A5087884887- Gene expression and cancer classification
- Single-cell and spatial transcriptomics
- RNA modifications and cancer
- Immune Cell Function and Interaction
- RNA Research and Splicing
- Bioinformatics and Genomic Networks
- Molecular Biology Techniques and Applications
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- Immune cells in cancer
- Immunotherapy and Immune Responses
- T-cell and B-cell Immunology
- Effects of Radiation Exposure
- Cell Image Analysis Techniques
- Genomics and Chromatin Dynamics
- Cancer Genomics and Diagnostics
- Melanoma and MAPK Pathways
- Genomics and Phylogenetic Studies
- Gene Regulatory Network Analysis
- Neuroinflammation and Neurodegeneration Mechanisms
- Childhood Cancer Survivors' Quality of Life
- Extracellular vesicles in disease
- Advanced Numerical Analysis Techniques
- Cytokine Signaling Pathways and Interactions
- Acute Lymphoblastic Leukemia research
Johannes Gutenberg University Mainz
2015-2025
University Medical Center of the Johannes Gutenberg University Mainz
2017-2025
Institute for Medical Informatics and Biostatistics
2020-2022
University Medical Center Freiburg
2022
University of Freiburg
2022
Hess (United States)
2022
University Medical Center
2022
Leibniz Institute for Prevention Research and Epidemiology - BIPS
2022
Institut für Medizinische Biometrie, Informatik und Epidemiologie
2021
Istituto di Matematica Applicata e Tecnologie Informatiche
2019
Principal component analysis (PCA) is frequently used in genomics applications for quality assessment and exploratory high-dimensional data, such as RNA sequencing (RNA-seq) gene expression assays. Despite the availability of many software packages developed this purpose, an interactive comprehensive interface performing these operations lacking. We pcaExplorer package to enhance commonly performed steps with user-friendly application, which provides state saving well automated creation...
Characterization of the immune responses to SARS-CoV-2 reveals a CD8 + T cell subset that likely establishes memory virus.
Palatine tonsils are secondary lymphoid organs (SLOs) representing the first line of immunological defense against inhaled or ingested pathogens. We generated an atlas human tonsil composed >556,000 cells profiled across five different data modalities, including single-cell transcriptome, epigenome, proteome, and immune repertoire sequencing, as well spatial transcriptomics. This census identified 121 cell types states, defined developmental trajectories, enabled understanding functional...
Immune evasion in the tumor microenvironment (TME) is a crucial barrier for effective cancer therapy, and plasticity of innate immune cells may contribute to failures targeted immunotherapies. Here, we show that rivaroxaban, direct inhibitor activated coagulation factor X (FX), promotes antitumor immunity by enhancing infiltration dendritic cytotoxic T at site. Profiling FX expression TME identifies monocytes macrophages as sources extravascular FX. By generating mice with lacking ability...
Data exploration is critical to the comprehension of large biological data sets generated by high-throughput assays such as sequencing. However, most existing tools for interactive visualisation are limited specific or analyses. Here, we present iSEE (Interactive SummarizedExperiment Explorer) software package, which provides a general visual interface exploring in object. directly compatible with many R/Bioconductor packages analysing data, and useful features simultaneous examination...
Diversification at the transcriptome 3'end is an important and evolutionarily conserved layer of gene regulation associated with differentiation dedifferentiation processes. Here, we identify extensive 3'end-alterations in neuroblastoma, a tumour entity paucity recurrent somatic mutations unusually high frequency spontaneous regression. Utilising RNAi-screening reveal landscape drivers 3'end-diversification, discovering PCF11 as critical regulator, directing alternative polyadenylation (APA)...
IL-17-producing CD8+ (Tc17) cells are enriched in active lesions of patients with multiple sclerosis (MS), suggesting a role the pathogenesis autoimmunity. Here we show that amelioration MS by dimethyl fumarate (DMF), mechanistically elusive drug, associates suppression Tc17 cells. DMF treatment results reduced frequency Tc17, contrary to Th17 cells, and decreased ratio regulators RORC-to-TBX21, along shift towards cytotoxic T lymphocyte gene expression signature from patients....
Abstract Polyphosphates are linear polymers and ubiquitous metabolites. Bacterial polyphosphates long chains of hundreds phosphate units. Here, we report that mouse survival peritoneal Escherichia coli sepsis is compromised by long-chain polyphosphates, improves with bacterial polyphosphatekinase deficiency or neutralization using recombinant exopolyphosphatase. Polyphosphate activities chain-length dependent, impair pathogen clearance, antagonize phagocyte recruitment, diminish phagocytosis...
The gut microbiota influences intestinal barrier integrity through mechanisms that are incompletely understood. Here we show the commensal weakens by suppressing epithelial neuropilin-1 (NRP1) and Hedgehog (Hh) signaling. Microbial colonization of germ-free mice dampens signaling Hh pathway Toll-like receptor (TLR)-2, resulting in decreased NRP1 protein levels. Following activation via TLR2/TLR6, NRP1, a positive-feedback regulator signaling, is lysosomally degraded. Conversely, elevated...
The proinflammatory cytokine interleukin 1 (IL-1) is crucially involved in the pathogenesis of multiple sclerosis (MS) and its animal model experimental autoimmune encephalomyelitis (EAE). Herein, we studied role IL-1 signaling blood-brain barrier (BBB) endothelial cells (ECs), astrocytes microglia for EAE development, using mice with conditional deletion receptor IL-1R1. We found that redundant development EAE, whereas IL-1R1 BBB-ECs markedly ameliorated disease severity. upregulated...
Abstract Palatine tonsils are secondary lymphoid organs representing the first line of immunological defense against inhaled or ingested pathogens. Here, we present a comprehensive census cell types forming human tonsil by applying single-cell transcriptome, epigenome, proteome and adaptive immune repertoire sequencing as well spatial transcriptomics, resulting in an atlas >357,000 cells. We provide glossary 121 annotated states, disentangle gene regulatory mechanisms that drive cells...
Significance Fibrosis is a consequence of most chronic liver diseases, but currently no approved antifibrotic treatment available. M2-type macrophages drive fibrosis progression and prevent regression, even when effective causal therapies have been employed. activate cascade fibrogenic effector cells can removal excess scar tissue. To switch these profibrogenic M2 to fibrolytic (regenerative) macrophages, we developed pH-degradable, nanogel-based delivery system which be covalently...
Abstract Recent developments in experimental technologies such as single-cell RNA sequencing have enabled the profiling a high-dimensional number of genome-wide features individual cells, inspiring formation large-scale data generation projects quantifying unprecedented levels biological variation at level. The generated exhibits unique characteristics, including increased sparsity and scale, terms both samples. Due to these specialized statistical methods are required along with fast...
Abstract Promoter-proximal pausing of RNA polymerase II (Pol II) is a widespread transcriptional regulatory step across metazoans. Here we find that the nuclear exon junction complex (pre-EJC) critical and conserved regulator this process. Depletion pre-EJC subunits leads to global decrease in Pol premature entry into elongation. This effect occurs, at least part, via non-canonical recruitment components promoters. Failure recruit promoters results increased binding positive transcription...
RNA sequencing (RNA-seq) is an ever increasingly popular tool for transcriptome profiling. A key point to make the best use of available data provide software tools that are easy but still flexibility and transparency in adopted methods. Despite availability many packages focused on detecting differential expression, a method streamline this type bioinformatics analysis comprehensive, accessible, reproducible way lacking.We developed ideal package, which serves as web application interactive...
ERK3 is a ubiquitously expressed member of the atypical mitogen activated protein kinases (MAPKs) and physiological significance its short half-life remains unclear. By employing gastrointestinal 3D organoids, we detect that levels steadily decrease during epithelial differentiation. not required for growth human gastric epithelium. However, stabilized in tumorigenic cells, but deteriorates over time primary cells response to lipopolysaccharide (LPS). necessary production several cellular...
The interpretation of results from transcriptome profiling experiments via RNA sequencing (RNA-seq) can be a complex task, where the essential information is distributed among different tabular and list formats-normalized expression values, differential analysis, functional enrichment analyses. A number tools databases are widely used for purpose identification relevant patterns, yet often their contextualization within data at hand not straightforward, especially if these analytic...
The liver's regenerative ability depends on injury extent. Minor injuries are repaired by hepatocyte self-duplication, while severe damage triggers cholangiocyte involvement in recovery. This paradigm is well-documented for adult animals but less explored during rapid growth. We design two new partial liver models zebrafish, which were investigated growth spurts: 1) ablation, killing half the hepatocytes; and 2) hepatectomy, removing a lobe. In both injuries, de novo hepatocytes emerged...
Fibrosis and persistent inflammation are interconnected processes that inhibit axon regeneration in the mammalian central nervous system (CNS). In zebrafish, by contrast, fibroblast-derived extracellular matrix deposition tightly regulated to facilitate regeneration. However, regulatory cross-talk between fibroblasts innate immune regenerating CNS remains poorly understood. Here, we show zebrafish possess a dual role inducing resolving inflammation, which both essential for We identify...
Background: Macrophages and tubular epithelial cell interactions are integral in kidney ischemia-incited interstitial inflammation leading to acute injury. Ischemia/reperfusion injury riggers cells express IL-34, a macrophage growth factor, that promotes subsequent chronic disease. IL-34 engages the cognate receptor, c-FMS, expressed by macrophages, recently discovered Protein-Tyrosine Phosphatase ζ (Ptprz). Ptprz, binds multiple ligands other than progressively increase their expression...
<title>Abstract</title> The emergence of post-COVID sequelae (PCS) represents a global challenge. However, understanding biological mechanisms and the definition quantifiable risk factors remains limited. This study harnessed power predictive machine learning models to explore potential proteomics in predicting individual symptoms their collective manifestation as PCS. analysis utilized panel approximately 2900 proteins measured 495 COVID-19 patients. identified 235 unique associated with 21...
Abstract Summary The Human BioMolecular Atlas Program (HuBMAP) constructs the worldwide available platform to research human body at cellular level. HuBMAP Data Portal encompasses a wide range of data resources measured on emerging experimental technologies spatial resolution. To broaden access Portal, we introduce an R client called HuBMAPR Bioconductor. This provides efficient and programmatic interface that enables researchers discover retrieve more easily quickly. Availability is...