scRNA-seq

Engineered microvessel networks -- Longitudinal transcriptomic profiling validates chip-grown tissues as a robust model for studying vasculature

The paper validates chip-grown vascular tissues as a model for studying vasculature by showing cell provenance affects network formation and transcriptomic profiles.

Uncertainty-Aware Personalised Gene Expression Prediction Improves Cell-Type-Specific Association Testing

ATTICUS improves gene expression prediction and association testing by incorporating uncertainty awareness and personalized training, enhancing accuracy and cell-type specificity in disease studies.

Host control and regulation of human anellovirus persistence

This study identifies host factors and cellular contexts governing anellovirus persistence through genomic, transcriptomic, and functional analyses.

A comparative transcriptomic framework across kidney organoid, assembloid, and transplantation models

The paper compares transcriptomic profiles across kidney organoid, assembloid, and transplantation models to evaluate their maturity and suitability for research.

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.

Caudate nucleus aging and its association with brain disorders

This study examines caudate nucleus aging across species and diseases, identifying shared and disorder-specific age-related changes in cell types and regulatory features.

The Reasoning Paradox in Scientific Sandboxes: Why Extended Reasoning Fails in Autonomous Bioinformatics and How to Fix It.

This paper identifies two failure modes in extended reasoning models within bioinformatics tasks and introduces DTDR to improve accuracy and reduce errors.

Integrated transcriptomic and epigenomic profiling of human cartilage reveals coordinated changes in fibronectin expression, splicing, and receptor signaling during osteoarthritis progression

This study profiles human cartilage across OA grades, revealing changes in fibronectin expression, splicing, and receptor signaling during disease progression.

Uncovering the Multifaceted Role of the Kinetochore Scaffold 1 (KNL1) in Hepatocellular Carcinoma: Integrative Bioinformatics Analysis and CRISPR-Cas9 Experimental Study

This study identifies KNL1 as a key driver of chromosomal instability and immune evasion in HCC through integrative bioinformatics and CRISPR-Cas9 experiments.

GraphExperiment: infrastructure for high-dimensional quantitative data and associated networks in R/Bioconductor

GraphExperiment provides an R/Bioconductor package to store and manipulate high-dimensional quantitative data alongside associated networks in a unified framework.

Single-cell transcriptome-wide association analysis reveals epithelial cell-specific genetic susceptibility to colorectal cancer

The paper performs single-cell transcriptome-wide association analysis to identify cell-type-specific genetic susceptibility genes for colorectal cancer, finding 546 gene-cell-type associations and 347 candidate susceptibility genes.

Integrative multi-omics re-analysis of public sequencing and metabolomics repositories defines the mucosal immune and metabolic landscape of Helicobacter pylori infection and supports CagW as a rational mRNA-LNP vaccine antigen

The paper re-analyses public multi-omics data to characterize the gastric mucosal immune and metabolic landscape of H. pylori infection and identifies CagW as a promising mRNA-LNP vaccine antigen.

Integrative multi-omics decoding of the host response to Klebsiella pneumoniae infection reveals an itaconate-centred metabolic-immune axis and a spatially organised inflammatory programme

This study integrates multi-omics data from Kp infection to identify an itaconate-centred metabolic-immune axis and a host-response signature with high diagnostic accuracy.

Influenza H1N1 Imprinting Uncouples Serological and B-Cell Responses in Mice

This study shows that immunological imprinting in mice uncouples serological and B-cell responses, with B-cell repertoires updating independently of serum antibody specificity.

De novo lipogenesis controls antigen presentation and metastatic immune escape in triple-negative breast cancer.

FASN-driven lipogenesis sustains EGFR palmitoylation and PI3K-AKT-mTOR signaling, suppressing tumor MHC-I antigen presentation; blocking it curbs TNBC metastasis in mice via CD8 T cell recognition.

IG-28 enables identification and quantification of high-confidence isoforms from large bulk and single-cell full-length cDNA datasets

IG-28 identifies and quantifies high-confidence isoforms from large bulk and single-cell full-length cDNA datasets more effectively than existing tools.

Multi-omics analysis reveals chromatin and transcriptomic remodeling in hippocampal CA1 following adolescent social isolation

Two weeks of post-weaning isolation in male mice altered expression of 106 CA1 genes, enriched for myelination, while chromatin accessibility shifted only at nominal significance and tracked expression weakly.

Transient Splicing-Associated Isoform Remodeling Defines Early MAPKi Resistance Adaptation in Melanoma

The paper identifies transient isoform remodeling as a key mechanism in early MAPKi resistance in melanoma, showing it is distinct from gene expression changes and linked to splicing regulators and developmental pathways.

IFNγ-CXCL9-CXCR3 axis links T cell recruitment to skeletal muscle remodelling in human physical frailty

This paper identifies an IFNγ-CXCL9-CXCR3 axis linking T cell recruitment to skeletal muscle remodelling in human physical frailty, showing its association with fibrosis and potential therapeutic targets.

Timed binary WNT activity is sufficient to model the early human neural axis

This paper shows that timed WNT pulses can specify distinct neural domains in human pluripotent stem cells, enabling the generation of specific neuron and progenitor types.

Increasing Cancer Stemness Drives Prostate Cancer Progression, Plasticity, Therapy Resistance and Poor Patient Survival

This study quantifies cancer stemness in prostate cancer across progression stages, showing its association with therapy resistance, poor survival, and lineage plasticity.

The epidermal growth factor (EGF) receptor family network in cardiac hypertrophy and heart failure

EGFR-family ligand mRNAs shift in failing human hearts; NRG1 and EGF drive distinct, differently ERBB2-dependent transcriptional programmes in rat cardiomyocytes; afatinib blunts mouse angiotensin II hypertrophy but worsens fibrosis.

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.

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.

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.

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.

Phenotype-cloud reorganization shapes cancer progression and therapeutic adaptation

This study identifies phenotype-cloud transitions as an organizational feature of cancer progression and therapeutic adaptation, showing how tumours reorganize phenotypic states during progression and treatment.

Tetraspanin changes in septic blood are organized by cell type, with monocyte CD82 induction and leukocyte CD37 loss associated with mortality

The paper identifies cell-type-specific tetraspanin changes in sepsis, finding CD37 loss and monocyte CD82 induction linked to mortality.

Gestational reorganization of cellular niches and communication revealed by a spatially resolved transcriptional atlas of the macaque maternal-fetal interface

This paper constructs a spatial transcriptomic atlas of the macaque maternal-fetal interface across gestation, revealing shifts in cellular composition and signaling pathways.

Survival-associated cellular communication networks in human solid cancers

The paper develops SKyNet to identify survival-associated cell-cell communication networks in solid cancers using single-cell and bulk RNA-seq data, finding specific interactions linked to patient outcomes.