Hanaé Carrié

Systematic benchmarking of multi-modal approaches for tumor-naive ctDNA detection and quantification

This study benchmarks tumor-naive ctDNA detection and quantification methods using WGS and methylation data from cancer patients, identifying performance trade-offs and optimal integration strategies.

Comprehensive benchmarking of methods for mutation calling in circulating tumor DNA

The paper benchmarks 9 somatic variant calling algorithms on cfDNA samples from cancer patients, identifying optimal methods based on ctDNA levels and sequencing depth.

A Computational Framework for Analysis of cfDNA Fragmentation Profiles

This study introduces NDRDiff, a computational framework for analyzing cfDNA fragmentation profiles to infer gene expression and identify differentially expressed genes in cancer.

Fragle: Universal ctDNA quantification using deep learning of fragmentomic profiles

Fragle quantifies ctDNA from fragment length profiles using deep learning, showing high accuracy and improved detection limits across multiple datasets and sequencing types.