A5017672883- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Cancer-related molecular mechanisms research
- Bacterial Genetics and Biotechnology
- Protein Structure and Dynamics
- Machine Learning in Bioinformatics
- Bacteriophages and microbial interactions
- Genomics and Chromatin Dynamics
- Advanced biosensing and bioanalysis techniques
- Genetics, Bioinformatics, and Biomedical Research
- Semantic Web and Ontologies
- Scientific Computing and Data Management
- Bioinformatics and Genomic Networks
- Enzyme Structure and Function
- Natural Language Processing Techniques
- MicroRNA in disease regulation
- Logic, programming, and type systems
- Photosynthetic Processes and Mechanisms
- Molecular Biology Techniques and Applications
- RNA regulation and disease
- Biomedical Text Mining and Ontologies
- RNA Interference and Gene Delivery
University of Freiburg
2016-2025
Kohler (New Zealand)
2014-2022
University of Copenhagen
2008-2021
Max Planck Institute of Immunobiology and Epigenetics
2019
Max Planck Institute for Molecular Genetics
2019
Institute of Bioinformatics
2012-2018
Helmholtz Centre for Environmental Research
2017
Martin Luther University Halle-Wittenberg
2017
German Centre for Integrative Biodiversity Research
2017
Life & Brain (Germany)
2015
The IntaRNA algorithm enables fast and accurate prediction of RNA-RNA hybrids by incorporating seed constraints interaction site accessibility. Here, we introduce IntaRNAv2, which enhanced parameterization as well fully customizable control over the modes output formats. Based on up to date benchmark data, predictive quality is shown further improvements due more restrictive are highlighted. extended web interface provides visualizations new minimal energy profiles for interactions. These...
During the last few years, several new small regulatory RNAs (sRNAs) have been discovered in bacteria. Most of them act as post-transcriptional regulators by base pairing to a target mRNA, causing translational repression or activation, mRNA degradation. Numerous sRNAs already identified, but number experimentally verified targets is considerably lower. Consequently, computational prediction great demand. Many existing programs neglect accessibility sites and existence seed, while other...
The RFAM database defines families of ncRNAs by means sequence similarities that are sufficient to establish homology. In some cases, such as microRNAs and box H/ACA snoRNAs, functional commonalities define classes RNAs characterized structural similarities, typically consist multiple RNA families. Recent advances in high-throughput transcriptomics comparative genomics have produced very large sets putative noncoding regulatory signals. For many them, evidence for stabilizing selection...
Abstract Motivation Generating publication ready plots to display multiple genomic tracks can pose a serious challenge. Making desirable and accurate figures requires considerable effort. This is usually done by hand or using vector graphic software. Results pyGenomeTracks (PGT) modular plotting tool that easily combines tracks. It enables reproducible standardized generation of highly customizable images. Availability implementation PGT available through graphical interface on...
Current genomic screens for noncoding RNAs (ncRNAs) predict a large number of regions containing potential structural ncRNAs. The analysis these data requires highly accurate prediction ncRNA boundaries and discrimination promising candidate ncRNAs from weak predictions. Existing methods struggle with goals because they rely on sequence-based multiple sequence alignments, which regularly misalign RNA structure therefore do not support identification similarities. To overcome this limitation,...
The RFAM database defines families of ncRNAs by means sequence similarities that are sufficient to establish homology.In some cases, such as microRNAs and box H/ACA snoRNAs, functional commonalities define classes RNAs characterized structural similarities, typically consist multiple RNA families.Recent advances in high-throughput transcriptomics comparative genomics have produced very large sets putative noncoding regulatory signals.For many them, evidence for stabilizing selection acting...
CopraRNA (Comparative prediction algorithm for small RNA targets) is the most recent asset to Freiburg Tools webserver. It incorporates and extends functionality of existing tool IntaRNA (Interacting RNAs) in order predict targets, interaction domains consequently regulatory networks bacterial molecules. The results are accompanied by extensive postprocessing methods such as functional enrichment analysis visualization interacting regions. Here, we introduce webservers give detailed...
Abstract The heart is a highly specialized organ with essential function for the organism throughout life. significance of DNA methylation in shaping phenotype remains only partially known. Here we generate and analyse methylomes from purified cardiomyocytes neonatal, adult healthy failing hearts. We identify large genomic regions that are differentially methylated during cardiomyocyte development maturation. Demethylation gene bodies correlates strongly increased expression. Silencing...
The molecular roles of many RNA-binding proteins in bacterial post-transcriptional gene regulation are not well understood. Approaches combining vivo UV crosslinking with RNA deep sequencing (CLIP-seq) have begun to revolutionize the transcriptome-wide mapping eukaryotic protein target sites. We applied CLIP-seq chart landscape two major regulators, Hfq and CsrA, model pathogen Salmonella Typhimurium. By detecting binding sites at single-nucleotide resolution, we identify preferences...
The Galaxy HiCExplorer provides a web service at https://hicexplorer.usegalaxy.eu. It enables the integrative analysis of chromosome conformation by providing tools and computational resources to pre-process, analyse visualize Hi-C, Capture Hi-C (cHi-C) single-cell (scHi-C) data. Since last publication, has been expanded considerably with new facilitate cHi-C provide an in-depth Moreover, it supports scHi-C data offering broad range tools. With help standard graphical user interface Galaxy,...
Abstract We present GraphProt, a computational framework for learning sequence- and structure-binding preferences of RNA-binding proteins (RBPs) from high-throughput experimental data. benchmark demonstrating that the modeled binding conform to literature, showcase biological relevance two applications GraphProt models. First, estimated affinities correlate with measurements. Second, predicted Ago2 targets display higher levels expression upon knockdown, whereas control do not. Computational...
Significance This study presents a unique approach (CopraRNA, for Comparative Prediction Algorithm sRNA Targets) towards reliably predicting the targets of bacterial small regulatory RNAs (sRNAs). These molecules are important regulators gene expression. Their detailed analysis thus far has been hampered by lack reliable algorithms to predict their mRNA targets. CopraRNA integrates phylogenetic information at genomic scale, reconstructs networks upon functional enrichment and network...
Galaxy HiCExplorer is a web server that facilitates the study of 3D conformation chromatin by allowing Hi-C data processing, analysis and visualization. With server, users with little bioinformatic background can perform every step in one workflow: mapping raw sequence data, creation contact matrices, quality assessment, correction matrices identification topological associated domains (TADs) A/B compartments. Users create publication ready plots matrix, compartments, TADs on selected...
Epigenetic mechanisms and transcription factor networks essential for differentiation of cardiac myocytes have been uncovered. However, reshaping the epigenome these terminally differentiated cells during fetal development, postnatal maturation, in disease remains unknown. Here, we investigate dynamics myocyte development chronic heart failure. We find that prenatal maturation are characterized by a cooperation active CpG methylation histone marks at cis-regulatory genic regions to shape...
Abstract Molecular classification of cancers into subtypes has resulted in an advance our understanding tumour biology and treatment response across multiple types. However, to date, cancer profiling largely focused on protein-coding genes, which comprise <1% the genome. Here we leverage a compendium 58,648 long noncoding RNAs (lncRNAs) subtype 947 breast samples. We show that lncRNA-based categorizes tumours by their known molecular cancer. identify cohort cancer-associated...
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...
Synonymous mutations have been viewed as silent mutations, since they only affect the DNA and mRNA, but not amino acid sequence of resulting protein. Nonetheless, recent studies suggest their significant impact on splicing, RNA stability, folding, translation or co-translational protein folding. Hence, we compile 659194 synonymous found in human cancer characterize properties. We provide user-friendly, comprehensive resource for cancer, SynMICdb ( http://SynMICdb.dkfz.de ), which also...
The Freiburg RNA tools web server integrates three for the advanced analysis of in a common web-based user interface. IntaRNA, ExpaRNA and LocARNA support prediction RNA–RNA interaction, exact matching alignment RNA, respectively. software packages stand-alone are freely accessible at http://rna.informatik.uni-freiburg.de.
The secondary structure of a pre-mRNA influences number processing steps including alternative splicing. Since most splicing regulatory proteins bind to single-stranded RNA, the sequestration RNA into double strands could prevent their binding. Here, we analyzed context experimentally determined enhancer and silencer motifs in natural context. We found that these are significantly more than controls. These findings were validated by transfection experiments, where effect or on exon skipping...