Ludmila Danilova

replicateFest uses negative binomial models for replicated and Fisher's exact tests for unreplicated FEST TCR-seq to call antigen-expanded clonotypes, recovering all nine published HIV-1 responders.

The paper develops a spatial biomarker, DONUTS, to predict treatment response in lung cancer by analyzing the niche surrounding CD8+FoxP3+ T-cells.

This paper presents a T-cell vaccine targeting conserved regions across Sarbecoviruses to provide cross-protection against evolving variants.

This study examines TLS in HCC treated with neoadjuvant immunotherapy, finding TLS correlate with better outcomes and show distinct morphological and functional features in tumor regression.

This study uses spatial multi-omics to identify TLS-associated immune niches in PDAC that correlate with improved survival in immunotherapy responders.

This paper introduces SpaceMarkers, a method to infer molecular changes from cell-cell interactions in spatial transcriptomics data, applied to tumor-immune interactions in metastasis and immunotherapy.

The paper uses integrated time course omics analysis to distinguish immediate therapeutic response from acquired resistance in head and neck cancer.

This study evaluates the diagnostic and prognostic value of telomere length measurement in a hospital setting, finding it alters treatment decisions in a subset of bone marrow failure patients.

This study develops a non-invasive test for upper tract urothelial carcinomas using urine-based molecular analysis of driver gene mutations and aneuploidy, showing high sensitivity compared to current methods.