Krishnaa T. A. Mahbubani

The paper generates organoid models of Barrett oesophagus and oesophageal adenocarcinoma to study disease progression and therapy response.

The paper reports mutation rates and mutational signatures across 53 normal human cell types, revealing variation in mutation accumulation and identifying known and unknown mutational processes.

This study uses spatial transcriptomics to map gene expression gradients in the human endometrium, revealing coordinated regeneration and niche architecture during menstrual breakdown.

This study develops human epithelioids as a 3D culture system that maintains architecture, heterogeneity, and clonal evolution over time, enabling long-term studies of tissue dynamics and therapeutic responses.

This study creates a comprehensive spatial atlas of the human ovarian cortex, revealing molecular mechanisms of primordial follicle activation and follicle niche organization.

This study shows hypoxia promotes airway differentiation in human lung epithelial progenitors through HIF pathways, with implications for lung disease.

The paper profiles immune cell RNA and protein expression across tissues and age to identify tissue-specific and age-related immune signatures.

This study examines the long-term effects of chemotherapy on normal blood cells by analyzing mutation burdens and cell population structure in treated individuals.

The immune response to human primary cholangiocyte organoids is ameliorated by donor-recipient HLA matching.

The paper identifies a VSMC transition linked to fibrous cap formation in atherosclerosis and shows PAR1 as a potential therapeutic target.

The paper creates a regulon atlas mapping TF activity across human cell types and uses it to link disease signatures to cell types and TFs, improving disease risk locus analysis.

This study uses whole-genome sequencing to analyze somatic mutations in normal gastric epithelium, revealing mutation rates, clonal dynamics, and associations with cancer risk factors.

This study generates HLA-edited cholangiocyte organoids with reduced immunogenicity and reports their mutation profiles and immune response in vitro and in vivo.

This study examines enhancer dynamics and spatial organization in the human spinal cord to understand cellular state transitions and identity.

Spapros selects optimal probe sets for targeted spatial transcriptomics to improve cell type identification and spatial variation detection across multiple datasets.

The paper introduces a high-accuracy sequencing method to detect somatic mutations in tissues, revealing extensive selection and driver mutations in oral epithelium and blood samples.

The paper integrates single-cell RNA-seq datasets across the GI tract to identify epithelial metaplasia in inflammatory diseases, showing its role in inflammation through immune cell interactions.

The paper constructs a high-resolution single-cell reference atlas of the human endometrium, identifying cell types, states, and signaling networks, and links them to endometriosis.

FlowAtlas.jl connects FlowJo with Julia-based computational tools for cytometry data analysis, demonstrating its capabilities on a human immune cell dataset.

The paper identifies and validates novel regulators of vascular smooth muscle cell proliferation using network analysis and experimental validation, highlighting RUNX1 and the TIMP1-CD74 axis as potential therapeutic targets.

The paper identifies CD8+FOXP3+ Tregs enriched in human tissues, expressing intracellular CD25 and tissue residency markers, and demonstrates their therapeutic potential and association with disease states.

This paper uses spatial transcriptomics and single-cell data to identify cellular niches in the human heart, revealing new insights into cardiac function and potential drug targets.

This study creates a single-cell atlas of human liver development, identifying pathways and factors that guide hepatic cell fates and improving hepatocyte-like cell functionality.

This study tracks clonal dynamics in human haematopoiesis across age, finding that clonal diversity sharply declines after 70, driven by positive selection on many genes and loss of Y chromosome in males.

This study creates a single-cell and single-nucleus transcriptomic atlas of human skeletal muscle ageing, revealing mechanisms in muscle stem cells, myofibers, and the microenvironment.

This study maps the temporal and spatial dynamics of the human endometrium using single-cell and spatial reference maps, identifying key signaling pathways regulating cell fate in vivo and in vitro.

The paper analyzes the mutational landscape of normal lymphocytes, revealing off-target effects of programmed genome engineering and the impact of differentiation and microenvironment exposure.

The paper characterizes the cellular composition and gene expression of the adult human heart using single-cell transcriptomics, identifying distinct cell types and their functional roles.

This study evaluates the impact of cold storage on scRNAseq data quality for lung, spleen, and oesophagus tissues, finding minimal effects within 24 hours but increased stress markers at 72 hours.