

This study integrates multi-omics data from Kp infection to identify an itaconate-centred metabolic-immune axis and a host-response signature with high diagnostic accuracy.

Functional Mammary Gland Organoids From Human Induced Pluripotent Stem Cells

This study develops a method to generate functional mammary gland organoids from human induced pluripotent stem cells, showing they can form layered epithelium and respond to hormonal signals.

A MultiOmics time-resolved systems map of gene regulation in Toxoplasma gondii

This study creates a time-resolved multi-omics map of gene regulation in Toxoplasma gondii by integrating perturbation data with single-cell measurements, revealing regulatory networks and novel interactions.

iPSC modeling of pulmonary arterial hypertension to uncover pathomechanisms and unrecognized modes of action of sotatercept

This study uses patient-derived iSMCs to uncover new mechanisms of PAH and sotatercept's effects beyond its known anti-proliferative actions.

Inflammation reshapes epidermal and leukocyte differentiation resulting in altered glucocorticoid responsiveness

The paper investigates how inflammation alters cell type-specific glucocorticoid responsiveness through single-cell RNA sequencing in zebrafish.

Anatomically matched spatial comparisons identify Trps1 as a regulator of knee interzone formation

The paper identifies Trps1 as a regulator of knee interzone formation through spatial comparisons and perturbation experiments in mice, showing its role in chondrogenic differentiation.

Defining cell type-specific diurnal gene expression in the mouse retina

The paper identifies cell-type-specific diurnal gene expression patterns in the mouse retina using single-nucleus RNA sequencing.

Single-nucleus multiome profiling reveals osteocyte-centered remodeling of human subchondral bone across osteoarthritis severity

The paper uses single-nucleus multiome sequencing to analyze subchondral bone in OA, finding increased osteocyte SMAD2/3 activity and chondrocyte-derived FN1 signaling with disease severity.

Digital twins forecast individual immune trajectories

The paper introduces ImmuneTwins, a digital twin framework that personalizes immune response models for individuals, improving prediction accuracy of immune trajectory changes.

Influenza H1N1 Imprinting Uncouples Serological and B-Cell Responses in Mice

This study shows that immunological imprinting in mice uncouples serological and B-cell responses, with B-cell repertoires updating independently of serum antibody specificity.

flashscenic: Accelerated GRN Analysis with RegDiffusion for Large-Scale Single-Cell Data

flashscenic accelerates single-cell GRN analysis using GPU acceleration, improving speed and enabling benchmarking of integration strategies in AML data.