Christoph Plass

The paper improves a tool for sorting DNA reads in xenograft models, enhancing efficiency for epigenetic analysis.

This study identifies LOY as a driver of aggressive PDAC through epigenetic reprogramming, linking it to EMT and metastasis, and highlights its clinical relevance as a biomarker.

The paper develops a hierarchical classification framework combining epigenetic and genetic data with machine learning to improve diagnosis and risk stratification in hematologic malignancies.

This study shows that loss of the Y chromosome in lung adenocarcinoma causes epigenetic and transcriptomic changes that increase lineage plasticity and poor clinical outcomes.

This study identifies GLYATL1 as a mediator of endocrine resistance in luminal breast cancer by promoting metabolic and epigenetic changes that counteract estrogen deprivation.

This study identifies epigenetic changes in AT2 cells from COPD patients that disrupt IFN and WNT pathways, impairing lung regeneration.

This study identifies oncofetal reprogramming in juvenile myelomonocytic leukemia, linking RAS-pathway activation to fetal gene expression and revealing CD52 as a therapeutic target.

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

This study integrates spatial and multi-omic data from bladder cancer patients to show L1 retrotransposition drives genomic instability, ecDNA formation, and a viral mimicry response.

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.

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

This study shows that inhibiting the DNMT/G9a complex targets specific epigenetic vulnerabilities in AML, inducing an IFN response and improving therapeutic outcomes.

The paper introduces epiCHAOS, a metric to quantify cell-to-cell epigenomic heterogeneity in single-cell data and shows its utility in assessing stemness and plasticity.

The paper identifies del(5q) AML as an epigenetically distinct subgroup driven by KDM3B haploinsufficiency, linked to DNA hypermethylation and H3K9me1/2 dysregulation.

This study shows that SRSF2 mutations cause DNA damage and cell cycle arrest, highlighting its role in transcription regulation during cell division.

The paper shows MNX1 overexpression in t(7;12)(q36;p13) AML is due to enhancer hijacking, not oncofusion, and is common in pediatric cases.

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.

Figeno generates publication-quality genomic figures with support for multi-region views, long reads, and epigenomic data.

This study shows that Dnmt3a1, but not Dnmt3a2, is required for hippocampus-dependent memory through its regulation of Nrp1.

The paper identifies sequence preferences of TET enzymes that target DNA demethylation to bHLH and bZIP transcription factor binding sites.

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.

This study benchmarks six sequencing-based and two array-based cell-type deconvolution methods for bulk DNA methylomes, identifying the best-performing method and factors affecting performance.

This paper introduces a reference-free deconvolution protocol for DNA methylomes to identify hidden cell populations in complex samples, applied to lung cancer data from TCGA.

The paper identifies DNA methylation differences in monozygotic twins discordant for multiple sclerosis, highlighting treatment effects and genetic confounders.