A5052739607- vaccines and immunoinformatics approaches
- Immunotherapy and Immune Responses
- Monoclonal and Polyclonal Antibodies Research
- Scientific Computing and Data Management
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Virology and Viral Diseases
- Cell Image Analysis Techniques
- Single-cell and spatial transcriptomics
- SARS-CoV-2 and COVID-19 Research
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Cancer Immunotherapy and Biomarkers
- Cancer Genomics and Diagnostics
- Glycosylation and Glycoproteins Research
- CAR-T cell therapy research
- Artificial Intelligence in Healthcare and Education
- Soft tissue tumor case studies
- Retinal and Optic Conditions
- Iron Metabolism and Disorders
- Otitis Media and Relapsing Polychondritis
- Head and Neck Surgical Oncology
- Nanoplatforms for cancer theranostics
- IgG4-Related and Inflammatory Diseases
- T-cell and B-cell Immunology
- Craniofacial Disorders and Treatments
Boehringer Ingelheim (Germany)
2024
Kliniken Essen-Mitte
2005-2022
University of Duisburg-Essen
2022
Quantitative Biology Center
2019-2022
University of Tübingen
2014-2019
University Children's Hospital Tübingen
2019
Bernstein Center for Computational Neuroscience Tübingen
2017
Leipzig University
2003-2005
Abstract Motivation: The human leukocyte antigen (HLA) gene cluster plays a crucial role in adaptive immunity and is thus relevant many biomedical applications. While next-generation sequencing data are often available for patient, deducing the HLA genotype difficult because of substantial sequence similarity within exceptionally high variability loci. Established approaches, therefore, rely on specific enrichment techniques, coming at an additional cost extra turnaround time. Result: We...
Although mutated HLA ligands are considered ideal cancer-specific immunotherapy targets, evidence for their presentation is lacking in hepatocellular carcinomas (HCCs). Employing a unique multi-omics approach comprising neoepitope identification pipeline, we assessed exome-derived mutations naturally presented as class I HCCs.
We report a novel experimental immunotherapeutic approach in patient with metastatic intrahepatic cholangiocarcinoma. In the 5year course of disease, initial tumor mass, two local recurrences and lung metastasis were surgically removed. Lacking alternative treatment options, aiming at induction anti-tumor T cells responses, we initiated personalized multi-peptide vaccination, based on in-depth analysis antigens (immunopeptidome) sequencing.Tumors characterized by immunohistochemistry,...
Personalized multipeptide vaccines are currently being discussed intensively for tumor immunotherapy. In order to identify epitopes—short, immunogenic peptides—suitable eliciting a tumor-specific immune response, human leukocyte antigen-presented peptides isolated by immunoaffinity purification from cancer tissue samples and analyzed liquid chromatography-coupled tandem mass spectrometry (LC–MS/MS). Here, we present MHCquant, fully automated, portable computational pipeline able process...
Abstract Summary: Immunoinformatics approaches are widely used in a variety of applications from basic immunological to applied biomedical research. Complex data integration is inevitable research and usually requires comprehensive pipelines including multiple tools sources. Non-standard input output formats immunoinformatics make the development such difficult. Here we present FRED 2, an open-source framework offering easy unified access methods for epitope prediction other applications. 2...
Modern biomedical research aims at drawing biological conclusions from large, highly complex datasets. It has become common practice to make extensive use of high-throughput technologies that produce big amounts heterogeneous data. In addition the ever-improving accuracy, methods are getting faster and cheaper, resulting in a steadily increasing need for scalable data management easily accessible means analysis. We present qPortal, platform providing users with an intuitive way manage...
Abstract Motivation The NanoString™ nCounter® technology platform is a widely used targeted quantification for the analysis of gene expression up to ∼800 genes. Whereas software tools by manufacturer can perform in an interactive and GUI driven approach, there no portable user-friendly workflow available that be reproducible multiple samples simultaneously scalable fashion on different computing infrastructures. Results Here, we present nf-core/nanostring open-source pipeline comprehensive...
Abstract Motivation Breast cancer is the second leading cause of death among women. Tumors, even same histopathological subtype, exhibit a high genotypic diversity that impedes therapy stratification and hence must be accounted for in treatment decision-making process. Results Here, we present ClinOmicsTrailbc, comprehensive visual analytics tool breast decision support provides holistic assessment standard-of-care targeted drugs, candidates drug repositioning immunotherapeutic approaches....
Immunoinformatics has become a crucial part in biomedical research. Yet many immunoinformatics tools have command line interfaces only and can be difficult to install. Web-based tools, on the other hand, are integrate with which is typically required for complex analysis prediction pipelines advanced applications.We present ImmunoNodes, an toolbox that fully integrated into visual workflow environment KNIME. By dragging dropping connecting them indicate data flow through pipeline, it...
Non-specific orbital inflammation (NSOI) and IgG4-related disease (IgG4-ROD) are currently treated with non-specific immunosuppressive agents based on non-randomized, uncontrolled studies. Therefore, relapses prolongated courses common remain challenging. For a more specific therapy, better understanding of the underlying pathophysiology is crucial. we aimed to analyze signaling pathways expand knowledge possibly identify targets in future, as occurred recently Graves' orbitopathy IGF-1...
The need for data privacy and security -- enforced through increasingly strict protection regulations renders the use of healthcare machine learning difficult. In particular, transfer between different hospitals is often not permissible thus cross-site pooling an option. Personal Health Train (PHT) paradigm proposed within GO-FAIR initiative implements 'algorithm to data' that ensures distributed can be accessed analysis without transferring any sensitive data. We present PHT-meDIC, a...
Modern biomedical research aims at drawing biological conclusions from large, highly complex datasets. Nowadays, it is common practice to make extensive use of high-throughput technologies that produce big amounts heterogeneous data. In addition the ever-improving accuracy, methods are getting faster and cheaper, resulting in a steadily increasing need for large storage, data management, easily accessible means analysis. We present qPortal, web-based science gateway providing users with an...
Modern biomedical research aims at drawing biological conclusions from large, highly complex datasets. Nowadays, it is common practice to make extensive use of high-throughput technologies that produce big amounts heterogeneous data. In addition the ever-improving accuracy, methods are getting faster and cheaper, resulting in a steadily increasing need for large storage, data management, easily accessible means analysis. We present qPortal, web-based science gateway providing users with an...
Abstract Current research has entered into an unprecedented territory of analytical possibilities represented by so called “omics” technologies, allowing the examination patients and their individual diseases on a previously unimaginable level. This development represents serious challenge considering established trial designs conduct, particularly in early phase clinical trials, since novel theranostics (biomarker based allocation therapies) principle would allow for patient selection far...
Abstract Background: We established a platform for the design of patient-individual peptide vaccination cocktails by combination whole exome sequencing tumor and normal tissue with in silico epitope prediction algorithms individual patient HLA types. Accumulation somatic mutations is one characteristic feature malignanT-cells. These single-nucleotide variants (SNVs) can lead to altered amino acid sequences translated proteins, which turn be presented malignant cells as antigenic peptides on...
Abstract We established a platform for the design of patient-individual peptide vaccination cocktails by combination whole exome sequencing tumor and normal tissue with in silico epitope prediction algorithms individual patient HLA types. Acute lymphoblastic leukemia (ALL) is most common pediatric malignancy. Standard chemotherapy successful treatment 80% patients, only about 20% develop relapse, however these patients have dismal prognosis. Prevention relapse after first-line or stem cell...