Benedikt Brors

The paper identifies genomic and transcriptomic features of telomere maintenance mechanisms in complex karyotype sarcomas, linking ALT status to therapeutic vulnerabilities.

This study shows that HSC dormancy, not apoptosis, limits mutagenesis in aging, with dormancy disruption accelerating mutation rates.

This study uses Nanopore whole-genome sequencing to show conserved chromosome-specific telomere length patterns across tissues and populations, revealing coordinated regulation and potential disease risk factors.

The paper investigates functional differences between EML4-ALK variants V1 and V3 in lung cancer using mouse models and human data, showing variant-specific effects on tumorigenesis.

The paper compares CCR8+ Treg cells in tumor and tumor-free tissues using chromatin accessibility and DNA methylation, finding high similarity suggesting tumor microenvironment activation of tissue Treg cells.

The paper identifies tertiary lymphoid structures in brain metastases from different cancer types and links their presence to patient survival.

Pyjacker detects enhancer hijacking in AML, identifying MNX1 activation via 7q deletion as a novel oncogenic mechanism.

This study identifies somatic mutations in ALS genes in the motor cortex of sporadic ALS patients, particularly in excitatory neurons, suggesting a role in disease initiation.

The paper introduces CFS, a method to compare cell groups across datasets without integration, identifying conserved astrocyte subpopulations in mouse motor cortex and spinal cord.

The paper evaluates and optimizes sequence-based gene regulatory deep learning models using a DREAM Challenge dataset, showing improvements through architectural and training strategy refinements.

The paper introduces REMIND-Cancer Pipeline and pSNV Hunter to identify and prioritize functional promoter SNVs, including lowly recurrent and singleton mutations, using multi-omics data from the PCAWG dataset.

This paper develops a computational framework to quantify telomere content and composition from scATAC-seq data, revealing patient-specific telomere maintenance patterns in cancer and immune cells.

The paper identifies previously overlooked activating promoter mutations in cancer using a computational workflow applied to the PCAWG dataset, validating several candidates through luciferase assays.

The paper shows that stromal cells, particularly fibroblasts, dominate EMT-related gene expression signature scores in cancer, rather than tumor-intrinsic properties.

The paper develops immune cell type signatures using multiple datasets and applies random forest classification to improve cell type assignment in single-cell RNA-seq data.

The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

The paper examines how somatic structural variations affect TAD boundaries and gene regulation in human cancers using whole genome sequencing data.

This study analyzes chromothripsis in 2,658 cancers using whole-genome sequencing, finding it prevalent across multiple cancer types with complex structural alterations.

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

The paper maps DNA methylation changes during differentiation of HL-60/S4 cells, showing enhancer and CTCF site methylation drives transcriptional reprogramming.

The paper integrates single cell RNA-seq with bulk epigenomic data to identify distinct regulatory states in bidirectional promoters and their associations with structural features and TF binding.

This study identifies MDM4 as a critical target of 1q gain in TP53wt Burkitt lymphoma, showing its role in evading cell cycle arrest and highlighting its therapeutic potential.

ACEseq estimates allele-specific copy numbers, tumor purity, ploidy, and homologous recombination deficiency scores from tumor whole-genome sequencing by combining GC-bias correction, replication-timing correction, and structural variant breakpoints.

This paper introduces TEPIC, a method that combines open-chromatin data with TF binding affinities to predict gene expression, achieving results comparable to TF ChIP-seq.

TelomereHunter estimates and characterizes telomere content from whole genome sequencing data in cancer studies.

This study benchmarks somatic mutation calling in cancer genomes, identifying inconsistencies and proposing solutions to improve accuracy.

This study compares whole genome sequencing pipelines across five centers using a uniform tumor-normal sample pair, identifying factors affecting output consistency.