scRNA-seq

RFind-sc maps single cells onto biological axes defined by external gene signatures

RFind-sc maps single cells onto biological axes defined by external gene signatures, revealing cell states and candidate genes for stress responses.

Disrupted glial-mediated synaptic refinement in Fragile X syndrome

This study identifies impaired glial-mediated synaptic refinement in FXS model mice, showing enhanced astrocyte-microglia signaling and synaptic over-engulfment as key features.

Effector-primed TCF1+ CD8+ T cells elicited by a networked epitope vaccine stratify protection against SHIV acquisition

This study identifies an effector-primed TCF1+ CD8+ T cell state linked to delayed SHIV acquisition and reduced viral load in vaccinated non-human primates.

Regulatory architecture tunes gene expression noise in the plant heat shock response

This study shows that the plant heat shock regulatory network controls both the magnitude and distribution of stress-responsive gene expression across cells.

Cardiomyocyte Identity Crisis Without Regenerative Re-entry: A Multi-Scale Atlas of Incomplete Dedifferentiation and Intercellular Communication Rewiring in the Infarcted Human Heart

The paper constructs a multi-scale atlas of cardiomyocyte changes in infarcted hearts, showing partial identity loss without regenerative proliferation and altered intercellular communication.

Large-scale integrated single-cell analysis reveals molecular subtypes and microenvironmental remodeling in cutaneous T cell lymphoma

This study integrates a large scRNA-seq dataset of CTCL to identify molecular subtypes and microenvironmental changes with clinical relevance.

Conserved Brain-Associated CD8+ T Cell Programs and Their Regulation by the Brain Microenvironment

This study identifies conserved functional features of brain-associated CD8+ T cells in mice and marmosets and shows how brain signals regulate their effector programs.

CDKL5 deficiency alters cell subtype-specific molecular programmes and intercellular signalling in the mouse hippocampus

This study uses snRNA-seq to analyze gene expression changes in the hippocampus of CDKL5-deficient mice, identifying cell-type-specific transcriptional alterations and intercellular signaling changes.

An integrative cardio-informatics approach identifies positionally conserved ancestors of human lncRNA genes transcribed across vertebrate hearts

The paper identifies conserved genomic positions of human heart-related lncRNA genes across vertebrates using integrative analysis and a neural network tool.

TMEM55B downregulation promotes neurodegeneration in Alzheimer disease models.

The paper shows TMEM55B downregulation contributes to neurodegeneration in Alzheimer's disease models by impairing lysosomal transport and autophagy.

Dosage-dependent disruption of corticofugal neuron development by Fezf2 loss

This study quantifies the cell-type-specific and temporal transcriptional effects of Fezf2 dosage loss in mouse cortical development using single-cell RNA-seq and ATAC-seq data.

A knowledge graph-guided framework for multitask single-cell analysis

scKNIFE integrates gene expression with functional annotations to identify tumor programs and treatment-related functional variation in breast cancer.

Integrative reanalysis of public intracellular and vaccine-challenge transcriptomes, informed by single-cell and metabolomic atlases, refines antigen prioritisation for next-generation veterinary Brucella vaccines

The paper reanalyzes public transcriptomic and metabolomic data to prioritize antigens for improved Brucella vaccines by integrating single-cell and metabolomic atlases.

Single-cell analysis of West Nile virus infection in brain organoids identified a serine synthesis enzyme as a determinant of viral neural tropism and a druggable antiviral target

This study uses human cerebral organoids to identify PHGDH as a key metabolic factor enabling WNV infection and a potential drug target.

Single-cell analysis of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-treated murine skin demonstrates that sebaceous gland differentiation precedes Ahr-dependent seboatrophy with elevated expression of infundibular Blimp1

This study shows TCDD induces Cyp1a1 in murine skin, enhancing sebaceous gland differentiation and lipid production before causing Ahr-dependent seboatrophy.

Single-Cell Sequencing in Pediatric Acute Leukemia: A Systematic Review of Biologic Insights and Translational Potential

This review evaluates single-cell sequencing findings in pediatric acute leukemia, highlighting insights into clonal evolution, chemoresistance, and immune dynamics, while noting limitations in study design and bias.

Recurrent leukaemia stem cell states define the antigenic landscape of paediatric Acute Myeloid Leukaemia

This study identifies three leukaemia stem cell subtypes in paediatric AML and shows that combining CLEC12A and CD84 targets all subtypes while sparing healthy cells.

OmniRE-seq: A Dual-Method Framework for Decoding RNA Editing Dynamics in Disease and Therapy

OmniRE-seq quantifies RNA editing across bulk and single-cell data, identifying disease-related patterns and therapeutic targets in multiple models.

Spatial multi-omics implicates vascular adipocytes proximal to tertiary lymphoid structures in human aortic aneurysm and B-cell autoreactivity.

This study uses spatial multi-omics to show that vascular adipocytes near tertiary lymphoid structures in human aortic aneurysms contribute to B-cell autoreactivity and inflammation.

Single-nucleus transcriptomics and phosphoproteomics identify misregulated sperm components in mice carrying a selfish supergene

The paper identifies misregulated sperm components in mice with a selfish supergene using single-nucleus transcriptomics and phosphoproteomics, revealing dysregulated phosphorylation and gene expression related to sperm motility.

A coordinated and reproducible multicellular response to AD pathology

The paper identifies robust multicellular axes associated with Alzheimer's disease pathology and sex using single-cell data from 427 donors, validated in an independent dataset.

Shared and distinct immunometabolic states link to divergent pathology in cutaneous mycobacterial infections

This study identifies shared and distinct innate immune programs in cutaneous mycobacterial infections and links them to divergent pathological outcomes through metabolic interactions.

A multi-omics resource of B cell activation reveals genetic mechanisms for immune-mediated diseases

This study profiles B cell activation states using multi-omics data to identify genetic mechanisms underlying immune-mediated diseases.

Elucidating changes in gene expression driving nuclear dynamics across a foraminiferal life cycle with Pheno2Seq

The paper develops Pheno2Seq to study gene expression changes in foraminifera life cycle transitions, identifying genes involved in nuclear dynamics and genome stability.

General Purpose AI for Public Data Analysis and Experimental Hypothesis Generation

The paper demonstrates how general-purpose AI can analyze public molecular datasets to generate hypotheses and identify biological relationships, though not all findings were validated experimentally.

LiverHomo: An Integrated and Interactive Human Liver Single-Cell Atlas with Protein Interaction and Cell-Cell Communication Networks

LiverHomo integrates human liver scRNA-seq data with PPI and cell-cell communication networks to provide an interactive resource for exploring liver health and disease.

Small-molecule ACOD1 inhibition attenuates colitis and tumor growth through a shared myeloid mechanism, diverging from genetic deletion

This study shows that ACOD1 inhibition reduces colitis and tumor growth via a shared myeloid mechanism, differing from genetic deletion effects.

Decoding Cell-level Circadian Phase and Rhythm-state Remodeling in Single-cell Transcriptomes With scRhythmBayes

scRhythmBayes infers cell-level circadian phase and rhythm-state remodeling in single-cell transcriptomes, revealing distinct temporal patterns in liver zonation and heart disease.

The hepatic mitochondrial landscape

This study maps mitochondrial gene expression across the liver lobule in mice and humans, revealing spatial and temporal heterogeneity in mitochondrial function and structure.

Cell-level integration of gene expression and B cell receptor data captures complementary B cell information

The paper integrates gene expression and B cell receptor data to capture complementary B cell information, revealing substructure supported by both transcriptional and receptor features.