scRNA-seq

Oncogenic fusions induce an extensive cancer-restricted cryptic proteome in Ewing sarcoma

The paper shows EWSR1::FLI1 fusion drives the production of cancer-specific neoproteins in Ewing sarcoma, revealing a reversible dark proteome with therapeutic potential.

Local Tumor Microenvironment Niches Correlate with Survival and Immunotherapy Response in Human Glioblastoma

The paper identifies six distinct tumor microenvironment niches in glioblastoma that correlate with patient survival and immunotherapy response.

Locat: Joint enrichment and depletion testing identifies localized marker genes in single-cell transcriptomics

Locat identifies localized marker genes by testing both enrichment within and depletion outside cell populations in single-cell transcriptomics.

Machine learning-driven decoding of maternal immune signatures in repeated pregnancy loss

The paper identifies maternal immune signatures in repeated pregnancy loss using single-cell RNA sequencing and machine learning, linking them to potential drug repurposing candidates.

A Gene-Program Architecture of Mouse T cells

The paper introduces immgenT-GP, a gene-program framework that identifies 200 reproducible gene programs in mouse T cells, capturing lineage identity, activation states, and tissue location.

In vivo HSPC gene therapy of hemoglobinopathies without drug selection of corrected cells

This study demonstrates in vivo gene therapy for hemoglobinopathies using EPOR editing to enhance the expansion of gene-corrected erythroid cells without drug selection.

Building dynamical models of multi-step state transitions from single cell gene expression trajectories

This paper introduces NetDes, a method to infer gene regulatory networks and build dynamical models from single-cell gene expression data, showing its effectiveness in reconstructing cell state transitions.

Post-hoc long-read sequencing links leukemic mutation status to single-cell transcriptomes

The paper develops a post-hoc method to link mutation status to single-cell transcriptomes using long-read sequencing, showing it can detect BCR::ABL1-positive cells in chronic myeloid leukemia.

miRNA-mediated regulation of lineage plasticity in YY1 knockout pro-B cells

This study identifies YY1-dependent miRNA networks that regulate B cell identity and lineage commitment through transcriptional and post-transcriptional mechanisms in pro-B cells.

Oncohistone inhibition reshapes tumor-microenvironment communication in Diffuse Midline Glioma (DMG)

This study shows that H3K27M oncohistone reshapes the tumor microenvironment in DMG by altering neuronal interactions and immune signaling, suggesting it as a therapeutic target.

A single nuclei expression resource for exploring dog brain cell transcriptomic diversity

The paper presents a single nuclei RNA sequencing resource of dog brain cells, identifying cell types and revealing differences in opioid receptor expression compared to humans and mice.

Generation and application of human pluripotent stem cells derived peri-nervoids

This study generates human pluripotent stem cell-derived Schwann cells and neural organoids to create a nerve-like construct, showing improved regeneration in mouse models.

Uncertainty-Aware Model Selection with a Calibrated Probability-Generating-Function-Based Bayesian Information Criterion

This paper introduces an uncertainty-aware Bayesian information criterion for selecting stochastic gene-expression models from single-cell counts, reducing incorrect selection of more complex models.

Integrative pipeline to profile and target endocrine therapy-insensitive cell populations in ER+ breast cancer

The paper develops an analytical pipeline to identify and target endocrine therapy-insensitive cells in ER+ breast cancer using single-cell RNA sequencing and functional validation in organoid models.

A frozen human wound-repair reference reveals heterogeneous tumor niches and conditional immunotherapy associations

The paper analyzes wound-repair modules in tumors to identify heterogeneous niches and conditional immunotherapy associations.

The Unreasonable Effectiveness of Cell Types in Describing Neuronal Physiological Features

On 495 human Patch-seq neurons, cell type means predicted electrophysiology better than neural networks on scGPT embeddings or gene panels; fusing scGPT embeddings with cell type labels predicted best.

Cell-specific dedifferentiation in Arabidopsis thaliana

The paper studies dedifferentiation in Arabidopsis thaliana using single-cell RNA sequencing, revealing cell-type-specific transcriptional changes and the role of phytohormones and chromatin remodeling.

Microglia modulate concussion biomarkers and cognitive recovery in male mice

This study shows microglia influence concussion recovery and identifies EV miRNA biomarkers affected by microglial presence.

Human skin fibrosis with iPSC-derived organoids reveals RUNX2-mediated fibroblast reprogramming

This study uses human iPSC-derived skin organoids to model fibrosis, identifies RUNX2 as a key driver, and finds a small molecule that suppresses fibrotic programs.

Comparison of cell-cycle gene expression dynamics and mRNA kinetics across mouse and human pluripotent systems

This study compares cell-cycle gene expression dynamics and mRNA kinetics across mouse and human pluripotent systems, revealing species-specific differences in transcriptional complexity and oscillatory control.

Environmental stress promotes entry into a pre-existing latent state in Plasmodium falciparum

The paper shows environmental stress promotes latency in Plasmodium falciparum parasites, identified through single-cell transcriptomics, and identifies molecular features of this latent state.

Early-life conditions shape baseline immune gene expression, but not pathogen-induced immune activation, in brown trout

This study shows that early-life conditions affect baseline immune gene expression in brown trout but not their response to pathogen exposure.

scACORN: Context-engineered agent orchestration of specialized small language models for single-cell transcriptomic interpretation

scACORN improves single-cell transcriptomic interpretation by combining specialized small language models with context-engineered agent orchestration, achieving higher accuracy and reducing unsupported gene citations.

Improvement of human donor retinal ganglion cell survival through modulation of microglia

This study improves human donor retinal ganglion cell survival by modulating host microglia using annexin V and soluble Fas ligand, increasing survival by 2.5-fold.

REN-former prioritizes candidate regulators of kidney disease-state transitions through single-cell foundation modeling and human genetics

REN-former identifies gene regulators of kidney disease transitions by combining single-cell modeling and human genetics.

Uncovering Heterogeneous Effects via Localized Feature Selection

This paper introduces a framework for identifying disease-associated features tailored to individual profiles using localized test statistics, applied to single-cell RNA sequencing data for Alzheimer's disease.

Allele-Resolved Hybrid Embryos Reveal the Fates of Regulatory Divergence

The paper tracks regulatory divergence in hybrid embryos of Ciona species, showing how allelic differences are maintained or remodeled in lineage-specific ways and how GRN hierarchy influences allelic divergence.

Glucocorticoids reprogram human AML leukemic stem cells to promote elimination through differentiation and apoptosis

This study shows glucocorticoids eliminate AML leukemic stem cells by inducing differentiation and apoptosis, with mechanisms involving the glucocorticoid receptor and inflammatory signatures.

LIGER2: Scalable Single-Cell Integration with On-Disk Datasets

LIGER2 improves single-cell data integration by enhancing scalability and efficiency while preserving biological variation.

ImmuneLens: linking transcriptional states and TCR clonotypes through disentangled multimodal learning

ImmuneLens links transcriptional states and TCR clonotypes using disentangled multimodal learning to improve antigen-specificity prediction and reveal T cell heterogeneity in immunotherapy.