A5085594740- MicroRNA in disease regulation
- Bioinformatics and Genomic Networks
- Monoclonal and Polyclonal Antibodies Research
- Computational Drug Discovery Methods
- Protein Structure and Dynamics
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Advanced Proteomics Techniques and Applications
- Gene Regulatory Network Analysis
- Genomics and Phylogenetic Studies
- Glycosylation and Glycoproteins Research
- Algorithms and Data Compression
- Computational Geometry and Mesh Generation
- Gene expression and cancer classification
- Genetics, Bioinformatics, and Biomedical Research
- RNA Interference and Gene Delivery
- Microbial Metabolic Engineering and Bioproduction
- Machine Learning in Bioinformatics
- Renal and related cancers
- Genomics and Chromatin Dynamics
- Mass Spectrometry Techniques and Applications
- Advanced Biosensing Techniques and Applications
- Data Management and Algorithms
- Immunotherapy and Immune Responses
Saarland University
2016-2025
Max Planck Institute for Informatics
1992-2019
Institute of Bioinformatics
2019
Johannes Gutenberg University Mainz
2013-2014
University of Tübingen
2009-2014
Friedrich Schiller University Jena
2011
Centrum Wiskunde & Informatica
2011
Max Planck Society
1993-2006
While the number of human miRNA candidates continuously increases, only a few them are completely characterized and experimentally validated. Toward determining total true miRNAs, we employed combined in silico high- experimental low-throughput validation strategy. We collected 28 866 small RNA sequencing data sets containing 363.7 billion reads excluded falsely annotated low quality data. Our high-throughput analysis identified 65% 24 127 mature as likely false-positives. Using northern...
Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the central nervous system, which heterogenous with respect to clinical manifestations and response therapy. Identification biomarkers appears desirable for an improved diagnosis MS as well monitoring activity treatment response. MicroRNAs (miRNAs) are short non-coding RNAs, have been shown potential serve different human diseases, most notably cancer. Here, we analyzed expression profiles 866 miRNAs. In detail,...
We present a comprehensive and efficient gene set analysis tool, called ‘GeneTrail’ that offers rich functionality is easy to use. Our web-based application facilitates the statistical evaluation of high-throughput genomic or proteomic data sets with respect enrichment functional categories. GeneTrail covers wide variety biological categories pathways, among others KEGG, TRANSPATH, TRANSFAC, GO. web server provides two common approaches, ‘Over-Representation Analysis’ (ORA) comparing...
Deregulation of cell signaling pathways plays a crucial role in the development tumors. The identification such requires effective analysis tools that facilitate interpretation expression differences. Here, we present novel and highly efficient method for identifying deregulated subnetworks regulatory network. Given score each node measures degree deregulation corresponding gene or protein, algorithm computes heaviest connected subnetwork specified size reachable from designated root node....
Abstract Since the initial release of miRPathDB, tremendous progress has been made in field microRNA (miRNA) research. New miRNA reference databases have emerged, a vast amount new candidates discovered and number experimentally validated target genes increased considerably. Hence, demand for major upgrade including extended analysis functionality intuitive visualizations query results emerged. Here, we present novel 2.0 Pathway Dictionary Database (miRPathDB) that is freely accessible at...
Which genes, gene sets or pathways are regulated by certain miRNAs? miRNAs regulate a particular target pathway in physiological context? Answering such common research questions can be time consuming and labor intensive. Especially for researchers without computational experience, the integration of different data sources, selection right parameters concise visualization demanding. A comprehensive analysis should central to present adequate answers complex biological questions. With...
We present a Lamarckian genetic algorithm (LGA) variant for flexible ligand-receptor docking which allows to handle large number of degrees freedom. Our hybrid method combines multi-deme LGA with recently published gradient-based local optimization molecular complexes. compared the performance our new two non search heuristics on Astex diverse set docking. results show that novel approach is clearly superior other LGAs employing stochastic method. The features shorter run time and gives...
Abstract Background MicroRNA (miRNA) signatures are not only found in cancer tissue but also blood of patients. Specifically, miRNA detection offers the prospect a non-invasive analysis tool. Methods Using microarray based approach we screened almost 900 human miRNAs to detect that deregulated their expression cells melanoma We analyzed 55 samples, including 20 samples healthy individuals, 24 patients as test set, and 11 independent validation set. Results A hypothesis approch detected 51...
Deregulated miRNAs are found in cancer cells and recently blood of patients. Due to their inherent stability may offer themselves for based tumor diagnosis. Here we addressed the question whether there is a sufficient number deregulated patients be able distinguish between controls. We synthesized 866 human miRNA star sequences as annotated Sanger miRBase onto microarray designed by febit biomed gmbh. Using fully automated Geniom Real Time Analyzer platform, analyzed expression 17 cell...
Gene set analysis has revolutionized the interpretation of high-throughput transcriptomic data. Nowadays, with comprehensive studies that measure multiple -omics from same sample, powerful tools for integrative multi-omics datasets are required.Here, we present GeneTrail2, a web service allowing integrated transcriptomic, miRNomic, genomic and proteomic datasets. It offers statistical tests, large number predefined reference sets, as well collection biological categories enables direct...
// Tim Kehl 1, * , Christina Backes 2, Fabian Kern 2 Tobias Fehlmann Nicole Ludwig 3 Eckart Meese Hans-Peter Lenhof 1 and Andreas Keller Center for Bioinformatics, Saarland University, Informatics Campus, Saarbrücken, Germany Chair Clinical Department of Human Genetics, Homburg, These authors have contributed equally to this work Correspondence to: Keller, email: andreas.keller@ccb.uni-saarland.de Keywords: non-coding RNA; systems biology; target gene; microRNA Received: July 27,...
In the last decade, miRNAs and their regulatory mechanisms have been intensively studied many tools for analysis of targets developed. We previously presented a dictionary on single putative target pathways. Since then, number has tripled knowledge grown substantially. This, along with changes in pathway resources such as KEGG, leads to an improved understanding miRNAs, genes related Here, we introduce miRNA Pathway Dictionary Database (miRPathDB), freely accessible at...
Abstract In many research disciplines, hypothesis tests are applied to evaluate whether findings statistically significant or could be explained by chance. The Wilcoxon–Mann–Whitney (WMW) test is among the most popular in medicine and life science analyze if two groups of samples equally distributed. This nonparametric statistical homogeneity commonly molecular diagnosis. Generally, solution WMW takes a high combinatorial effort for large sample cohorts containing number ties. Hence, P value...
Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance has to be detected and removed. We show here this severe restriction the is not necessary. Building upon recent advances in mathematical phylogenetics we demonstrate gene duplications convey meaningful phylogenetic information allow inference plausible trees, provided orthologs paralogs can distinguished with degree...
<h3>Importance</h3> The overall low survival rate of patients with lung cancer calls for improved detection tools to enable better treatment options and patient outcomes. Multivariable molecular signatures, such as blood-borne microRNA (miRNA) may have high rates sensitivity specificity but require additional studies large cohorts standardized measurements confirm the generalizability miRNA signatures. <h3>Objective</h3> To investigate use miRNAs potential circulating markers detecting in an...
The continuous increase of available biological data as consequence modern high-throughput technologies poses new challenges for analysis techniques and database applications. Especially miRNAs, one class small non-coding RNAs, many algorithms have been developed to predict candidates from next-generation sequencing data. While the amount publications describing novel miRNA keeps steadily increasing, current gold standard miRNAs - miRBase has not updated since June 2014. As a result, in last...
We present GeneTrail 3, a major extension of our web service that offers rich functionality for the identification, analysis, and visualization deregulated biological processes. Our provides comprehensive collection processes signaling pathways 12 model organisms can be analyzed with powerful framework enrichment network analysis transcriptomic, miRNomic, proteomic, genomic data sets. Moreover, novel workflows epigenetic marks, time series experiments, single cell data. demonstrate...
Abstract Blood-borne small non-coding (sncRNAs) are among the prominent candidates for blood-based diagnostic tests. Often, high-throughput approaches applied to discover biomarker signatures. These have be validated in larger cohorts and evaluated by adequate statistical learning approaches. Previously, we published sequencing based microRNA (miRNA) signatures Alzheimer’s disease (AD) patients United States (US) Germany. Here, determined abundance levels of 21 known circulating miRNAs 465...
Article Free Access Share on q-gram based database searching using a suffix array (QUASAR) Authors: Stefan Burkhardt MPI für Informatik, Im Stadtwald, 66123 Saarbrücken, Germany GermanyView Profile , Andreas Crauser Paolo Ferragina Dipartimento di Informatica, Università Pisa, Corso Italia 56125 Italy ItalyView Hans-Peter Lenhof Eric Rivals Deutsches Krebsforschungszentrum, Abt. Theoretische Bioinformatik INF 280, D-69120 Heidelberg, Martin Vingron Authors Info & Claims RECOMB '99:...
While in the last decade mRNA expression profiling was among most popular research areas, over past years study of non-coding RNAs, especially microRNAs (miRNAs), has gained increasing interest. For almost 900 known human miRNAs hundreds pretended targets are known. However, there is only limited knowledge about putative systemic effects changes and their regulatory influence. We determined for each miRNA biochemical pathways KEGG TRANSPATH database Gene Ontology categories that enriched...
Abstract NF-κB functions as modulator of T cell receptor-mediated signaling and transcriptional regulator miR-34a. Our in silico analysis revealed that miR-34a impacts the signalosome with binding sites 14 key members pathway. Functional identified five target genes including PLCG1 , CD3E PIK3CB TAB2 NFΚBIA . Overexpression CD4 + CD8 cells led to a significant decrease most downstream cytoplasmic member, reduced surface abundance TCRA CD3E, reduction killing capacity. Inhibition caused an...
MicroRNAs are regulators of gene expression. A wide-spread, yet not validated, assumption is that the targetome miRNAs non-randomly distributed across transcriptome and targets share functional pathways. We developed a computational experimental strategy termed high-throughput miRNA interaction reporter assay (HiTmIR) to facilitate validation target First, pathways predicted prioritized by means increase specificity positive predictive value. Second, novel webtool miRTaH facilitates guided...
Abstract A major challenge of precision oncology is the identification and prioritization suitable treatment options based on molecular biomarkers considered tumor. In pursuit this goal, large cancer cell line panels have successfully been studied to elucidate relationship between cellular features response. Due high dimensionality these datasets, machine learning (ML) commonly used for their analysis. However, choosing a algorithm set input can be challenging. We performed comprehensive...
Caspases and granzyme B are proteases that share the primary specificity to cleave at carboxyl terminal of aspartate residues in their substrates. Both, caspases enzymes involved fundamental cellular processes play a central role apoptotic cell death. Although various targets described, many substrates still await identification cleavage sites known not identified or experimentally verified. A more comprehensive knowledge caspase is essential understand biological roles these detail. The...