A5088111641- Genomics and Phylogenetic Studies
- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- Gene expression and cancer classification
- Insect and Arachnid Ecology and Behavior
- Insect and Pesticide Research
- Plant and animal studies
- Extracellular vesicles in disease
- Machine Learning in Bioinformatics
- Scientific Computing and Data Management
- Neuroinflammation and Neurodegeneration Mechanisms
- Microbial Natural Products and Biosynthesis
- RNA modifications and cancer
- Microbial Community Ecology and Physiology
- Single-cell and spatial transcriptomics
- Metabolomics and Mass Spectrometry Studies
- Antenna Design and Analysis
- Evolution and Genetic Dynamics
- Environmental DNA in Biodiversity Studies
- Circular RNAs in diseases
- Millimeter-Wave Propagation and Modeling
- Science and Climate Studies
- Microbial Metabolic Engineering and Bioproduction
- Insect Pheromone Research and Control
- RNA Research and Splicing
Saarland University
2019-2025
Helmholtz Institute for Pharmaceutical Research Saarland
2021-2022
Helmholtz Centre for Infection Research
2021-2022
Senckenberg Biodiversity and Climate Research Centre
2022
University of Tasmania
2015-2018
Health Sciences and Nutrition
2018
Data61
2018
Commonwealth Scientific and Industrial Research Organisation
2015
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...
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....
MiRNAs represent a non-coding RNA class that regulate gene expression and pathways. While miRNAs are evolutionary conserved most data stems from Homo sapiens Mus musculus. As miRNA is highly tissue specific, we developed miRNATissueAtlas to comprehensively explore this landscape in H. sapiens. We expanded the repertoire included M. In past years, number of public datasets has grown substantially. Our previous releases great framework for uniformly pre-processed label-harmonized resource...
Since the initial discovery of microRNAs as post-transcriptional, regulatory key players in 1990s, a total number $2656$ mature have been publicly described for Homo sapiens. As new miRNAs is still on-going, target identification remains to be an essential and challenging step preceding functional annotation analysis. One challenge researchers seems selection most appropriate tool out larger multiverse published solutions given research study set-up.In this review we collectively describe...
This paper introduces both a hardware and software system designed to allow low-cost electronic monitoring of social insects using RFID tags. Data formats for individual insect identification their associated experiment are proposed facilitate data sharing from experiments conducted with this system. The antennas’ configuration duty cycle ensure high degree detection rates. Other advantages limitations discussed in detail the paper.
Analyzing all features of small non-coding RNA sequencing data can be demanding and challenging. To facilitate this process, we developed miRMaster. After the analysis over 125 000 human samples 1.5 trillion reads 4 years, present miRMaster 2 with a wide range updates new features. We extended our reference sets so that now supports eight species (e.g. human, mouse, chicken, dog, cow) 10 classes microRNAs, piRNAs, tRNAs, rRNAs, circRNAs). also incorporated downstream modules such as batch...
Abstract The clinical course and treatment of neurodegenerative disease are complicated by immune-system interference chronic inflammatory processes, which remain incompletely understood. Mapping immune signatures in larger human cohorts through single-cell gene expression profiling supports our understanding observed peripheral changes neurodegeneration. Here, we employ over 909k blood mononuclear cells (PBMCs) from 121 healthy individuals, 48 patients with mild cognitive impairment (MCI),...
Abstract The human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration analysis its biosynthetic landscape, we present ABC-HuMi: the Atlas Biosynthetic Gene Clusters (BGCs) in Human Microbiome. ABC-HuMi integrates data from major sequence databases provides an expansive repository BGCs compared to limited coverage offered by existing resources. Employing...
Abstract The identification of targetomes remains a challenge given the pleiotropic effect miRNAs, limited effects miRNAs on individual targets, and sheer number estimated miRNA–target gene interactions (MTIs), which is around 44,571,700. Currently, targetome for single relies computational evidence functional studies covering smaller numbers targets. To ensure that analysis could be experimentally verified by assays, we employed systematic approach explored four (miR-129-5p, miR-129-1-3p,...
Abstract Plasmids are extrachromosomal DNA molecules in bacteria and archaea, playing critical roles horizontal gene transfer, antibiotic resistance, pathogenicity. Since its first release 2018, our database on plasmids, PLSDB, has significantly grown enhanced content scope. From 34 513 records contained the 2021 version, PLSDB now hosts 72 360 entries. Designed to provide life scientists with convenient access extensive plasmid data support computer by offering curated datasets for...
A significant fraction of mature miRNA transcripts carries sequence and/or length variations, termed isomiRs. IsomiRs are differentially abundant in cell types, tissues, body fluids or patients' samples. Not surprisingly, multiple studies describe a physiological and pathophysiological role. Despite their importance, systematically collected annotated isomiR information available databases remains limited. We thus developed isomiRdb, comprehensive resource that compiles expression data at...
Despite recent methodology and reference database improvements for taxonomic profiling tools, metagenomic assembly genomic binning remain important pillars of analysis workflows. In case information is lacking, considered to be a state-of-the-art method in mixed culture data analysis. this light, our previously published tool BusyBee Web implements composition-based efficient enough function as rapid online utility. Handling assembled contigs long nanopore generated reads alike, the...
Abstract Selecting proper genome assembly is key for downstream analysis in genomics studies. However, the availability of many tools and huge variety their running parameters challenge this task. The existing online evaluation are limited to specific taxa or provide just a one-sided view on quality. We present WebQUAST, web server multifaceted quality assessment comparison assemblies based state-of-the-art QUAST tool. freely available at https://www.ccb.uni-saarland.de/quast/. WebQUAST can...
This paper proposes a method to address misreadings and consequent inadequacy of radio-frequency identification data for social insect monitoring. Six-month worth field experiment were collected demonstrate the application method. The are transformed into linear combination Gaussian model curve-fitted using an evolutionary algorithm. results show that proposed allows us improve quality infer honey bee behavior at colony level.
Abstract The molecular causes and mechanisms of neurodegenerative diseases remain poorly understood. A growing number single-cell studies have implicated various neural, glial, immune cell subtypes to affect the mammalian central nervous system in many age-related disorders. Integrating this body transcriptomic evidence into a comprehensive reproducible framework poses several computational challenges. Here, we introduce ZEBRA, large single-nucleus RNA-seq database. ZEBRA integrates...
Single-cell RNA sequencing (RNA-seq) has revolutionized our understanding of cell biology, developmental and pathophysiological molecular processes, paving the way toward novel diagnostic therapeutic approaches. However, most gene regulatory processes on single-cell level are still unknown, including post-transcriptional control conferred by microRNAs (miRNAs). Like established expression analysis, advanced computational expertise is required to comprehensively process newly emerging...
This paper introduces both a hardware and software system designed to allow low-cost electronic monitoring of social insects using RFID tags. Data formats for individual insect identification their associated experiment are proposed facilitate data sharing from experiments conducted with this system. The antenna's configuration duty cycle ensure high degree detection rates. Other advantages limitations discussed in detail the paper.
Abstract With Aviator, we present a web service and repository that facilitates surveillance of online tools. Aviator consists user-friendly website two modules, literature-mining based general manually curated module. The module currently checks 9417 websites twice day with respect to their availability stores many features (frontend backend response time, required RAM size the page, security certificates, analytic tools trackers embedded in webpage others) data warehouse. is also equipped...
Quantifying microbiome species and composition from metagenomic assays is often challenging due to its time-consuming nature computational complexity. In Bioinformatics, k-mer-based approaches were long established expedite the analysis of large sequencing data are now widely used annotate data. We make use k-mer counting techniques for efficient accurate compositional microbiota whole metagenome sequencing. Mibianto solves this problem by operating directly on read files, without manual...
ABSTRACT The human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration analysis its biosynthetic landscape, we present ABC-HuMi: the Atlas Biosynthetic Gene Clusters (BGCs) in Human Microbiome. ABC-HuMi integrates data from major sequence databases provides an expansive repository BGCs compared to limited coverage offered by existing resources. Employing...