scRNA-seq

A multimodal perturbation atlas defines the phenotypic resolution of cellular morphology.

The paper presents a multimodal perturbation atlas using CRISPR knockouts in A549 cells, combining microscopy, phase imaging, and scRNA-seq to assess phenotypic resolution.

Transcriptional landscape of direct reprogramming toward the hematopoietic lineage

The paper develops a single-cell transcriptomic reference atlas and evaluates a transcription factor recipe for reprogramming fibroblasts into hematopoietic stem cells, revealing intermediate transcriptomic states and transcriptional remodeling.

Early life stress affects the transcription and chromatin accessibility of spermatogonial cells

This study shows early-life stress alters the transcriptome and chromatin accessibility of mouse spermatogonial cells, with molecular signatures persisting into adulthood.

Single-cell roadmap of bovine oogenesis and somatic niche interactions during fetal ovarian development

This study creates a single-cell RNA-seq atlas of bovine fetal ovarian development, identifying cell populations and developmental stages, and showing parallels with human fetal ovaries.

T cell repertoire diversity measurement; inferences from a dynamical systems model, Fourier Analysis of the T cell repertoire

This study uses Fourier analysis of T cell receptor V gene segment usage to quantify repertoire diversity in healthy donors and recipients, finding shifts in spectral patterns in recipients.

The transcription factor Bhlhe40 promotes inflammatory functions of ILC2s through inducing GM-CSF while inhibiting IL-10 expression

This study shows Bhlhe40 promotes GM-CSF and inhibits IL-10 in ILC2s, enhancing eosinophil recruitment during type 2 immune responses.

MultiFlow: coupled flow matching for predicting single-cell multiomic perturbation responses in unseen cellular contexts

MultiFlow predicts single-cell multiomic perturbation responses by jointly modeling gene expression and chromatin accessibility across cellular contexts.

A statistical framework for disease classification with scRNA-Seq Data

This paper introduces a statistical framework for disease classification using scRNA-seq data, achieving better interpretability and performance compared to existing methods.

Dissecting context-dependent cancer vulnerabilities using Perturb-seq

The paper uses Perturb-seq to analyze gene knockouts in cancer cell lines, identifying context-specific gene dependencies and transcriptional responses.

C1Q-associated adaptive myeloid remodelling accompanies early response to BCMA CAR-T therapy in multiple myeloma

In a ten-patient multiple myeloma reanalysis, myeloid pseudobulk from day-30 BCMA CAR-T responders showed C1Q enrichment with interferon-γ signalling, not cholesterol efflux; patient-level composite scores stayed exploratory.

GATA3-extension mutants rewire lineage identity in luminal breast cancer

The paper shows that eGATA3 mutations alter transcriptional regulation and lineage identity in luminal breast cancer without losing DNA-binding function.

Neutrophil remodeling is associated with human meibomian gland dysfunction and enables IFN-γ- and PAD4-dependent gland obstruction in mice

This study identifies a remodeled neutrophil state associated with meibomian gland dysfunction, showing IFN-γ and PAD4-dependent obstruction in mice.

Diverse Intestinal Injuries Drive Heterogeneous Transcriptional Responses and Limited Reactivation of Developmental Gene Programs in Human Enteroids

This study examines how human enteroids respond to various injuries, finding limited reactivation of developmental gene programs and highlighting the role of specific signaling pathways.

Identifying memory gene expression from single sample scRNA-seq data using power law signatures

This paper introduces Power-Seek, an algorithm to identify memory genes from single-sample scRNA-seq data by detecting power-law signatures in covariance matrices, validated on melanoma and breast cancer data.

Public-Data Reanalysis Links MS4A4A to M2-like Human Myeloid States and Supports a Predicted Four-Pass Transmembrane Fold

The paper reanalyzes public datasets to show MS4A4A is associated with M2-like myeloid states and finds AlphaFold does not support a predicted MS4A4A-MS4A6A interaction.

An ncBAF-ETS2 Chromatin-Remodelling Axis Drives Vascular Smooth Muscle Cell Osteogenic Reprogramming in Vascular Calcification

A single-cell transcriptomic atlas of the Echinococcus multilocularis metacestode reveals cellular diversity and molecular specialization

This study creates a single-cell transcriptomic atlas of Echinococcus multilocularis metacestodes, identifying 26 cell populations and revealing molecular specialization and heterogeneity.

A Cytokine Receptor Signaling Atlas Reveals How STAT Mosaics Fine-Tune T Cell Function

A fully orthogonal IL-2 receptor platform isolates 36 cytokine receptors in T cells; receptor-specific STAT combinations specify distinct fates, and STAT3-dominant programs give curative antitumor responses.

Unbiased and Epicardial-Specific Lineage Tracing Reveal Epicardial Contribution to Vascular Endothelial Cells in Heart Development

The paper identifies epicardial cells' contribution to vascular endothelial cells in heart development using a CRISPR-based lineage-tracing system and a novel marker gene, Lrrn4.

Renin is critical for Renin Lineage Cell Plasticity and Migration in experimental crescentic Glomerulonephritis

This study shows that renin in renin-lineage cells protects against crescentic glomerulonephritis by supporting cell migration and reducing inflammation.

The diverse functions of viral microproteins

A >50,000-element viral smORF library screened by growth, MHC-I, ER stress, Perturb-seq and mass spectrometry yields >2,000 active microproteins and shows EBV BNLF2b inhibits PKA by mimicry.

A scalable human neuromuscular organoid platform enables lineage-specific analysis of drug responses in spinal muscular atrophy.

This study develops a scalable neuromuscular organoid platform to analyze drug responses in spinal muscular atrophy, showing distinct muscle and neuronal responses to SMN2 splicing modulators.

Conditional polygenic enrichment distinguishes causal from tagging disease-critical cell populations in single-cell RNA-seq

This paper introduces scDRS-FM, a method to distinguish causal from tagging disease associations in scRNA-seq data, showing it improves power and accuracy in identifying disease-relevant cell populations.

Time-resolved operator archetypes characterize dynamical sensitivity during cell-state transitions

This paper introduces scJDO, a framework for analyzing dynamical sensitivity during cell-state transitions, and applies it to iPSC reprogramming to distinguish productive from diverted fates.

Imaging guided single-cell multiomics unveils shared autoreactive CD4+ T-cell responses in blood, locoregional lymph node and affected tissues of patients with systemic autoimmunity

The paper uses imaging-guided single-cell multiomics to identify shared autoreactive CD4+ T-cell responses in blood, lymph nodes, and tissues of patients with systemic autoimmune diseases.

Functional Pairing of TCR-peptide-MHC Interactomes by Single-cell Clonal Expansion

The paper develops LINC-seq to identify functional TCR-pMHC pairs by clonal expansion and deep mutational scanning, achieving high accuracy in recovering known cognate pairs and resolving co-evolutionary interactions.

Single-cell and spatial transcriptomics resolve airway obliteration in bronchiolitis obliterans syndrome

This study uses single-cell and spatial transcriptomics to identify structural cell circuits in BOS lungs and their spatial organization during airway obliteration.

A Centimeter-Scale, Peristaltic Human Intestinal Organoid with Integrated Neuro-Immune-Vascular Systems Recapitulates Enteritis and Orthotopic Colorectal Cancer

This paper develops centimeter-scale human intestinal organoids with neuro-immune-vascular systems that model enteritis and colorectal cancer.

sc-pcQTL: hurdle-based co-expression modeling for multi-gene QTL mapping in single-cell RNA-seq data

sc-pcQTL identifies multi-gene QTLs in single-cell RNA-seq data by combining hurdle modeling and principal-component analysis, revealing cell-type-specific regulatory effects.

On the robustness of scRNA-seq foundation models for plant perturbation response prediction under cross-experiment shift

This study evaluates scRNA-seq foundation models for plant perturbation response prediction, finding that performance varies significantly with evaluation protocol and that preserving gene identity improves generalization.