A5067743298- MicroRNA in disease regulation
- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- vaccines and immunoinformatics approaches
- Immunotherapy and Immune Responses
- RNA and protein synthesis mechanisms
- Microbial Metabolic Engineering and Bioproduction
- RNA modifications and cancer
- Computational Drug Discovery Methods
- Immune cells in cancer
- Gene expression and cancer classification
- Genetics, Bioinformatics, and Biomedical Research
- Monoclonal and Polyclonal Antibodies Research
- Extracellular vesicles in disease
- Melanoma and MAPK Pathways
- Cancer Immunotherapy and Biomarkers
- CAR-T cell therapy research
- Mathematical Biology Tumor Growth
- Immune Cell Function and Interaction
- RNA Interference and Gene Delivery
- Single-cell and spatial transcriptomics
- Cytokine Signaling Pathways and Interactions
- Advanced biosensing and bioanalysis techniques
Universitätsklinikum Erlangen
2016-2025
Friedrich-Alexander-Universität Erlangen-Nürnberg
2016-2025
Comprehensive Cancer Center Erlangen
2020-2024
German Climate Computing Centre
2020-2024
Ludwig-Maximilians-Universität München
2024
LMU Klinikum
2024
University of Rostock
2007-2023
Stanford University
2009-2020
Case Western Reserve University
2020
Progress (Ireland)
2020
We present a new version of Babelomics, complete suite web tools for functional analysis genome-scale experiments, with and improved tools. New functionally relevant terms have been included such as CisRed motifs or bioentities obtained by text-mining procedures. An indexing has considerably speeded up several the modules. FatiScan method studying coordinate behaviour groups related genes is presented, along similar tool, Gene Set Enrichment Analysis. Babelomics now more oriented to test...
The discovery of microRNAs (miRNAs) has added a new player to the regulation gene expression. With increasing number molecular species involved in regulatory networks, it is hard obtain an intuitive understanding network dynamics. Mathematical modelling can help dissecting role miRNAs and we shall here review most recent developments that utilise different mathematical approaches provide quantitative insights into function Key miRNA features have been elucidated via include: (i)...
Cancer is a disease of subverted regulatory pathways. In this paper, we reconstruct the network around E2F, family transcription factors whose deregulation has been associated to cancer progression, chemoresistance, invasiveness, and metastasis. We integrate gene expression profiles cell lines from two E2F1-driven highly aggressive bladder breast tumors, use analysis methods identify tumor type-specific core network. By combining logic-based modeling, in vitro experimentation, patient...
Abstract Activation of proinflammatory macrophages is associated with the inflammatory state rheumatoid arthritis. Their polarization and activation are controlled by transcription factors such as NF-κB AP-1 factor member c-Fos. Surprisingly, little known about role c-Jun in macrophage activation. In this study, we show that mRNA protein levels increased following pro- or anti-inflammatory stimulations. Gene Ontology Kyoto Encyclopedia Genes Genomes pathway enrichment cluster analyses...
Epigenetic deregulation remarkably triggers mechanisms associated with tumor aggressiveness like epithelial-mesenchymal transition (EMT). Since EMT is a highly complex, but also reversible event, epigenetic processes such as DNA methylation or chromatin alterations must be involved in its regulation. It was recently described that loss of the cell cycle regulator p21 gain characteristics and an upregulation master transcription factor ZEB1. In this study, silico analysis performed...
The Gene Expression Profile Analysis Suite (GEPAS) has been running for more than four years. During this time it evolved to keep pace with the new interests and trends in still changing world of microarray data analysis. GEPAS designed provide an intuitive although powerful web-based interface that offers diverse analysis options from early step preprocessing (normalization Affymetrix two-colour experiments other options), final functional annotation experiment (using Ontology, pathways,...
MicroRNA (miRNA) target hubs are genes that can be simultaneously targeted by a comparatively large number of miRNAs, class non-coding RNAs mediate post-transcriptional gene repression. Although the details hub regulation remain poorly understood, recent experiments suggest pairs miRNAs cooperate if their binding sites reside in close proximity. To test this and other hypotheses, we established novel approach to investigate mechanisms collective miRNA The presented here combines prediction...
// Animesh Bhattacharya 1 , Ulf Schmitz 2 Yvonne Raatz Madeleine Schönherr Tina Kottek Marianne Schauer Sandra Franz Anja Saalbach Anderegg Olaf Wolkenhauer Dirk Schadendorf 3 Jan C. Simon Thomas Magin 4 Julio Vera 5 and Manfred Kunz Department of Dermatology, Venereology Allergology, University Leipzig, Germany Systems Biology Bioinformatics, Rostock, Hospital Essen, Institute Translational Centre for Regenerative Medicine (TRM), Laboratory Tumor Immunology, Faculty Medicine,...
MicroRNAs (miRNAs) are an integral part of gene regulation at the post-transcriptional level. Recently, it has been shown that pairs miRNAs can repress translation a target mRNA in cooperative manner, which leads to enhanced effectiveness and specificity repression. However, remains unclear miRNA synergize genes regulation. In this paper, we present computational workflow for prediction analysis cooperating their mutual genes, refer as RNA triplexes. The integrates methods prediction;...
High rates of lethal outcome in tumour metastasis are associated with the acquisition invasiveness and chemoresistance.Several clinical studies indicate that E2F1 overexpression across high-grade tumours culminates unfavourable prognosis chemoresistance patients.Thus, fine-tuning expression could be a promising approach for treating patients showing chemoresistance.Methods: We integrated bioinformatics, structural kinetic modelling, experiments to study cooperative regulation by microRNA...
The polarization of macrophages is regulated by transcription factors such as nuclear factor kappa B (NF-κB) and activator protein 1 (AP-1). In this manuscript, we delineated the role Fos-related antigen (Fra-1) during macrophage activation development arthritis. Network level interaction analysis microarray data derived from Fra-1- or Fra-2-deficient revealed a central Fra-1, but not Fra-2 in orchestrating expression genes related to wound response, toll-like receptor interleukin signaling....
The bone marrow niche has a pivotal role in progression, survival, and drug resistance of multiple myeloma cells. Therefore, it is important to develop means for targeting the microenvironment. Myeloma-associated macrophages (MAM) are M2 like. They provide nurturing signals cells promote immune escape. Reprogramming M2-like toward tumoricidal M1 phenotype represents an intriguing therapeutic strategy. This especially interesting view successful use mAbs against cells, as these therapies hold...
During development of myelin-forming oligodendrocytes in the central nervous system two closely related transcription factors Sox9 and Sox10 play essential roles that are partly shared unique. Whereas primarily functions during oligodendroglial specification, is uniquely required to induce terminal differentiation myelination. this process, protein levels rise substantially. As coincides with a reciprocal decrease Sox9, we postulated influences amounts differentiating oligodendrocytes. Here...