Zarko Manojlovic

Analysis of Naturally Arising Simple Deletions in Single Human Colon Crypts with Age

The paper analyzes simple deletions in single human colon crypts across age, finding most are due to strand slippage and NHEJ, with age-related accumulation and radiation effects.

SWI/SNF Alterations Define a Chromatin-Dependent Subtype of Urothelial Carcinoma

This paper identifies a chromatin-altered subtype of urothelial carcinoma defined by SWI/SNF alterations, showing it is sensitive to HDAC inhibition and immunotherapy.

Mutation count and mutation profile analyses of single-nucleotide variants in single human colon crypts

The paper analyzes mutation counts and profiles in single human colon crypts to assess somatic mutation rates and their implications for aging and disease.

Complex Indel Detection: A Simulation-Based Framework and Parsing with FreeBayes

This paper evaluates complex indel detection methods, finding FreeBayes best represents simulated complex indels as single variant records and develops a parsing workflow to extract complex indels from VCF output.

Germline VCF Annotator: a lightweight pipeline for processing germline VCFs with robust variant extraction and read evidence quality control

The paper develops a lightweight pipeline to process germline VCF files, enabling robust variant extraction and read evidence quality control for DDR loci analysis in colon crypts.

Fine Structural Features of Complex InDels and NHEJ Repair at Naturally Occurring Damage Sites in Normal Human Colon Crypts

The paper identifies complex indels and NHEJ repair in human colon crypt stem cells using whole-genome sequencing to study DNA damage repair in a physiologically relevant context.

High-depth Whole Genome Sequencing of Single Human Colon Crypts Uncovers New View on Crypt Clonality

This study uses high-depth whole genome sequencing of single colon crypts to show they are often polyclonal, revealing cell-to-cell heterogeneity previously unattainable with lower sensitivity methods.

Analysis of Naturally Occurring Somatic Insertions in the Human Genome

The paper analyzes naturally occurring somatic insertions in the human genome using whole-genome sequencing, finding replication slippage as a dominant mechanism for these events.