Publications

Data-driven soft labeling scales DNA read classification to whole-body cell-type deconvolution.

The molecular heterogeneity and clinical impact of genomic driver alterations in prostate cancer.

Integrated signatures define mutational processes in prostate cancer.

Recurrent mechanisms of biallelic epigenetic inactivation reveal new putative tumour suppressor genes in prostate cancer.

GLYATL1 is associated with metabolic and epigenetic changes and with endocrine resistance in luminal breast cancer.

Molecular Plasticity Results in Oncofetal Reprogramming and Therapeutic Vulnerabilities in Juvenile Myelomonocytic Leukemia.

Methylation reprogramming associated with aggressive prostate cancer and ancestral disparities.

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

Epigenetic clues from cancer's past foretell its future.

DNA demethylation-mediated downregulation of MNX1 in acute myeloid leukemia.

Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q.

Causes of evolutionary divergence in prostate cancer.

MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model.

EpiCHAOS: a metric to quantify epigenomic heterogeneity in single-cell data.

SRSF2 safeguards efficient transcription of DNA damage and repair genes.

Altered enhancer-promoter interaction leads to MNX1 expression in pediatric acute myeloid leukemia with t(7;12)(q36;p13).

Dnmt3a1 regulates hippocampus-dependent memory via the downstream target Nrp1.

scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data.

ARID1A regulates DNA repair through chromatin organization and its deficiency triggers DNA damage-mediated anti-tumor immune response.

Figeno: multi-region genomic figures with long-read support.

Aberrant MNX1 expression associated with t(7;12)(q36;p13) pediatric acute myeloid leukemia induces the disease through altering histone methylation.

Discovery of non-genomic drivers of YAP signaling modulating the cell plasticity in CRC tumor lines.

Clinical impact of the genomic landscape and leukemogenic trajectories in non-intensively treated elderly acute myeloid leukemia patients.

Heterogeneity in the gene regulatory landscape of leiomyosarcoma.

Translocation t(6;7) in AML-M4 cell line GDM-1 results in MNX1 activation through enhancer-hijacking.

TAL1 activation in T-cell acute lymphoblastic leukemia: a novel oncogenic 3' neo-enhancer.

The GAPDH redox switch safeguards reductive capacity and enables survival of stressed tumour cells.

Dynamic DNA methylation reveals novel cis-regulatory elements in mouse hematopoiesis.

Global DNA Methylation Analysis of Cancer-Associated Fibroblasts Reveals Extensive Epigenetic Rewiring Linked with RUNX1 Upregulation in Breast Cancer Stroma.

Genetic and methylation profiles distinguish benign, malignant and spitzoid melanocytic tumors.

Epigenomic technologies for precision oncology.

Genetic and Methylation Analysis of CTNNB1 in Benign and Malignant Melanocytic Lesions.

Club cells employ regeneration mechanisms during lung tumorigenesis.

Histone H3K27 demethylase KDM6A is an epigenetic gatekeeper of mTORC1 signalling in cancer.

Systematic evaluation of cell-type deconvolution pipelines for sequencing-based bulk DNA methylomes.

A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation.

ID3 promotes homologous recombination via non-transcriptional and transcriptional mechanisms and its loss confers sensitivity to PARP inhibition.

Epigenetic reprogramming of airway macrophages promotes polarization and inflammation in muco-obstructive lung disease.

AmpliconDesign - an interactive web server for the design of high-throughput targeted DNA methylation assays.

Epigenetic analysis of patients with T-ALL identifies poor outcomes and a hypomethylating agent-responsive subgroup.

Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction.

Epigenetic Modulation of Radiation-Induced Diacylglycerol Kinase Alpha Expression Prevents Pro-Fibrotic Fibroblast Response.

Methrix: an R/Bioconductor package for systematic aggregation and analysis of bisulfite sequencing data.

Versatile workflow for cell type-resolved transcriptional and epigenetic profiles from cryopreserved human lung.

Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction.

Globally altered epigenetic landscape and delayed osteogenic differentiation in H3.3-G34W-mutant giant cell tumor of bone.

Reference-free deconvolution, visualization and interpretation of complex DNA methylation data using DecompPipeline, MeDeCom and FactorViz.

Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL.

Neuronal ensemble-specific DNA methylation strengthens engram stability.

Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software.

DNA methylation signatures of monozygotic twins clinically discordant for multiple sclerosis.

Integrative Analysis Defines Distinct Prognostic Subgroups of Intrahepatic Cholangiocarcinoma.

RnBeads 2.0: comprehensive analysis of DNA methylation data.

Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands.

Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories.

From Basic Knowledge to Effective Therapies.

DNA methylation analysis on purified neurons and glia dissects age and Alzheimer's disease-specific changes in the human cortex.

MeDeCom: discovery and quantification of latent components of heterogeneous methylomes.

Mitochondrial DNA Variation and Heteroplasmy in Monozygotic Twins Clinically Discordant for Multiple Sclerosis.

Epigenome data release: a participant-centered approach to privacy protection.

AKSmooth: enhancing low-coverage bisulfite sequencing data via kernel-based smoothing.

Comprehensive analysis of DNA methylation data with RnBeads.

BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives.

Bi-PROF: bisulfite profiling of target regions using 454 GS FLX Titanium technology.

Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles.

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing.

Assisted reproductive technologies do not enhance the variability of DNA methylation imprints in human.