A5086419862- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Gut microbiota and health
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- Scientific Computing and Data Management
- Environmental DNA in Biodiversity Studies
- Legume Nitrogen Fixing Symbiosis
- Distributed and Parallel Computing Systems
- Microbial Metabolic Engineering and Bioproduction
- Plant Pathogenic Bacteria Studies
- Bacteriophages and microbial interactions
- Metabolomics and Mass Spectrometry Studies
- Genetics, Bioinformatics, and Biomedical Research
- Metal Extraction and Bioleaching
- Machine Learning in Bioinformatics
- Biomedical Text Mining and Ontologies
- Research Data Management Practices
- Cloud Computing and Resource Management
- Bacterial Genetics and Biotechnology
- Soil Carbon and Nitrogen Dynamics
- Plant nutrient uptake and metabolism
- Bacterial biofilms and quorum sensing
- Mine drainage and remediation techniques
University of Duisburg-Essen
2020-2025
Artificial Intelligence in Medicine (Canada)
2024
Essen University Hospital
2020-2024
University of Chicago
2010-2023
Argonne National Laboratory
2012-2023
Institut für Medizinische Informatik, Biometrie und Epidemiologie
2020
University of Illinois Chicago
2014-2019
Newcastle University
2018
University of Newcastle Australia
2018
Wellcome Centre for Mitochondrial Research
2018
Abstract Background The number of prokaryotic genome sequences becoming available is growing steadily and faster than our ability to accurately annotate them. Description We describe a fully automated service for annotating bacterial archaeal genomes. identifies protein-encoding, rRNA tRNA genes, assigns functions the predicts which subsystems are represented in genome, uses this information reconstruct metabolic network makes output easily downloadable user. In addition, annotated can be...
Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, major challenge associated with metagenomics shifted from generating analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access a wide range of researchers. A high-throughput pipeline been constructed provide high-performance computing all researchers interested using metagenomics. The produces automated functional assignments...
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of Minimum Information about Any (x) Sequence (MIxS). The a Single Amplified Genome (MISAG) Metagenome-Assembled (MIMAG), including, but not limited to, assembly quality, estimates completeness contamination. These can be used in combination with other GSC checklists, including (MIGS), Metagenomic (MIMS), Marker Gene (MIMARKS). Community-wide...
To the Editor: Over past two decades, scale and complexity of genomics technologies data have advanced from sequencing genomes a few organisms to generating metagenomes, genome variation, gene expression, metabolites, phenotype for thousands their communities.A major challenge in this data-rich age biology is integrating heterogeneous distributed into predictive models biological function, ranging single entire ecologies.The US Department Energy (DOE) has invested substantially efforts...
Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content entire communities organisms. The field metagenomics has been responsible for substantial advances in microbial ecology, evolution, diversity over past 5 10 years, many research laboratories are actively engaged it now. With growing numbers activities also comes plethora methodological knowledge expertise that should guide future developments field. This review summarizes...
We present the Biological Observation Matrix (BIOM, pronounced "biome") format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated and metadata. As number of categories comparative omics data types (collectively, "ome-ome") grows rapidly, general to represent archive this will facilitate interoperability existing bioinformatics tools future meta-analyses. The BIOM is supported an independent open-source software project (the...
The flood of sequence data resulting from the large number current genome projects has increased need for a flexible, open source annotation system, which so far not existed. To account individual needs different projects, such system should be modular and easily extensible. We present prokaryote genomes, is well tested readily adaptable to tasks. was developed using an object-oriented approach, it relies on relational database backend. Using defined application programmers interface (API),...
Alcanivorax borkumensis is a cosmopolitan marine bacterium that uses oil hydrocarbons as its exclusive source of carbon and energy. Although barely detectable in unpolluted environments, A. becomes the dominant microbe oil-polluted waters. SK2 has streamlined genome with paucity mobile genetic elements energy generation–related genes, but plethora genes accounting for wide hydrocarbon substrate range efficient oil-degradation capabilities. The further specifies systems scavenging nutrients,...
The genus Sorangium synthesizes approximately half of the secondary metabolites isolated from myxobacteria, including anti-cancer metabolite epothilone. We report complete genome sequence model strain S. cellulosum So ce56, which produces several natural products and has morphological physiological properties typical genus. circular genome, comprising 13,033,779 base pairs, is largest bacterial sequenced to date. No global synteny with Myxococcus xanthus apparent, revealing an unanticipated...
Summary Members of the Bacteroidetes , formerly known as Cytophaga‐Flavobacteria‐Bacteroides (CFB) phylum, are among major taxa marine heterotrophic bacterioplankton frequently found on macroscopic organic matter particles (marine snow). In addition, they have been shown to also represent a significant part free‐living microbial assemblages in nutrient‐rich microenvironments. Their abundance and distribution pattern combination with enzymatic activity studies has led notion that organisms...
Predatory bacteria remain molecularly enigmatic, despite their presence in many microbial communities. Here we report the complete genome of Bdellovibrio bacteriovorus HD100, a predatory Gram-negative bacterium that invades and consumes other bacteria. Its surprisingly large shows no evidence recent gene transfer from its prey. A plethora paralogous families coding for enzymes, such as hydrolases transporters, are used throughout life cycle B. prey entry, killing, uptake complex molecules.
The gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria is the causative agent of bacterial spot disease in pepper and tomato plants, which leads to economically important yield losses. This pathosystem has become a well-established model for studying infection strategies. Here, we present whole-genome sequence pepper-pathogenic strain 85-10, comprises 5.17-Mb circular chromosome four plasmids. genome high G+C content (64.75%) signatures extensive plasticity....
Abstract Background Computing of sequence similarity results is becoming a limiting factor in metagenome analysis. Sequence search encoded an open, exchangeable format have the potential to limit needs for computational reanalysis these data sets. A prerequisite sharing common reference. Description We introduce mechanism automatically maintaining comprehensive, non-redundant protein database and creating quarterly release this resource. In addition, we present tools translating searches...
INTRODUCTION Shotgun metagenomics creates millions of fragments short DNA reads, which are meaningless unless analyzed appropriately. The Metagenomics RAST server (MG-RAST) is a web-based, open source system that offers unique suite tools for analyzing these data sets. After de-replication and quality control, mapped against comprehensive nonredundant database (NR). Phylogenetic metabolic reconstructions computed from the set hits NR. resulting made available browsing, download, most...
Between July 18(th) and 24(th) 2010, 26 leading microbial ecology, computation, bioinformatics statistics researchers came together in Snowbird, Utah (USA) to discuss the challenge of how best characterize world using next-generation sequencing technologies. The meeting was entitled "Terabase Metagenomics" sponsored by Institute for Computing Science (ICiS) summer 2010 workshop program. aim explore fundamental questions relating ecology that could be addressed advances potential....
Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high diversity and large spatial variability most soil characteristics. We investigated bacterial structure in a switchgrass stand planted on with history grassland vegetation at resolution determine whether biogeographic trends occurred the centimeter scale. Moreover, we tested such heterogeneity, if present, influenced within or among...
Microbes hold the key to life. They secrets our past (as descendants of earliest forms life) and prospects for future we mine their genes solutions some planet's most pressing problems, from global warming antibiotic resistance). However, piecemeal approach that has defined efforts study microbial genetic diversity over 20 years in 30,000 genome projects risks squandering promise. These have covered less than 20% cultured archaeal bacterial species, which represent just 15% overall known...
A vast and rich body of information has grown up as a result the world's enthusiasm for 'omics technologies. Finding ways to describe make available this that maximise its usefulness become major effort across world. At heart is Genomic Standards Consortium (GSC), an open-membership organization drives community-based standardization activities, Here we provide short history GSC, overview range current call scientific community join forces improve quality quantity contextual about our public...
MG-RAST (http://metagenomics.anl.gov) is an open-submission data portal for processing, analyzing, sharing and disseminating metagenomic datasets. The system currently hosts over 200 000 datasets continuously updated. volume of submissions has increased 4-fold the past 24 months, now averaging 4 terabasepairs per month. In addition to several new features, we report changes analysis workflow technologies used scale pipeline up required throughput levels. To show possible uses from MG-RAST,...
Abstract MOTIVATION: We present a new probabilistic model of the evolution RNA-, DNA-, or protein-like sequences and software tool, Rose, that implements this model. Guided by an evolutionary tree, family related is created from common ancestor sequence insertion, deletion substitution characters. During artificial process, 'true' history logged 'correct' multiple alignment simultaneously. The also allows for varying rates mutation within sequences, making it possible to establish so-called...
ABSTRACT Sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. These autotrophic and mixotrophic sulfur-oxidizing bacteria believed to contribute substantially the oxidative portion global sulfur cycle. In order better understand ecology roles epsilonproteobacteria, particular those widespread genus Sulfurimonas , biogeochemical cycles, genome denitrificans DSM1251 was sequenced. This has many features, including larger size (2.2 Mbp), that suggest...