Burçak Otlu

Identification and Validation of a Previously Missed Mutational Signature in Colorectal Cancer

The paper identifies and validates a previously missed mutational signature in microsatellite-stable colorectal cancer, showing it is distinct from known signatures and not caused by canonical DNA repair defects.

Mutation-centric Network Construction using Long-Range Interactions

The paper introduces a graph-based framework to construct mutation-centric networks using long-range genomic interactions, demonstrating its ability to cluster cancer subtypes and prioritize non-coding driver mutations.

A Robust Framework for Predicting Mutation Effects on Transcription Factor Binding: Insights from Mutational Signatures in 560 Breast CancerGenomes

The paper develops a framework to predict mutation effects on transcription factor binding using mutational signatures in breast cancer genomes, revealing subtype-specific rewiring of gene regulatory networks.

Evaluating topography of mutational signatures with SigProfilerTopography

SigProfilerTopography evaluates how chromatin organization and other genomic features influence mutational signatures in cancer genomes.

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

SigProfilerExtractor is a tool for de novo mutational signature extraction that outperforms existing methods and identifies four novel signatures, including one linked to tobacco smoking.

The genomic and epigenomic evolutionary history of papillary renal cell carcinomas

This study examines intratumor heterogeneity and clonal evolution in papillary renal cell carcinomas using whole-genome sequencing and DNA methylation data, revealing distinct patterns of genomic and epigenomic evolution across subtypes.