Bogac Aybey

The paper identifies a fetal-like stem cell trajectory in colorectal cancer using multi-omics and organoid models, linked to poor prognosis and SRC/mTOR dependency.

The paper shows that stromal cells, particularly fibroblasts, dominate EMT-related gene expression signature scores in cancer, rather than tumor-intrinsic properties.

The paper develops immune cell type signatures using multiple datasets and applies random forest classification to improve cell type assignment in single-cell RNA-seq data.

CONET infers tumor evolutionary trees and copy number calls from single-cell data using a probabilistic model with MCMC and regularization.