A5019620266- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Single-cell and spatial transcriptomics
- RNA modifications and cancer
- Scientific Computing and Data Management
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Genomics and Chromatin Dynamics
- Machine Learning in Bioinformatics
- Gene expression and cancer classification
- Genetics, Bioinformatics, and Biomedical Research
- Research Data Management Practices
- Molecular Biology Techniques and Applications
- Advanced Electron Microscopy Techniques and Applications
- MicroRNA in disease regulation
- Distributed and Parallel Computing Systems
- Software Engineering Research
- Software System Performance and Reliability
- Gene Regulatory Network Analysis
- Phagocytosis and Immune Regulation
- Cell Image Analysis Techniques
- Software Testing and Debugging Techniques
- Advanced Proteomics Techniques and Applications
- Cancer Mechanisms and Therapy
- Algorithms and Data Compression
University of Freiburg
2014-2025
Munich Leukemia Laboratory (Germany)
2014
Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues use, maintain contribute the project, support from multiple national infrastructure providers that enable freely analysis training services. The Training Network supports free, self-directed, virtual >230 integrated tutorials. Project engagement metrics have continued grow...
The primary problem with the explosion of biomedical datasets is not data, computational resources, and required storage space, but general lack trained skilled researchers to manipulate analyze these data. Eliminating this requires development comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching data analytics in life sciences facilitates training materials. key feature our system it static continuously improved...
Histone acetyl transferases (HATs) play distinct roles in many cellular processes and are frequently misregulated cancers. Here, we study the regulatory potential of MYST1-(MOF)-containing MSL NSL complexes mouse embryonic stem cells (ESCs) neuronal progenitors. We find that both influence transcription by targeting promoters TSS-distal enhancers. In contrast to flies, complex is not exclusively enriched on X chromosome, yet it crucial for mammalian chromosome regulation as specifically...
Cortical development is controlled by transcriptional programs, which are orchestrated transcription factors. Yet, stable inheritance of spatio-temporal activity factors influencing cell fate and localization in different layers only partly understood. Here we find that deletion Dot1l the murine telencephalon leads to cortical layering defects, indicating DOT1L chromatin methylation at H3K79 impact on cycle, influence programs conferring upper layer identity early progenitors. Specifically,...
Abstract Background Bioinformatics is fundamental to biomedical sciences, but its mastery presents a steep learning curve for bench biologists and clinicians. Learning code while analyzing data difficult. The may be flattened by separating these two aspects providing intermediate steps budding bioinformaticians. Single-cell analysis in great demand from scientists, as evidenced the proliferation of training events, materials, collaborative global efforts like Human Cell Atlas. However,...
RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if not taken into account. Thus, it increasingly important but yet standard to combine RNA-centric tools with other types experimental such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, comprehensive set consolidated workflows that enable researcher these two worlds. Based on Galaxy framework workbench guarantees simple access, easy...
Rett syndrome is a complex neurodevelopmental disorder that mainly caused by mutations in MECP2. However, FOXG1 cause less frequent form of atypical syndrome, called syndrome. key transcription factor crucial for forebrain development, where it maintains the balance between progenitor proliferation and neuronal differentiation. Using genome-wide small RNA sequencing quantitative proteomics, we identified affects biogenesis miR200b/a/429 interacts with ATP-dependent helicase, DDX5/p68. Both...
Abstract Summary: Non-coding RNAs (ncRNAs) play a vital role in many cellular processes such as RNA splicing, translation, gene regulation. However the vast majority of ncRNAs still have no functional annotation. One prominent approach for putative function assignment is clustering transcripts according to sequence and secondary structure. information changed by post-transcriptional modifications, structure only proxy true 3D conformation polymer. A different type that does not suffer from...
RNA has become one of the major research topics in molecular biology. As a central player key processes regulating gene expression, is focus many efforts to decipher pathways that govern transition genetic information fully functional cell. more and researchers join this endeavour, there rapidly growing demand for comprehensive collections tools cover diverse layers RNA-related research. However, increasing amounts data, from types experiments, addressing different aspects biological...
Abstract The primary problem with the explosion of biomedical datasets is not data itself, computational resources, and required storage space, but general lack trained skilled researchers to manipulate analyze these data. Eliminating this requires development comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching analytics in life sciences facilitates training materials. key feature our system it static continuously...
Abstract Background With the advances in next-generation sequencing technologies, it is possible to determine RNA-RNA interaction and RNA structure predictions on a genome-wide level. The reads from these experiments usually are chimeric, with each arm generated one of partners. Owing short read lengths, often sequenced arms ambiguously map multiple locations. Thus, inferring origin can be quite complicated. Here we present ChiRA, generic framework for sensitive annotation chimeric reads,...
In quantitative proteomics, peptide mapping is a valuable approach to combine positional information with topographical and domain of proteins. Quantitative proteomic analysis cell surface shedding an exemplary application area this approach. We developed ImproViser ( http://www.improviser.uni-freiburg.de ) for fully automated proteomics data in the protXML data. The tool generates sortable graphically annotated output, which can be easily shared further users. As application, we show its...
Abstract Background RNA–RNA interactions are key to a wide range of cellular functions. The detection potential helps understand the underlying processes. However, identified via in silico or experimental high-throughput methods can lack precision because high false-positive rate. Results We present CheRRI, first tool evaluate biological relevance putative interaction sites. CheRRI filters candidates machine learning–based model trained on interactome data. Its unique setup combines data and...
<title>Abstract</title> Cell-type specific gene expression programs and response to stimuli are modulated by <italic>cis-</italic>regulatory elements (CREs). CREs modulate the activity of spatially interacting promoters. Heart disease is a major cause death worldwide. Here, we aim decode CRE-promoter interactions in atrial ventricular cardiomyocytes link them heart genetic risk factors. Therefore, analyze epigenetic features chromatin human atrial, ventricular, failing (CM). In CM limited...
<title>Abstract</title> Cell-type specific gene expression programs and response to stimuli are modulated by cis-regulatory elements (CREs). CREs modulate the activity of spatially interacting promoters. Heart disease is a major cause death worldwide. Here, we aim decode CRE-promoter interactions in atrial ventricular cardiomyocytes link them heart genetic risk factors. Therefore, analyze epigenetic features chromatin human atrial, ventricular, failing (CM). In CM limited number genes,...
<ns3:p>Single-cell omics (SCO) has revolutionized the way and level of resolution by which life science research is conducted, not only impacting our understanding fundamental cell biology but also providing novel solutions in cutting-edge medical research. The rapid development single-cell technologies been accompanied active data analysis methods, resulting a plethora new tools strategies every year. Such SCO methods poses several challenges standardization, benchmarking, computational...