Kourosh Saeb‐Parsy

Evaluation of Densified Collagen Tubes as an Interposition Graft in Abdominal Aorta

This study evaluates densified collagen tubes as interposition grafts in rat abdominal aorta, showing patent grafts for 17 weeks with neointima formation and re-endothelialization but late thrombosis.

A comprehensive atlas of somatic mutation rates and mutational signatures in normal human cells

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.

Full-thickness spatial transcriptomics of the human uterus reveals basalis niche architecture and regeneration gradients during menstrual breakdown

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

Human 3D epithelioids enable continuous long-term clonal evolution studies across multiple epithelial tissues

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.

Spatial atlas of the ovary identifies molecular events in primordial follicle activation in humans

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

A network medicine framework for multi-modal data integration in therapeutic target discovery

This paper presents a network medicine framework integrating multi-modal data to identify therapeutic targets in clear cell renal cell carcinoma, recovering established targets and predicting five candidates, with ENO2 inhibition showing the strongest anti-tumour effect.

Systemic mutagen exposures reported by normal kidney cell genomes

The paper identifies mutational signatures in normal kidney cells from multiple countries, revealing exposure to exogenous mutagens including aristolochic acids and unknown agents prevalent in Japan.

Hypoxia promotes airway differentiation in the human lung epithelium

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

The long-term effects of chemotherapy on normal blood cells

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

An atlas of TF driven gene programs across human cells

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.

The somatic mutation landscape of normal gastric epithelium

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.

Immune and Mutational Profile of Gene-Edited Low-Immunogenic Human Primary Cholangiocyte Organoids

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

Enhancer Dynamics and Spatial Organization Drive Anatomically Restricted Cellular States in the Human Spinal Cord

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

Somatic mutation and selection at epidemiological scale

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.

Single Cell Integration Characterises Metaplasia in Inflammatory Intestinal Diseases

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.

An integrated single-cell reference atlas of the human endometrium

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: an interactive tool bridging FlowJo with computational tools in Julia

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

Spatially resolved multiomics of human cardiac niches

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.

Single-cell atlas of human liver development reveals pathways directing hepatic cell fates

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.

Generation of functional hepatocytes by forward programming with nuclear receptors

This study generates functional hepatocytes from human pluripotent stem cells using forward programming with nuclear receptors, bypassing the limitations of traditional differentiation methods.

Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells

This study shows that inherited MUTYH mutations increase somatic mutation rates and specific mutational signatures in normal human cells, contributing to cancer risk without causing premature aging.

Clonal dynamics of haematopoiesis across the human lifespan

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.

Human skeletal muscle ageing atlas

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.

Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

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.

Genome-wide mutational signatures of immunological diversification in normal lymphocytes

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.

Cells and gene expression programs in the adult human heart

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.

Distance and Colour-based Scores for Blood Test Risk Stratification

The paper introduces numerical and colour-based risk stratification scores to quantify abnormal blood analyte values and tests their effectiveness in distinguishing healthy individuals from those with diseases.

Lung, spleen and oesophagus tissue remains stable for scRNAseq in cold preservation

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.