Julia Markowski

The paper introduces CoPhasing, a method to phase chromatin contacts with haplotype specificity, revealing structural differences between homologous chromosomes.

The paper benchmarks somatic variant and indel detection at low allele fractions using short- and long-read data, finding sensitivity and precision around 80% at 300x coverage.

The paper introduces a knowledge graph framework for integrating and querying biomedical data across domains, demonstrating its utility in eight use cases.

The paper uses GAM to study haplotype-specific 3D chromatin structures in mESCs, finding extensive allelic differences in chromatin architecture and gene expression mediated by Polycomb repression.

GAMIBHEAR reconstructs haplotypes from Genome Architecture Mapping data to enable allele-specific chromatin conformation analysis.

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

The paper analyzes RNA alterations across 27 cancer types using whole-genome sequencing data, identifying gene expression associations with DNA variants and structural fusions.

This study analyzes whole genome and RNA-Seq data from 1,188 cancer patients to map the effects of somatic and germline genetic variation on gene expression in cancer.