Roland F. Schwarz

Chromosomal instability shapes spatial and temporal phenotypic diversity in a malignant peripheral nerve sheath tumour

This study uses single-cell and spatial multi-omics to analyze a malignant peripheral nerve sheath tumor, revealing chromosomal instability drives phenotypic diversity and spatial-temporal evolution.

pyfraglib: An integrated cfDNA fragmentomics platform

pyfraglib provides a platform for cfDNA fragmentomics analysis, including fragment extraction, feature modeling, cohort comparison, and simulation, and identifies a high-risk subgroup in CNSL patients.

Haplotype-resolved genome architecture mapping uncovers pervasive structural heterogeneity between human homologous chromosomes

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

PhytClust: Efficient and Optimal Monophyletic Partitioning of Rooted Phylogenetic Trees

PhytClust partitions rooted phylogenetic trees into monophyletic clusters without user-defined thresholds, achieving optimal and reproducible results across diverse biological datasets.

SC-BIG: A Hierarchical Bayesian Model for Bulk-Informed Single Nucleotide Variant Calling in Single Cells

SC-BIG improves single-cell SNV detection by integrating bulk sequencing data, outperforming existing methods in simulated scenarios.

Deciphering selection patterns of somatic copy-number events

This paper introduces SPICE, a framework to infer copy-number events and model selection in cancer genomes, revealing 460 loci under selection and expanding the known cancer-related loci.

Phylogenetic analysis of paired breast carcinomas identifies genetic events associated with clonal recurrence and invasive progression

The paper analyzes paired breast carcinomas to determine if recurrences are clonal or new tumors, finding 7% are non-clonal by whole exome sequencing.

Ongoing genome doubling promotes evolvability and immune dysregulation in ovarian cancer

This study shows that ongoing whole-genome doubling in ovarian cancer promotes cell diversity and immune dysregulation through chromosomal instability and quiescent states.

Extensive folding variability between homologous chromosomes in mammalian cells

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.

CNSistent integration and feature extraction from somatic copy number profiles

CNSistent integrates and analyzes somatic copy number profiles across cancer cohorts to improve classification accuracy and identify key alterations.

Copy-number dosage regulates telomere maintenance and disease-associated pathways in neuroblastoma

The paper identifies gene dosage effects on telomere maintenance and disease pathways in neuroblastoma using genomic and transcriptomic data from 115 tumors.

Refphase: Multi-sample reference phasing reveals haplotype-specific copy number heterogeneity

Refphase uses multi-sample reference phasing to infer haplotype-specific copy numbers and reveal intra-tumour heterogeneity in cancer samples.

SMITH: Spatially Constrained Stochastic Model for Simulation of Intra-Tumour Heterogeneity

SMITH simulates cancer evolution with spatial constraints, showing that confinement mechanisms can reproduce clonal dynamics efficiently.

The rate of spontaneous mutations in yeast deficient for MutSβ function

The paper shows that in yeast lacking MutSβ function, mutations in simple sequence repeats are mostly deletions and occur at different rates depending on repeat length.

MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution

MEDICC2 infers cancer phylogenies from copy-number data, accounting for whole-genome doubling and parallel evolution, and performs well on simulated and real datasets.

Smoking-dependent expression alterations in nasal epithelium reveal immune impairment linked to germline variation and lung cancer risk

The paper identifies persistent smoking-related immune alterations in airway tissues and links them to genetic risk factors and lung cancer risk using transcriptomic data and GWAS integration.

GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data

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

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

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

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

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

Assessing the Gene Regulatory Landscape in 1,188 Human Tumors

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.