Eszter Lakatos

This study uses whole genome sequencing of endometrial cancers to identify novel subgroups, drivers, and actionable alterations, improving precision medicine approaches.

This paper introduces BayesCNA, a Bayesian method for detecting copy number alterations in low-pass liquid biopsy sequencing data, showing improved sensitivity in low-quality cases.

This paper identifies long deletion signatures in repetitive regions as markers of microsatellite instability and develops a classifier to detect MSI in low-quality sequencing data.

This study shows that immune evasion in colorectal cancer follows a 'Big Bang' pattern, where early genetic and epigenetic changes drive subsequent tumor-immune evolution.

This paper identifies mutational signatures caused by formalin fixation and introduces FFPEsig, a method to correct these artefacts in genome sequencing data.

The paper introduces rapidly oscillating molecular clocks to quantify human stem cell dynamics and finds differences in stem cell replacement rates between small intestine and colon, as well as effects of germline mutations.

LiquidCNA tracks subclonal evolution from liquid biopsies using somatic copy number alterations, revealing new subpopulations in metastatic lung cancer.

The paper quantifies tumor immunogenicity using dN/dS ratios in the immunopeptidome and shows it predicts immunotherapy response by distinguishing adaptation from escape mechanisms.

NeoPredPipe predicts and assesses neoantigen recognition potential from tumor variants in single and multi-region samples, providing insights into neoantigen burden and tumor heterogeneity.

This study develops a mathematical model to analyze spatial interactions in ovarian cancer microenvironments and shows how niche composition affects treatment response.

The paper analyzes dynamical systems models of stem-cell differentiation to explore transition states and their role in cell fate changes.

The paper develops a reachability analysis framework to study control mechanisms in stochastic biochemical systems, providing bounds on population statistics despite parameter uncertainty and non-linearity.