A5046176085- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Genetics, Bioinformatics, and Biomedical Research
- Gut microbiota and health
- Scientific Computing and Data Management
- Bacteriophages and microbial interactions
- Gene expression and cancer classification
- Research Data Management Practices
- Anaerobic Digestion and Biogas Production
- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- SARS-CoV-2 detection and testing
- Microbial Metabolites in Food Biotechnology
- Radiomics and Machine Learning in Medical Imaging
- Online Learning and Analytics
- Biofuel production and bioconversion
- Metabolomics and Mass Spectrometry Studies
- Wastewater Treatment and Nitrogen Removal
- Cloud Computing and Resource Management
- Ethics in Clinical Research
- COVID-19 diagnosis using AI
- Cancer Immunotherapy and Biomarkers
- Advanced Data Storage Technologies
- SARS-CoV-2 and COVID-19 Research
Forschungszentrum Jülich
2022-2023
Bielefeld University
2015-2022
Helmholtz Centre for Infection Research
2017-2019
The Critical Assessment of Metagenome Interpretation (CAMI) community initiative presents results from its first challenge, a rigorous benchmarking software for metagenome assembly, binning and taxonomic profiling. Methods profiling are key to interpreting data, but lack consensus about complicates performance assessment. challenge has engaged the global developer benchmark their programs on highly complex realistic data sets, generated ∼700 newly sequenced microorganisms ∼600 novel viruses...
Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation underlying biological systems, but also differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, effectively assess performance metagenomic analysis software, a wide range benchmark required.We describe CAMISIM community simulator. The software can model different abundance profiles, multi-sample time series, differential studies, includes...
Software is now both central and essential to modern biology, yet lack of availability, difficult installations, complex user interfaces make software hard obtain use. Containerisation, as exemplified by the Docker platform, has potential solve problems associated with sharing software. We propose bioboxes: containers standardised bioinformatics interchangeable.
Reconstructing the genomes of microbial community members is key to interpretation shotgun metagenome samples. Genome binning programs deconvolute reads or assembled contigs such samples into individual bins. However, assessing their quality difficult due lack evaluation software and standardized metrics. Here, we present Assessment Metagenome BinnERs (AMBER), an package for comparative assessment genome reconstructions from benchmark datasets. It calculates performance metrics...
The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. Open-community Profiling Assessment tooL (OPAL) implements commonly used metrics, including those of first challenge initiative Critical Metagenome Interpretation (CAMI), together with convenient visualizations. In addition, we perform in-depth seven profilers on datasets CAMI and Human Microbiome Project. OPAL is freely...
Abstract Background The production of biogas takes place under anaerobic conditions and involves microbial decomposition organic matter. Most the participating microbes are still unknown non-cultivable. Accordingly, shotgun metagenome sequencing currently is method choice to obtain insights into community composition genetic repertoire. Findings Here, we report on deeply sequenced metatranscriptome a complex biogas-producing from an agricultural production-scale plant. We assembled and, as...
Abstract In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets evaluation metrics complicates proper performance assessment. The Critical Assessment Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on unprecedented complexity realism. Benchmark metagenomes were...
A common Authentication and Authorisation Infrastructure (AAI) that would allow single sign-on to services has been identified as a key enabler for European bioinformatics. ELIXIR AAI is an service portfolio authenticating researchers assisting these on user privileges during research usage. It relieves the scientific providers from managing identities authorisation themselves, enables researcher have set of credentials all supports meeting requirements imposed by data protection laws. was...
Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation underlying biological systems, but also differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, effectively assess performance metagenomic analysis software, a wide range benchmark required. Here, we describe CAMISIM community simulator. The software can model different abundance profiles, multi-sample time series differential studies,...
The academic de.NBI Cloud offers compute resources for life science research in Germany. At the beginning of 2017, started to implement a federated cloud consisting five centers, with aim acting as one resource their users. A introduces multiple challenges, such central access and project management point, unified account across all sites an interchangeable setup federation. In order federation concept, integrated ELIXIR authentication authorization infrastructure system (ELIXIR AAI)...
Genomic surveillance of the SARS-CoV-2 pandemic is crucial and mainly achieved by amplicon sequencing protocols. Overlapping tiled-amplicons are generated to establish contiguous genome sequences, which enable precise resolution infection chains outbreaks. We investigated a outbreak in local hospital used nanopore with modified ARTIC protocol employing 1200 bp long amplicons. detected deletion 168 nucleotides ORF8 gene 76 samples from outbreak. This difficult identify classical procedures...
The metagenome analysis of complex environments with thousands datasets, such as those available in the Sequence Read Archive, requires immense computational resources to complete work within an acceptable time frame. Such large-scale analyses require that underlying infrastructure is used efficiently. In addition, any should be fully reproducible and workflow must publicly allow other researchers understand reasoning behind computed results. Here, we introduce Metagenomics-Toolkit, a...
Abstract Reconstructing the genomes of microbial community members is key to interpretation shotgun metagenome samples. Genome binning programs deconvolute reads or assembled contigs such samples into individual bins, but assessing their quality difficult due lack evaluation software and standardized metrics. We present AMBER, an package for comparative assessment genome reconstructions from benchmark data sets. It calculates performance metrics visualizations used in first benchmarking...
Abstract Taxonomic metagenome profilers predict the presence and relative abundance of microorganisms from shotgun sequence samples DNA isolated directly a microbial community. Over past years, there has been an explosive growth software algorithms for this task, resulting in need more systematic comparisons these methods based on relevant performance criteria. Here, we present OPAL, package implementing commonly used metrics, including those first challenge Initiative Critical Assessment...
<ns4:p>The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the Federal Ministry of Education Research (BMBF). The de.NBI provides (i) service, (ii) training, (iii) cloud computing to users in life sciences research biomedicine Germany Europe (iv) fosters cooperation bioinformatics community with international network structures. members also run node (ELIXIR-DE) within European ELIXIR network. / ELIXIR-DE training platform, known...
In recent years, modern life sciences research underwent a rapid development driven mainly by the technical improvements in analytical areas leading to miniaturization, parallelization, and high throughput processing of biological samples. This has led generation huge amounts experimental data. To meet these rising demands, German Network for Bioinformatics Infrastructure (de.NBI) was established 2015 as national bioinformatics consortium aiming provide quality services, comprehensive...
<ns4:p>The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the Federal Ministry of Education Research (BMBF). The de.NBI provides (i) service, (ii) training, (iii) cloud computing to users in life sciences research biomedicine Germany Europe (iv) fosters cooperation bioinformatics community with international network structures. members also run node (ELIXIR-DE) within European ELIXIR infrastructure. / ELIXIR-DE training platform,...
Research on biogas-producing microbial communities aims at elucidation of correlations and dependencies between the anaerobic digestion (AD) process corresponding microbiome composition in order to optimize performance biogas output. Previously, Lachnospiraceae species were frequently detected mesophilic moderately thermophilic reactors. To analyze adaptive genome features a representative strain, Anaeropeptidivorans aminofermentans M3/9 T was isolated from laboratory-scale plant its...