Roman Jaksik

This study assesses microhomology-associated deletions in cancer genomes, identifies their prognostic significance, and optimizes detection parameters for improved patient stratification.

This study evaluates methods to correct cytosine deamination artifacts in FFPE sequencing, finding enzymatic repair is most effective and FFPErase is the best computational method.

DECODE improves tumor clonality and expansion mode detection by accounting for sequencing biases and neutral tail in SFS, showing better performance on synthetic data and clinical relevance in glioma.

The paper analyzes FFPE breast cancer specimens to assess recoverable molecular evolution features using computational methods despite sequencing artifacts.

The paper identifies a novel mechanism where focal deletions of an intronic element in FTO lead to IRX3 activation in T-ALL through enhancer hijacking.

This study identifies molecular changes in bladder mucosa that initiate cancer, revealing inflammation's role and mutation patterns linked to early carcinogenesis.

The paper identifies replication origins in human tumors using mutation patterns and compares them across methods to define a consensus set.

This study evaluates the accuracy of somatic variant detection workflows in WGS experiments using real and synthetic data, finding DRAGEN excels in sensitivity while CGP-WGS performs better in precision.