Alexander Goesmann
A5088085534- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Plant Pathogenic Bacteria Studies
- Plant-Microbe Interactions and Immunity
- Legume Nitrogen Fixing Symbiosis
- Bacteriophages and microbial interactions
- Probiotics and Fermented Foods
- Microbial Metabolic Engineering and Bioproduction
- Antibiotic Resistance in Bacteria
- RNA and protein synthesis mechanisms
- Gut microbiota and health
- Plant Disease Resistance and Genetics
- Bioinformatics and Genomic Networks
- Bacterial Infections and Vaccines
- Biofuel production and bioconversion
- Gene expression and cancer classification
- Bacterial Genetics and Biotechnology
- Plant Pathogens and Fungal Diseases
- Viral Infectious Diseases and Gene Expression in Insects
- Bacterial biofilms and quorum sensing
- Algal biology and biofuel production
- Protist diversity and phylogeny
- Plant nutrient uptake and metabolism
- Machine Learning in Bioinformatics
- Anaerobic Digestion and Biogas Production
Justus-Liebig-Universität Gießen
2016-2025
Institute of Bioinformatics
2025
Giessen School of Theology
2014-2024
German Center for Infection Research
2016-2024
Bielefeld University
2008-2021
Heinrich Heine University Düsseldorf
2021
Institute of Bioinformatics and Systems Biology
2015-2020
University of Cologne
2016
Federal Institute for Risk Assessment
2016
Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures
2016
Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% the world's annual sugar production and a source for bioethanol animal feed. The species belongs to order Caryophylalles, diploid with 2n = 18 chromosomes, has estimated genome size 714-758 megabases shares ancient triplication other eudicot plants. Leafy beets have been cultivated since Roman times, but one most recently domesticated crops. It arose in late eighteenth century when...
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...
Command-line annotation software tools have continuously gained popularity compared to centralized online services due the worldwide increase of sequenced bacterial genomes. However, results existing command-line pipelines heavily depend on taxon-specific databases or sufficiently well annotated reference Here, we introduce Bakta, a new tool for robust, taxon-independent, thorough and, nonetheless, fast Bakta conducts comprehensive workflow including detection small proteins taking into...
Meeting the increasing food and energy demands of a growing population will require development ground-breaking strategies that promote sustainable plant production. Host-induced gene silencing has shown great potential for controlling pest diseases in crop plants. However, while delivery inhibitory noncoding double-stranded (ds)RNA by transgenic expression is promising concept, it requires generation plants which may cause substantial delay application depending on transformability genetic...
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...
The introduction of next generation sequencing approaches has caused a rapid increase in the number completely sequenced genomes. As one result this development, it is now feasible to analyze large groups related genomes comparative approach. A main task genomics identification orthologous genes different and classification as core or singletons.To support these studies EDGAR - "Efficient Database framework for Genome Analyses using BLAST score Ratios" was developed. designed automatically...
Lactococcus lactis is of great importance for the nutrition hundreds millions people worldwide. This paper describes genome sequence subsp. cremoris MG1363, lactococcal strain most intensively studied throughout world. The 2,529,478-bp contains 81 pseudogenes and encodes 2,436 proteins. Of 530 unique proteins, 47 belong to COG (clusters orthologous groups) functional category "carbohydrate metabolism transport," by far largest novel proteins in comparison with L. IL1403. Nearly one-fifth 71...
ABSTRACT Bacterioplankton of the marine Roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with plankton. Comparative genome sequence analysis three cultured representatives suggests cellular requirements for nitrogen are largely provided by regenerated ammonium organic compounds (polyamines, allophanate, urea), while typical sources carbon include amino acids, glyoxylate, aromatic metabolites. An unexpectedly large number genes predicted to encode...
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 rapidly increasing availability of microbial genome sequences has led to a growing demand for bioinformatics software tools that support the functional analysis based on comparison closely related genomes. By utilizing comparative approaches gene level it is possible gain insights into core genes which represent set shared features organisms under study. Vice versa singleton can be identified elucidate specific properties an individual genome. Since initial publication, EDGAR platform...
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....
Metagenomics is providing striking insights into the ecology of microbial communities. The recently developed massively parallel 454 pyrosequencing technique gives opportunity to rapidly obtain metagenomic sequences at a low cost and without cloning bias. However, phylogenetic analysis short reads produced represents significant computational challenge. algorithm CARMA for predicting source organisms environmental described. searches conserved Pfam domain protein families in unassembled...
Biogas production from renewable resources is attracting increased attention as an alternative energy source due to the limited availability of traditional fossil fuels. Many countries are promoting use sources for sustainable production. In this study, a metagenome production-scale biogas fermenter was analysed employing Roche's GS FLX Titanium technology and compared previous dataset obtained same community DNA sample that sequenced on platform. Taxonomic profiling based 16S rRNA-specific...
Listeria monocytogenes is an important food-borne pathogen and model organism for host-pathogen interaction, thus representing invaluable target considering research on the forces governing evolution of such microbes. The diversity this species has not been exhaustively explored yet, as previous efforts have focused analyses serotypes primarily implicated in human listeriosis. We conducted complete genome sequencing 11 strains employing 454 GS FLX technology, thereby achieving full coverage...
Plasmids are extrachromosomal genetic elements that replicate independently of the chromosome and play a vital role in environmental adaptation bacteria. Due to potential mobilization or conjugation capabilities, plasmids important vehicles for antimicrobial resistance genes virulence factors with huge increasing clinical implications. They therefore subject large genomic studies within scientific community worldwide. As result rapidly improving next-generation sequencing methods, quantity...
Antimicrobial resistance (AMR) is one of the biggest global problems threatening human and animal health. Rapid accurate AMR diagnostic methods are thus very urgently needed. However, traditional antimicrobial susceptibility testing (AST) time-consuming, low throughput viable only for cultivable bacteria. Machine learning may pave way automated prediction based on genomic data comparing different machine encodings whole-genome sequencing without previously known knowledge remains to be...
Azoarcus sp. strain BH72, a mutualistic endophyte of rice and other grasses, is agrobiotechnological interest because it supplies biologically fixed nitrogen to its host colonizes plants in remarkably high numbers without eliciting disease symptoms. The complete genome sequence 4,376,040-bp long contains 3,992 predicted protein-coding sequences. Genome comparison with the Azoarcus-related soil bacterium EbN1 revealed surprisingly low degree synteny. Coding sequences involved synthesis...