Ivana Holcátová

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.

Revealing the Drivers Underlying Distinct Evolutionary Trajectories in Lung Adenocarcinoma

This study identifies three distinct evolutionary trajectories in lung adenocarcinomas using whole-genome sequencing, revealing that some never-smoking tumors follow smoking-like paths driven by KRAS mutations.

Cross-ancestral GWAS identifies 29 novel variants across Head and Neck Cancer subsites

This study conducts a cross-ancestral GWAS and fine mapping of head and neck squamous cell carcinoma subsites, identifying 29 novel variants and highlighting gene-environment interactions.

A prognostic signature for lung adenocarcinoma in people who have never smoked

The paper identifies three subtypes of NS-LUAD using RNA-seq data and develops a 60-gene signature that predicts survival across subgroups.

Deciphering lung adenocarcinoma evolution and the role of LINE-1 retrotransposition

This study analyzes 1024 lung adenocarcinomas to identify evolutionary patterns and mutational mechanisms, revealing distinct trajectories linked to smoking, ancestry, and retrotransposition.

Needlestack: an ultra-sensitive variant caller for multi-sample next generation sequencing data

Needlestack is a variant caller that improves sensitivity for low abundance mutations by learning sequencing error rates from multi-sample data.