A5087586426- Biomedical Text Mining and Ontologies
- Scientific Computing and Data Management
- Research Data Management Practices
- Microbial Metabolic Engineering and Bioproduction
- Advanced Proteomics Techniques and Applications
- Genomics and Phylogenetic Studies
- Plant Disease Resistance and Genetics
- Chromosomal and Genetic Variations
- Genetics, Bioinformatics, and Biomedical Research
- Plant nutrient uptake and metabolism
- Bioinformatics and Genomic Networks
- Machine Learning in Bioinformatics
- Genetic diversity and population structure
- Semantic Web and Ontologies
- Biofuel production and bioconversion
- Wheat and Barley Genetics and Pathology
- Photosynthetic Processes and Mechanisms
- Advanced Computational Techniques and Applications
- Plant Micronutrient Interactions and Effects
- Gene Regulatory Network Analysis
- Lipid metabolism and biosynthesis
- Light effects on plants
- Edcuational Technology Systems
- Image Retrieval and Classification Techniques
- Evolutionary Algorithms and Applications
Leibniz Institute of Plant Genetics and Crop Plant Research
2009-2017
Leibniz Association
2012-2015
Friedrich-Alexander-Universität Erlangen-Nürnberg
2012
Heinrich Heine University Düsseldorf
2012
Martin Luther University Halle-Wittenberg
2011
Cereal grasses of the Triticeae tribe have been major food source in temperate regions since dawn agriculture. Their large genomes are characterized by a high content repetitive elements and pericentromeric that virtually devoid meiotic recombination. Here we present high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive linear order sequences across space investigate spatial organization chromatin nucleus at megabase...
Abstract Crop plant development is strongly dependent on the availability of nitrogen (N) in soil and efficiency N utilization for biomass production yield. However, knowledge about molecular responses to deprivation derives mainly from study model species. In this article, metabolic adaptation source leaves low was analyzed maize (Zea mays) seedlings by parallel measurements transcriptome metabolome profiling. Inbred lines A188 B73 were cultivated under sufficient (15 mm) or limiting (0.15...
Abstract We systematically analyzed a developmental gradient of the third maize (Zea mays) leaf from point emergence into light to tip in 10 continuous slices study organ development and physiological biochemical functions. Transcriptome analysis, oxygen sensitivity photosynthesis, photosynthetic rate measurements showed that undergoes sink-to-source transition without an intermediate phase C3 photosynthesis or operation photorespiratory carbon pump. Metabolome transcriptome chlorophyll...
Abstract Barley ( Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by International Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report experimental computational procedures to (i) assemble more than 80,000 bacterial artificial chromosome (BAC) clones along minimum tiling path genome-wide physical map, (ii) find...
Abstract Background Abiotic stress causes disturbances in the cellular homeostasis. Re-adjustment of balance carbon, nitrogen and phosphorus metabolism therefore plays a central role adaptation. However, it is currently unknown which parts primary cell follow common patterns under different conditions represent specific responses. Results To address these questions, changes transcriptome, metabolome ionome were analyzed maize source leaves from plants suffering low temperature, (N) (P)...
The life-science community faces a major challenge in handling "big data", highlighting the need for high quality infrastructures capable of sharing and publishing research data. Data preservation, analysis, publication are three pillars data life cycle". currently available managing often designed to meet domain-specific or project-specific requirements, resulting repeated development proprietary solutions lower preservation overall.e!DAL is lightweight software framework Its main features...
MetaCrop is a manually curated repository of high-quality data about plant metabolism, providing different levels detail from overview maps primary metabolism to kinetic enzymes. It contains information seven major crop plants with high agronomical importance and two model plants. intended support research aimed at the improvement crops for both nutrition industrial use. can be accessed via web, web services an add-on Vanted software. Here, we present several novel developments system...
Abstract Brassica napus (oilseed rape, canola) is one of the world’s most important sources vegetable oil for human nutrition and biofuel, also a model species studies investigating evolutionary consequences polyploidisation. Strong bottlenecks during its recent origin from interspecific hybridisation, subsequently through intensive artificial selection, have severely depleted genetic diversity available breeding. On other hand, high-throughput genome profiling technologies today provide...
Abstract Background Maize is a major crop plant, grown for human and animal nutrition, as well renewable resource bioenergy. When looking at the problems of limited fossil fuels, growth world’s population or climate change, it important to find ways increase yield biomass maize study how reacts specific abiotic biotic stress situations. Within OPTIMAS systems biology project plants were under large set controlled conditions, phenotypically characterised plant material was harvested analyse...
With the number of sequenced plant genomes growing, predicted genes and functional annotations is also increasing. The association between phenotypic traits currently great interest. Unfortunately, information available today widely scattered over a different databases. Information retrieval (IR) has become an all-encompassing bioinformatics methodology for extracting knowledge from complex, heterogeneous distributed databases, therefore can be useful tool obtaining comprehensive view...
Crop plants play a major role in human and animal nutrition increasingly contribute to chemical or pharmaceutical industry renewable resources. In order achieve important goals, such as the improvement of growth yield, it is indispensable understand biological processes on detailed level. Therefore, well-structured management fine-grained information about metabolic pathways high interest. Thus, we developed MetaCrop system, manually curated repository quality concerning metabolism crop...
Efficient and effective information retrieval in life sciences is one of the most pressing challenge bioinformatics. The incredible growth science databases to a vast network interconnected systems same extent big great chance for research. knowledge found Web, particular life-science databases, are valuable major resource. In order bring it scientist desktop, essential have well performing search engines. Thereby, not response time nor number results important. crucial factor millions query...
In modern life science research it is very important to have an efficient management of high throughput primary lab data. To realise such management, four main aspects be handled: (I) long term storage, (II) security, (III) upload and (IV) retrieval.In this paper we define central requirements for a data discuss best practices these requirements. As proof concept, introduce pipeline that has been implemented in order manage at the Leibniz Institute Plant Genetics Crop Research (IPK). It...
Background: Life sciences are data intensive. High throughput technologies, like "Next-Generation-Sequencing", "Phenotyping" and other -omics technologies produce a huge amount of primary data. In classic scientific publication process, is usually aggregated to number paragraphs in journal article proven by figures, tables supplementary material. So it that the value data, on which conclusions based on, do not get proper attention. But, responsible use efficient availability digital...
The paper presents e!DAL-API, a comprehensive storage backend for primary data management. It stands (Electronical Data Archive Library) and implements infrastructure, but with an intuitive usability like classical file system.
Summary Crop plants play a major role in human and animal nutrition increasingly contribute to chemical or pharmaceutical industry renewable resources. In order achieve important goals, such as the improvement of growth yield, it is indispensable understand biological processes on detailed level. Therefore, well-structured management fine-grained information about metabolic pathways high interest. Thus, we developed MetaCrop system, manually curated repository quality concerning metabolism...
Summary Efficient and effective information retrieval in life sciences is one of the most pressing challenge bioinformatics. The incredible growth science databases to a vast network interconnected systems same extent big great chance for research. knowledge found Web, particular life-science databases, are valuable major resource. In order bring it scientist desktop, essential have well performing search engines. Thereby, not response time nor number results important. crucial factor...