scRNA-seq

Benchmarking Imputation Methods for Single-Cell RNA Sequencing Data Using Peripheral Blood Mononuclear Cells from Acute Myocardial Infarction Patients

The paper benchmarks imputation methods on scRNA-seq data from AMI patients to assess their impact on downstream analysis.

In vivo virus-free lineage tracing and live imaging 1 reveal that NeuroD1 does not reprogram microglia into neurons

The paper shows NeuroD1 does not convert microglia into neurons, instead causing apoptosis, using lineage tracing and single-cell RNA sequencing.

Comparative Single-Cell Profiling of CRISPR Knockout and Interference Defines Modality-Specific Strengths in Functional Genomics

This study compares CRISPR knockout and interference methods using single-cell RNA sequencing to evaluate their strengths in functional genomics.

Deciphering the combinatorial expression pattern and genetic regulatory mechanisms of Beats and Sides in the olfactory circuits of Drosophila

The paper investigates the combinatorial expression of Beat and Side genes in Drosophila olfactory circuits and their role in synaptic specificity and development.

Erosion of regenerative regulation: age-associated shifts in the skeletal muscle fiber epigenome and transcriptome

The paper identifies age-associated changes in the skeletal muscle epigenome and transcriptome, revealing shifts in chromatin accessibility and gene expression linked to metabolic and senescence pathways.

Single-cell mapping of the fallopian tube reveals a genomically unstable secretory cell state enriched in carriers of germline BRCA1/2 mutations

The paper identifies genomically unstable secretory cells in fallopian tubes of BRCA1/2 carriers using single-cell transcriptomics, linking them to replication stress and early cancer transformation.

Skeletal Muscle Stem Cell-Derived Myonuclei Adopt Divergent Terminal Transcriptional States in Adult and Aged Muscle In Response to a Hypertrophic Stimulus

The paper identifies age-related differences in the transcriptional states of MuSC-derived myonuclei in response to mechanical overload.

A Subset of G Protein-Coupled Serotonin Receptor Genes is Linked to a Neuronal Gene Expression Signature and Clinically Favorable Biology in IDH-Mutant Gliomas

The paper identifies four serotonin receptor genes linked to favorable clinical and molecular features in IDH-mutant lower-grade gliomas, suggesting a neuronal/synaptic differentiation state.

The cortical microenvironment drives early immune organization and controls early osteoclastogenesis in bone healing

This study identifies a cortical niche-specific macrophage subset that drives early osteoclastogenesis in bone healing through spatial immune-stromal interactions in young mice.

The cellular and genetic basis of inflorescence divergence between maize and teosinte

This study identifies cellular and genetic changes in maize and teosinte ears, showing how cytokinin signaling and transcription factor expression differences drive cob thickening and increased kernel number during domestication.

High-avidity TCR signaling drives an NKG2A-positive CD8 T cell exhaustion state in human tumors

This study identifies high-avidity TCR signaling via NFAT as a key driver of NKG2A-positive CD8 T cell exhaustion in human tumors, with implications for immunotherapy.

BatchRefiner: fast, significant improvement in batch integration of single-cell embeddings with ensemble refinement

BatchRefiner improves batch integration of scRNA-seq and scATAC-seq embeddings by ensemble refinement, showing significant performance gains across datasets and metrics.

Longitudinal single-cell modeling reveals monocyte reprogramming in juvenile systemic sclerosis following autologous stem cell transplantation

This study uses longitudinal single-cell data to show changes in monocyte gene expression and metabolic state after ASCT in jSSc patients.

Malignant epithelial diversification and inflammatory neutrophil remodeling define a transitional stage between tumor cell dissemination and overt metastatic outgrowth in breast cancer

The paper identifies a transitional stage in breast cancer metastasis characterized by malignant epithelial diversification and inflammatory neutrophil remodeling, linking these to poor clinical outcomes.

AI-driven framework modeling perturbation in brain organoids reveals candidate genes for autism

The paper uses an AI-driven framework to model perturbations in brain organoids and identifies candidate genes for autism using genomic and clinical data.

Likelihood-Based Inference and Model Selection for Stochastic Gene Expression in Probability-Generating-Function Space

This paper develops a likelihood-based framework using probability generating functions for parameter inference and model selection in stochastic gene expression from single-cell counts.

A mechanism-annotated benchmark reveals limited fidelity to drug-response signatures in single-cell perturbation models

This paper introduces a benchmark to evaluate single-cell drug perturbation models by assessing their fidelity to drug-response signatures, finding that expression similarity is a poor proxy for mechanism preservation.

Uni-TINT: Unifying T and Innate Lymphoid Cell Taxonomy with a high resolution, pan-disease and pan-tissue single-cell transcriptomic atlas

Uni-TINT creates a unified single-cell atlas of T and innate lymphoid cells across diseases and tissues, identifying new cell subtypes and functional associations.

Multiscale biological interactions define clinical trajectories in acute myeloid leukemia

This study links multiscale biological interactions to clinical outcomes in AML by analyzing single-cell data and developing an analytical framework.

scDisent: regulatory-aware disentangled representation learning for multi-omic single-cell analysis

scDisent separates regulatory and expression variables in multi-omic single-cell data, improving integration and interpretability.

Robustness to nuisance perturbations enables unsupervised evaluation of single-cell foundation models

This paper evaluates single-cell foundation models using an unsupervised framework that assesses their robustness to nuisance perturbations, revealing significant differences in structural stability between models ranked similarly by standard benchmarks.

In Luminal~A breast cancer, bulk FOXC1 reports the tumour vasculature, while a proliferation-independent basal-lineage axis marks the tumour cells

The paper adjusts bulk gene correlations for stromal and vascular compartments, showing FOXC1 in Luminal A breast cancer reflects vascular rather than tumour-cell biology.

Protein aggregation inhibitors induce divergent transcriptional responses in a cellular model of a-synuclein seeded aggregation

The paper evaluates three Syn aggregation inhibitors in a cellular model of a-synuclein aggregation using single-cell RNA sequencing to identify transcriptional changes and potential druggable pathways.

Hypothalamic Cell Type Evolution across Vertebrates

This study identifies conserved and clade-specific hypothalamic cell types across vertebrates using single-cell transcriptomics, revealing conserved transcription factors and rewired regulatory linkages.

Fusion-driven oncogenic programs shape the immune landscape in translocation renal cell carcinoma

This study identifies fusion-driven oncogenic programs in translocation renal cell carcinoma (tRCC) that shape an immunosuppressive tumor microenvironment, explaining its reduced immunotherapy response.

Identification of a set of endogenous retroviruses linked to IL-1-mediated immunopathology in severe COVID-19.

This study identifies ERVs linked to IL-1-mediated immunopathology in severe COVID-19 using bulk and single-cell RNA-sequencing data from multiple cohorts.

Long noncoding RNA NRAV can regulate interferon-stimulated gene expression in melanoma

This study shows that NRAV, a long noncoding RNA, suppresses interferon-stimulated gene expression in melanoma, contributing to immune evasion.

ClustoCell reveals cell states and their markers from single-cell transcriptomes

ClustoCell identifies cell states and markers from single-cell transcriptomes by analyzing transcriptional architecture, improving accuracy and stability over existing methods.

Leukemic Stem Cell Subtypes Drive Distinct Niche Remodeling in Acute Myeloid Leukemia

This study identifies a specific leukemic stem cell (LSC) subtype that drives niche remodeling in AML by altering fibroblast states and suppressing osteolineage differentiation.

CCIDeconv: Hierarchical model for deconvolution of subcellular cell-cell interactions in single-cell data

The paper introduces CCIDeconv, a method to deconvolve whole-cell cell-cell interactions into subcellular compartments using scRNA-seq data and spatial transcriptomics datasets.