A5075631508- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- Circular RNAs in diseases
- RNA Research and Splicing
- Extracellular vesicles in disease
- Single-cell and spatial transcriptomics
- Genomics and Phylogenetic Studies
- Wound Healing and Treatments
- Bioinformatics and Genomic Networks
- RNA regulation and disease
- Gene expression and cancer classification
- Neuroinflammation and Neurodegeneration Mechanisms
- RNA Interference and Gene Delivery
- Cancer Genomics and Diagnostics
- Immune cells in cancer
- Molecular Biology Techniques and Applications
- Adipose Tissue and Metabolism
- Sex and Gender in Healthcare
- Long-Term Effects of COVID-19
- CRISPR and Genetic Engineering
- Renal cell carcinoma treatment
- CAR-T cell therapy research
- Mesenchymal stem cell research
- Diversity and Career in Medicine
Saarland University
2016-2025
Crohn's and Colitis Foundation
2024
Institute of Bioinformatics
2019
We present a human miRNA tissue atlas by determining the abundance of 1997 miRNAs in 61 biopsies different organs from two individuals collected post-mortem. One thousand three hundred sixty-four were discovered at least one tissue, 143 each tissue. To define distribution miRNAs, we utilized specificity index (TSI). The majority (82.9%) fell middle TSI range i.e. neither specific for single tissues (TSI > 0.85) nor housekeeping < 0.5). Nonetheless, observed many and families that...
Fast and reliable detection of patients with severe heterogeneous illnesses is a major goal precision medicine1,2. Patients leukaemia can be identified using machine learning on the basis their blood transcriptomes3. However, there an increasing divide between what technically possible allowed, because privacy legislation4,5. Here, to facilitate integration any medical data from owner worldwide without violating laws, we introduce Swarm Learning-a decentralized machine-learning approach that...
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...
Abstract The study of bacterial isolates or communities requires the analysis therein included plasmids in order to provide an extensive characterization organisms. Plasmids harboring resistance and virulence factors are especial interest as they contribute dissemination antibiotic resistance. As number newly sequenced genomes is growing a comprehensive resource required which will allow browse filter available plasmids, perform sequence analyses. Here, we present PLSDB, containing 13 789...
In this study, we aimed to clinically and genetically characterize LVNC patients investigate the prevalence of variants in known novel disease genes.Left ventricular non-compaction cardiomyopathy (LVNC) is an increasingly recognized cause heart failure, arrhythmia, thromboembolism, sudden cardiac death. We sought here dissect its genetic causes, phenotypic presentation outcome.In our registry with follow-up median 61 months, analysed 95 (68 unrelated index 27 affected relatives; definite...
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...
Plasmids are known to contain genes encoding for virulence factors and antibiotic resistance mechanisms. Their relevance in metagenomic data processing is steadily growing. However, with the increasing popularity scale of metagenomics experiments, number reported plasmids rapidly growing as well, amassing a considerable false positives due undetected misassembles. Here, our previously published database PLSDB provides reliable resource researchers quickly compare their sequences against...
Abstract Gene set enrichment analysis has become one of the most frequently used applications in molecular biology research. Originally developed for gene sets, same statistical principles are now available all omics types. In 2016, we published miRNA and annotation tool (miEAA) human precursor mature miRNAs. Here, present miEAA 2.0, supporting input from ten investigated organisms. To facilitate inclusion workflow systems, implemented an Application Programming Interface (API). Users can...
Recent studies indicate that the adaptive immune system plays a role in Lewy body dementia (LBD). However, mechanism regulating T cell brain homing LBD is unknown. Here, we observed cells adjacent to bodies and dopaminergic neurons postmortem brains. Single-cell RNA sequencing of cerebrospinal fluid (CSF) identified up-regulated expression C-X-C motif chemokine receptor 4 (CXCR4) CD4+ LBD. CSF protein levels CXCR4 ligand, ligand 12 (CXCL12), were associated with neuroaxonal damage...
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...
Abstract Small non-coding RNAs (sncRNAs) are pervasive regulators of physiological and pathological processes. We previously developed the human miRNA Tissue Atlas, detailing expression miRNAs across organs in body. Here, we present an updated resource containing sequencing data 188 tissue samples comprising 21 organ types retrieved from six humans. Sampling same bodies minimizes intra-individual variability facilitates making a precise high-resolution body map transcriptome. The allow...
MicroRNAs (miRNAs) are small non-coding RNAs that play a critical role in regulating diverse biological processes. Extracting functional insights from list of miRNAs is challenging, as each miRNA can potentially interact with hundreds genes. To address this challenge, we developed miEAA, flexible and comprehensive enrichment analysis tool based on direct indirect annotation. The latest release miEAA includes data warehouse 19 repositories, covering 10 different organisms 139 399 categories....
Abstract Breast cancer is a heterogeneous disease with distinct molecular subtypes including the aggressive subtype triple-negative breast (TNBC). We compared blood-borne miRNA signatures of early-stage basal-like (cytokeratin-CK5-positive) TNBC patients to age-matched controls. The miRNAs were assessed prior and following platinum-based neoadjuvant chemotherapy (NCT). After an exploratory genome-wide study on 21 cases controls using microarrays, identified verified independently in two...
// 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,...
We present the first sequencing data using combinatorial probe-anchor synthesis (cPAS)-based BGISEQ-500 sequencer. Applying cPAS, we investigated repertoire of human small non-coding RNAs and compared it to other techniques. Starting with repeated measurements different specimens including solid tissues (brain heart) blood, generated a median 30.1 million reads per sample. 24.1 mapped genome 23.3 miRBase. Among six technical replicates brain samples, observed correlation 0.98. Comparing...
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...
<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...
Information on miRNA targeting genes is growing rapidly. For high-throughput experiments, but also for targeted analyses of few or miRNAs, easy analysis with concise representation results facilitates the work life scientists. We developed miRTargetLink, a tool automating respective procedures that are frequently applied. Input web-based solution either single gene miRNA, sets can be entered. Validated and predicted targets extracted from databases an interaction network presented. Users...
Conventional white-light endoscopy has high interobserver variability for the diagnosis of gastric precancerous conditions.Here we present a deeplearning (DL) approach atrophic gastritis developed and trained using real-world endoscopic images from proximal stomach.The model achieved an accuracy 93% (area under curve (AUC): 0.98; F-score 0.93) in independent data set, outperforming expert endoscopists.DL may overcome conventional appraisal support human decision making.The algorithm is...
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...
Significance We report a systematic unbiased analysis of small RNA molecule expression in 11 different tissues the model organism mouse. discovered uncharacterized noncoding molecules and identified that ∼30% total transcriptome are distributed across body tissue-specific manner with some also being sexually dimorphic. Distinct distribution patterns suggest existence mechanisms involved processing.
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...