Matthias Schlesner

Multi-omic dissection of reversible and persistent molecular alterations in diet-induced obesity

This study identifies reversible and persistent molecular changes in diet-induced obesity using multi-omic analysis, showing that microbial functional profiles drive persistent alterations.

Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold-standard

The paper benchmarks DNA methylation sequencing workflows against an experimental gold-standard, identifying superior workflows and developing a sustainable benchmarking platform.

Pyjacker identifies enhancer hijacking events in acute myeloid leukemia including MNX1 activation via deletion 7q

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

Dynamic DNA methylation reveals novel cis-regulatory elements in murine hematopoiesis

The paper develops a computational framework for analyzing DNA methylation data in mouse hematopoiesis, identifying novel cis-regulatory elements associated with gene expression during differentiation.

Endothelial Dnmt3a controls placenta vascularization and function to support fetal growth

This study shows that Dnmt3a regulates placental vascularization and fetal growth by controlling DNA methylation in endothelial cells, identifying it as a key factor in placental function.

Cell segmentation-free inference of cell types from in situ transcriptomics data

This paper introduces SSAM, a cell segmentation-free method for cell-type identification and tissue domain detection in in situ transcriptomics data, showing it detects known and discovers new cell types in mouse brain tissues.

Integrated phospho-proteogenomic and single-cell transcriptomic analysis of meningiomas establishes robust subtyping and reveals subtype-specific immune invasion

This study integrates phospho-proteogenomic and single-cell transcriptomic data to subtype meningiomas and identify subtype-specific immune infiltration patterns.

Framework For Quality Assessment Of Whole Genome, Cancer Sequences

The paper introduces a framework for assessing the quality of whole genome cancer sequences using a star rating system based on five QC measures, providing a tool for researchers to evaluate and exclude low-quality data.

Genomic footprints of activated telomere maintenance mechanisms in cancer

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.

pheno-seq - linking morphological features to gene expression in 3D cell culture systems

The paper introduces pheno-seq, a method that links morphological features to gene expression in 3D cell cultures, showing its ability to identify morphology-specific genes and regulatory states not captured by scRNA-seq.

HTSlib-js: Developer toolkit for a client-side JavaScript interface for HTSlib

HTSlib-js provides a JavaScript interface for processing BAM and VCF files in web browsers, enabling fast and interactive analysis of high-throughput sequencing data.

Questioning unexpected CRISPR off-target mutations in vivo

The paper questions the claim that unexpected SNVs and indels in CRISPR-treated mice are caused by CRISPR-Cas9, highlighting the lack of validation for these off-target effects.

Identification and prioritisation of causal variants in human genetic disorders from exome or whole genome sequencing data

This paper presents a pipeline for identifying and prioritizing causal variants in genetic disorders using exome or whole genome sequencing data, achieving success in over 35% of neurodevelopmental disorder cases.

ACEseq - allele specific copy number estimation from whole genome sequencing

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.

Deciphering programs of transcriptional regulation by combined deconvolution of multiple omics layers

The paper introduces a method to disentangle multi-omics data and identifies regulatory mechanisms in human blood cells.

Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments

The paper describes the PCAWG project's large-scale analysis of cancer whole genomes across multiple computing environments, producing validated consensus variants for downstream research.

A comprehensive multicenter comparison of whole genome sequencing pipelines using a uniform tumor-normal sample pair

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