Batuhan Çakır

The paper presents the Human Gut Cell Atlas v1.0, a unified reference of gut cell diversity, revealing how tissue structure influences cellular composition and enabling disease and organoid analysis.

TERRA is a foundation model for spatial transcriptomics that predicts tissue behavior under perturbation and identifies multi-scale biological insights across tissues.

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.

inVAE improves cell state identification by disentangling biological and technical variation in single-cell data, outperforming existing methods across multiple human tissues.

This study creates a single-cell spatial atlas of the developing human reproductive tract, identifying genes and mechanisms involved in sexual dimorphism and organ development.

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.

This study constructs a multiomic atlas of human early skeletal development using single-nuclei transcriptomics, epigenomics, and spatial transcriptomics to uncover regulatory mechanisms and cell states involved in bone and joint formation.

This study compares web-based visualization tools for scRNA-seq data and introduces an R package to standardize data formats for sharing.