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  • Courses
  • Blog
    • A new review on spatial cell-cell communication analysis
    • MOPRED Symposium 2026
  • Open Theses
    • Incorporating deep learning TF models into SNEEP
    • Modifying SNEEP to account for averaged differential TF Binding
    • Placing regulatory variants into tissue context
    • Enabling allele-specific analysis of epigenome data
    • Expanding a Nextflow pipeline for histone-association studies
    • Expanding a Nextflow pipeline for single-cell data
    • Statistical analysis of liver disease transcriptomes
  • Publications
    • A categorization of spatial transcriptomics methods for cell–cell communication analysis
    • AtlasLens: Metadata-centric exploration and analysis of single-cell atlases
    • Comparing machine learning methods predicting transcriptome from epigenome with applications to association studies
    • Improved RNA-DNA interaction calling suggests RNA-based gene regulation of phenotypic transitions
    • Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data
    • Prediction and evaluation of Split-ORFs using Ribo-seq data
    • Probing transcription factor subsets in gene regulatory networks
    • Quantifying Components in a Model Vaccine with Machine-Learning-Augmented Raman Spectroscopy
    • RANKOR: Direct Drug Prioritization from Bulk and Single-Cell Transcriptomic Signatures
    • Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci
    • Enhancing KLF15 activity in cardiomyocytes: a novel approach to prevent pathological reprogramming and fibrosis via nuclease-deficient dCas9VPR
    • Comparative cross-methodological analysis of the IDH-wildtype glioblastoma tumor microenvironment
    • Hierarchical Representation Learning for Drug Mechanism-of-Action Prediction from Gene Expression Data
    • miRXplain: explainable isomiR-aware microRNA target prediction using CLIP-L experiments and hybrid attention transformers
    • Cystine import and oxidative catabolism fuel vascular growth and repair via nutrient-responsive histone acetylation
    • Epigenetic control of metabolic identity across cell types
    • The transaminase-ω-amidase pathway senses oxidative stress to control glutamine metabolism and α-ketoglutarate levels in endothelial cells
    • TripLexicon: prediction and analysis of gene regulatory RNA-DNA interactions
    • Decoding heart failure subtypes with neural networks via differential explanation analysis
    • Vascular Niches Are the Primary Hotspots in Cardiac Aging
    • Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard
    • Revealing microRNA regulation in single cells
    • STAT3 expression is reduced in cardiac pericytes in HFpEF and its loss reduces cellular adhesion and induces pericyte senescence
    • A cell type-specific expression atlas of small and total RNA in the heart after myocardial infarction
    • GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data
    • Learning Enhancer-Gene associations from Bulk Transcriptomic and Epigenetic Sequencing Data with STITCHIT
    • Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers
    • Prediction of Enhancer-Gene Interactions Using Chromatin-Conformation Capture and Epigenome Data Using STARE
    • Temporal Expression Analysis to Unravel Gene Regulatory Dynamics by microRNAs
    • A statistical approach for identifying single nucleotide variants that affect transcription factor binding
    • BI-3231, an enzymatic inhibitor of HSD17B13, reduces lipotoxic effects induced by palmitic acid in murine and human hepatocytes
    • A systematic analysis of circRNAs in subnuclear compartments
    • An AI-based cell segmentation pipeline for studying immune markers from brightfield microscopy images
    • Improved integration of single-cell transcriptome data demonstrates common and unique signatures of heart failure in mice and humans
    • Multiomics analysis identifies novel facilitators of human dopaminergic neuron differentiation
    • Computational tools for inferring transcription factor activity
    • The challenges of research data management in cardiovascular science: a DGK and DZHK position paper-executive summary
    • Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models
    • Alterations in the hepatocyte epigenetic landscape in steatosis
    • Circular RNA circPLOD2 regulates pericyte function by targeting the transcription factor KLF4
    • CVD-associated SNPs with regulatory potential reveal novel non-coding disease genes
    • Pathogenetic mechanisms and therapeutic approaches of acute-to-chronic liver failure
    • Efficiently quantifying DNA methylation for bulk- and single-cell bisulfite data
    • A combined computational and functional approach identifies IGF2BP2 as a driver of chemoresistance in a wide array of pre-clinical models of colorectal cancer
    • Interaction of inherited genetic variants in the NLRP3 inflammasome/IL-6 pathway with acquired clonal hematopoiesis to modulate mortality risk in patients with HFrEF
    • TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors
    • Dataset of single nucleotide polymorphisms of immune-associated genes in patients with SARS-CoV-2 infection
    • Multimodal analysis methods in predictive biomedicine
    • The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data
    • The endothelial-enriched lncRNA LINC00607 mediates angiogenic function
    • DOT1L regulates chamber-specific transcriptional networks during cardiogenesis and mediates postnatal cell cycle withdrawal
    • A universal model of RNA.DNA:DNA triplex formation accurately predicts genome-wide RNA-DNA interactions
    • HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex
    • Broad domains of histone marks in the highly compact Paramecium macronuclear genome
    • Nuclear receptor activation shapes spatial genome organization essential for gene expression control: lessons learned from the vitamin D receptor
    • Energy efficient convolutional neural networks for arrhythmia detection
    • Comparative analysis of common alignment tools for single-cell RNA sequencing
    • Two Piwis with Ago-like functions silence somatic genes at the chromatin level
    • Dysregulation of cholesterol homeostasis in human lung cancer tissue and tumour-associated macrophages
    • Integrative analysis of epigenetics data identifies gene-specific regulatory elements
    • Computational prediction of CRISPR-impaired non-coding regulatory regions
    • Machine learning based disease prediction from genotype data
    • Fast detection of differential chromatin domains with SCIDDO
    • Fostering accessible online education using Galaxy as an e-learning platform
    • A hierarchical regulatory network analysis of the vitamin D induced transcriptome reveals novel regulators and complete VDR dependency in monocytes
    • Machine learning for deciphering cell heterogeneity and gene regulation
    • SPONGEdb: a pan-cancer resource for competing endogenous RNA interactions
    • CpG content-dependent associations between transcription factors and histone modifications
    • Single cell sequencing reveals endothelial plasticity with transient mesenchymal activation after myocardial infarction
    • Synthesis of Power-Efficient Analog Neural Networks for Signal Processing
    • Deletion of NoxO1 limits atherosclerosis development in female mice
    • Prediction of single-cell gene expression for transcription factor analysis
    • EpiRegio: analysis and retrieval of regulatory elements linked to genes
    • Altered glucocorticoid metabolism represents a feature of macroph-aging
    • The endocannabinoid anandamide has an anti-inflammatory effect on CCL2 expression in vascular smooth muscle cells
    • Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data
    • Improved linking of motifs to their TFs using domain information
    • SRSF7 maintains its homeostasis through the expression of Split-ORFs and nuclear body assembly
    • Feeding exogenous dsRNA interferes with endogenous sRNA accumulation in Paramecium
    • Integrative prediction of gene expression with chromatin accessibility and conformation data
    • Yeast Viral Killer Toxin K1 Induces Specific Host Cell Adaptions via Intrinsic Selection Pressure
    • AERON: Transcript quantification and gene-fusion detection using long reads
    • The mRNA-binding Protein TTP/ZFP36 in Hepatocarcinogenesis and Hepatocellular Carcinoma
    • Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data
    • Exogenous RNAi mechanisms contribute to transcriptome adaptation by phased siRNA clusters in Paramecium
    • Phenotypic Plasticity of Fibroblasts during Mammary Carcinoma Development
    • The lncRNA Locus Handsdown Regulates Cardiac Gene Programs and Is Essential for Early Mouse Development
    • Large-scale inference of competing endogenous RNA networks with sparse partial correlation
    • Transcriptomics of a KDELR1 knockout cell line reveals modulated cell adhesion properties
    • TEPIC 2-an extended framework for transcription factor binding prediction and integrative epigenomic analysis
    • Improving in-silico normalization using read weights
    • Identification of transcription factor binding sites using ATAC-seq
    • On the problem of confounders in modeling gene expression
    • Temporal enhancer profiling of parallel lineages identifies AHR and GLIS1 as regulators of mesenchymal multipotency
    • Automated analysis of small RNA datasets with RAPID
    • Hepatocellular Carcinoma and Nuclear Paraspeckles: Induction in Chemoresistance and Prediction for Poor Survival
    • Transcriptome Kinetics of Saccharomyces cerevisiae in Response to Viral Killer Toxin K1
    • Analysis of Cell Type-Specific Effects of MicroRNA-92a Provides Novel Insights Into Target Regulation and Mechanism of Action
    • Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters
    • In silico read normalization using set multi-cover optimization
    • Transgenic expression of the RNA binding protein IMP2 stabilizes miRNA targets in murine microsteatosis
    • An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets
    • JAMI: fast computation of conditional mutual information for ceRNA network analysis
    • Environmental Temperature Controls Accumulation of Transacting siRNAs Involved in Heterochromatin Formation
    • More than the \"Killer Trait\": Infection with the Bacterial Endosymbiont Caedibacter taeniospiralis Causes Transcriptomic Modulation in Paramecium Host
    • Predicting transcription factor binding using ensemble random forest models
    • The long non-coding RNA H19 suppresses carcinogenesis and chemoresistance in hepatocellular carcinoma
    • RegulatorTrail: a web service for the identification of key transcriptional regulators
    • Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction
    • Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development
    • The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery
    • Two sets of RNAi components are required for heterochromatin formation in trans triggered by truncated transgenes
    • Informed kmer selection for de novo transcriptome assembly
    • De novo ChIP-seq analysis
    • Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia
    • A general concept for consistent documentation of computational analyses
    • Fiona: a parallel and automatic strategy for read error correction
    • Letting the data speak for themselves: a fully Bayesian approach to transcriptome assembly
    • Assessment of transcript reconstruction methods for RNA-seq
    • Reconstructing dynamic microRNA-regulated interaction networks
    • Probabilistic error correction for RNA sequencing
    • Bayesian ontology querying for accurate and noise-tolerant semantic searches
    • DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data
    • Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
    • Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS
    • Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts
    • A tandem sequence motif acts as a distance-dependent enhancer in a set of genes involved in translation by binding the proteins NonO and SFPQ
    • Exact score distribution computation for ontological similarity searches
    • DECOD: fast and accurate discriminative DNA motif finding
    • Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions
    • Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments
    • Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
    • Short ultraconserved promoter regions delineate a class of preferentially expressed alternatively spliced transcripts
    • Clinical diagnostics in human genetics with semantic similarity searches in ontologies
    • A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
    • Mapping translocation breakpoints by next-generation sequencing
    • A short ultraconserved sequence drives transcription from an alternate FBN1 promoter
    • The generalised k-Truncated Suffix Tree for time-and space-efficient searches in multiple DNA or protein sequences
  • Projects
    • Prediction of single cell gene expression
    • Exploring the regulatory impact of non-coding genetic variants
    • Quality control for imaging-based spatial transcriptomics
    • Categorization of Spatial Transcriptomics Methods for Cell-Cell Communication Analysis
    • Enhancer-gene interactions and transcription factor affinities
    • MISPIL and/or PCMultiome
    • Prediction and evaluation of Split open reading frames
    • Prediction of gene expression from epigenome data
    • Signature reversal based drug ranking from expression data
    • A unified single-cell atlas of mouse tissue damage
  • Team
    • Christian Kolland
    • Carolin Becker
    • Christina Wrobel (formerly Kalk)
    • David Rodriguez Morales
    • Dennis Hecker
    • Laura Rumpf
    • Lea Sarial
    • Marcel Weinberg
    • Maxim Evsioukov
    • Nikoletta Katsaouni
    • Nina Baumgarten
    • Paula Kilp
    • Paulina Kunz
    • Prof. Dr. Marcel Schulz
    • Sasha Soustova
    • Shamim Ashrafiyan
    • Yaroslav Kosaretskii
    • Zlatka Fischer
    • Seda Nurhayat Öztürk
    • Florian Neukamm
  • Tools
    • AtlasLens
    • MetaFR
    • RANKOR
    • SNEEP
    • FAME
    • STARE
    • STITCHIT
    • EpiRegio
    • ORNA
    • TEPIC
    • KREATION
    • Fiona
    • SEECER
    • DREM 2.0
    • Oases
    • ALF
    • SplazerS
    • Phenomizer
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