scRNA-seq

SPECHTacle: An Efficient Detection and Visualization of Cell Specific Regulation in Single Cell-Based Experiments Using a Novel Combinatorial Computational Tool

SPECHTacle efficiently identifies and visualizes cell-specific regulatory changes in single-cell experiments using optimal transport and entropy analysis.

Lineage tracing in rhabdoid tumor organoids and orthotopic xenografts reveals convergent transcriptional states

The paper uses lineage tracing and single-cell RNA sequencing to show that rhabdoid tumors converge on a limited set of transcriptional states despite clonal diversity.

Vorinostat Can Reduce an Ongoing Fibrosis and Preserve Key Liver Metabolic Functions by Selectively Altering Mesenchymal Cell Differentiation

This study shows Vorinostat reduces ongoing liver fibrosis and preserves metabolic functions by altering mesenchymal cell differentiation in a human iPSC-derived model.

Decoding Cell-type Specific Gene Regulation with CellReg3D by Integrating DNA Large Language Models and 3D Genome Structure

CellReg3D integrates DNA language models and 3D genome structure to model cell-type-specific gene regulation, achieving state-of-the-art performance in predicting epigenetic marks and gene expression.

Spectral Adaptive Repositioning for Flow-Based Single-Cell Perturbation Modeling

SPEAR predicts cellular responses to perturbations by adaptively repositioning genes in a co-expression network using spectral encoding and generative modeling.

Aging activates latent enhancers that can be reversed withexercise

This study identifies age-acquired enhancers in mouse hearts and shows that exercise can reverse their activation.

scPCIP: cross-species annotation of plant cell types with conserved gene programs

scPCIP annotates plant cell types across species using conserved gene programs, outperforming marker-based and deep-learning methods in held-out datasets.

brisc: a multithreaded CPU toolkit for single-cell analysis

brisc is a multithreaded CPU toolkit for single-cell analysis that is faster and more reproducible than existing tools like Scanpy and Seurat.

Single-cell transcriptomics of enriched rare neural lineages of Tribolium castaneum

The paper develops workflows for targeted single-cell and single-nucleus RNA sequencing of rare neural populations in Tribolium castaneum using reporter and antibody-based enrichment strategies.

Single-Cell RNA Sequencing Reveals Distinct Cellular and Molecular Features of Steroid-Induced Osteonecrosis of the Femoral Head Compared to Alcohol-Induced Osteonecrosis and Hip Osteoarthritis

This study uses single-cell RNA sequencing to compare cellular and molecular features of steroid-induced and alcohol-induced osteonecrosis of the femoral head with hip osteoarthritis, identifying distinct immune and stromal cell signatures.

Uncovering cross-signal interactions in single-cell and spatial omics

CRISP identifies and localizes interactions between biological signals in single-cell and spatial transcriptomic data, revealing their effects on tissue function and gene regulation.

A fibroblast-CD8+ T cell circuit drives a Type 1 shift in allergic inflammatory memory

This study identifies a fibroblast-CD8+ T cell circuit that drives a Type 1 immune shift in allergic inflammatory memory through mechanistic and translational analysis in murine and human models.

High-fat diet promotes exhaustion-associated T-cell remodeling across vascular and lymphoid tissues in atherosclerosis-prone mice

This study shows that a high-fat diet causes T-cell exhaustion in multiple tissues of atherosclerosis-prone mice, which partially reverses with dietary changes.

Where single-cell foundation models help: a benchmark of annotation, perturbation and regulatory inference against simple baselines

This paper benchmarks single-cell foundation models against baselines for annotation, perturbation and regulatory inference using diverse datasets.

Live Droplet Single-Cell RNA Sequencing

The paper introduces Live D-seq, a method for longitudinal, non-destructive single-cell RNA sequencing, and demonstrates its ability to track cellular dynamics over time.

MET inhibition exploits conserved regulatory dependencies in malignant rhabdoid tumors

This study identifies MET signaling as a targetable vulnerability in rhabdoid tumors through integrated single-cell multi-omic and spatial transcriptomics analyses.

A subtype-specific gene regulatory program controls differential circuit integration of deep CA3 pyramidal neurons

The paper identifies ST18 as a regulator of deep CA3 pyramidal neuron identity, showing its role in restricting a superficial-like program and shaping circuit integration through molecular and electrophysiological changes.

Early Progression Cells mark a stem-like state associated with pancreatic cancer initiation and progression

The paper identifies Early Progression Cells (EPCs) as stem-like cells in pancreatic cancer that drive progression and are associated with specific gene programs and interactions.

Comparative molecular analysis of histopathologic subtypes reveals shared epithelial remodeling yet distinct fibroblast programs in scleroderma lung disease

This study compares molecular features of SSc-NSIP and SSc-UIP with IPF, finding shared epithelial changes and distinct fibroblast programs.

Perturbation-induced gene programs map the hidden regulatory architecture of complex diseases

This paper introduces Perturbscape, a framework that uses perturbation-induced gene programs to identify disease-relevant genes and pathways, showing higher heritability informativeness than steady-state approaches.

CD200R1 Marks a Branchpoint During Human Natural Killer Cell Development in Tonsils

The paper identifies CD200R1 as a marker for an immature NK-cell precursor in tonsils, distinguishing between oligopotent and more restricted developmental stages.

RAPTORGraph: graph-based pathway modeling for causal discovery in single-cell perturbations

RAPTORGraph improves causal discovery in single-cell perturbations by modeling gene interactions and isolating perturbation effects, outperforming existing methods on downstream analyses.

Single-cell geometry of drug responses across malignant glioma states

The paper analyzes drug response direction across glioma states using single-cell RNA-seq data, finding that response direction is consistent across states but magnitude varies.

Sex-specific bone marrow populations regulate skeletal phenotype and identify CD74-marked osteoclast precursor subsets

The paper identifies sex-specific bone marrow cell populations that regulate bone mass and shows CD74 marks osteoclast precursor subsets.

Disentangling Context-Specific Alzheimer's Disease Progression Signatures through an Explainable AI Framework

ADVISE identifies context-specific Alzheimer's disease progression signatures using an explainable AI framework and validates ROBO2 as a candidate regulator in excitatory neurons.

BioTrajX: evaluating biological plausibility in single-cell trajectory inference

BioTrajX evaluates biological plausibility of single-cell trajectories using three metrics to compare different trajectory inference results.

gcat, its_a_scam: modular tools for single cell data processing and per-cellquality control

The paper introduces gcat and its_a_scam, modular tools for single cell genomic data processing and quality control, showing they produce results comparable to proprietary pipelines.

CloneVI: A deep generative model for deciphering the relationships between cell state and mitochondrial genotype

CloneVI infers clonal structure from cell states in single-cell RNA-seq and ATAC-seq data, linking mitochondrial DNA mutations to specific cell states.

Distinct processing of visual motion by transcriptomic cell types in the superior colliculus

The paper identifies how three transcriptomic cell types in the superior colliculus process visual motion with distinct feature selectivity, morphology, and connectivity.

Endogenous PROM1 activation redistributes liver cancer cells along a preexisting differentiation axis

The paper shows PROM1 activation in liver cancer cells shifts their state along a preexisting differentiation axis, suggesting CD133's role extends beyond being a stem-like marker.