A5010196918- Insect Resistance and Genetics
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- RNA and protein synthesis mechanisms
- Cancer Genomics and Diagnostics
- Genomics and Phylogenetic Studies
- Computational Drug Discovery Methods
- Insect Utilization and Effects
- Genomics and Rare Diseases
- Gene Regulatory Network Analysis
- CRISPR and Genetic Engineering
- Machine Learning in Bioinformatics
- Gene expression and cancer classification
- Insect Pest Control Strategies
- Genomics and Chromatin Dynamics
- Semantic Web and Ontologies
- Neurobiology and Insect Physiology Research
- Pediatric health and respiratory diseases
- Neonatal Respiratory Health Research
- Animal Genetics and Reproduction
- Ubiquitin and proteasome pathways
- Blood Pressure and Hypertension Studies
- Microbial Natural Products and Biosynthesis
- Epigenetics and DNA Methylation
- Genetically Modified Organisms Research
Universitätsmedizin Göttingen
2012-2025
University of Göttingen
2015-2025
Intelligent Transport Systems Niedersachsen
2023-2025
Charité - Universitätsmedizin Berlin
2024
University Medical Center
2024
University Hospital Cologne
2024
University of Helsinki
2024
University Hospital Leipzig
2024
Abstract Genetic screens are powerful tools to identify the genes required for a given biological process. However, technical reasons, comprehensive have been restricted very few model organisms. Therefore, although deep sequencing is revealing of ever more insect species, functional studies predominantly focus on candidate previously identified in Drosophila , which biasing research towards conserved gene functions. RNAi other organisms promise reduce this bias. Here we present results...
TFClass (http://tfclass.bioinf.med.uni-goettingen.de/) provides a comprehensive classification of human transcription factors based on their DNA-binding domains. Transcription constitute large functional family proteins directly regulating the activity genes. Most them are sequence-specific proteins, thus reading out information encoded in cis-regulatory DNA elements promoters, enhancers and other regulatory regions genome. is database that classifies by six-level schema, four which...
Insect pest control is challenged by insecticide resistance and negative impact on ecology health. One promising specific alternative the generation of transgenic plants, which express double stranded RNAs targeting essential genes a species. Upon feeding, dsRNA induces gene silencing in resulting its death. However, identification efficient RNAi target remains major challenge as genomic tools breeding capacity limited most insects impeding whole-animal-high-throughput-screening.We use red...
The iBeetle-Base (http://ibeetle-base.uni-goettingen.de) makes available annotations of RNAi phenotypes, which were gathered in a large scale screen the red flour beetle Tribolium castaneum (iBeetle screen). In addition, it provides access to sequence information and links for all genes. contains phenotypes several thousands genes knocked down during embryonic metamorphic epidermis muscle development addition linked oogenesis stink gland biology. are described according EQM (entity, quality,...
TFClass is a resource that classifies eukaryotic transcription factors (TFs) according to their DNA-binding domains (DBDs), available online at http://tfclass.bioinf.med.uni-goettingen.de. The classification scheme of was originally derived for human TFs and expanded here the whole taxonomic class mammalia. Combining information from different resources, checking manually retrieved mammalian sequences applying extensive phylogenetic analyses, >39 000 up 41 species were assigned Superclasses,...
Motile multiciliated cells (MCCs) have critical roles in respiratory health and disease are essential for cleaning inhaled pollutants pathogens from airways. Despite their significance human disease, the transcriptional control that governs multiciliogenesis remains poorly understood. Here we identify TP73, a p53 homolog, as governing program airway multiciliogenesis. Mice with TP73 deficiency suffer chronic tract infections due to profound defects ciliogenesis complete loss of mucociliary...
The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, ecological evolutionary genomics, pest control a plethora other topics. RNA interference (RNAi), transgenesis genome editing are well established resources genome-wide RNAi screening have become available this model. All these techniques depend on high quality assembly precise models. However, first version was generated by Sanger sequencing, with...
TFClass aims at classifying eukaryotic transcription factors (TFs) according to their DNA-binding domains (DBDs). For this, a classification schema comprising four generic levels (superclass, class, family and subfamily) was defined that could accommodate all known human TFs. They were assigned (sub-)families as instances two different levels, the corresponding TF genes individual gene products (protein isoforms). In present version, mouse rat orthologs have been linked TFs, arranged in an...
Abstract Background Most of the known genes required for developmental processes have been identified by genetic screens in a few well-studied model organisms, which considered representative related species, and informative—to some degree—for human biology. The fruit fly Drosophila melanogaster is prime insect genetics, while conservation many gene functions has observed among bilaterian animals, plethora data show evolutionary divergence function more closely-related groups, such as within...
The iBeetle-Base provides access to sequence and phenotype information for genes of the beetle Tribolium castaneum. It has been updated including more data new functions. RNAi phenotypes are now available >50% genes, which represents an expansion 60% compared previous version. Gene based on official gene set OGS3 covers all genes. Interoperability with FlyBase enhanced: First, pages homologous interlinked between both databases. Second, some steps a query pipeline allow transforming lists...
Abstract An increasing human population, the emergence of resistances against pesticides and their potential impact on environment call for development new eco-friendly pest control strategies. RNA interference (RNAi) based have emerged as option with first products entering market. Essentially, double stranded RNAs targeting essential genes pests are either expressed in plants or sprayed surface. Upon feeding, mount an RNAi response die. However, it has remained unclear, whether...
Identifying and validating genotype-guided drug combinations for a specific molecular subtype in cancer therapy represents an unmet medical need is important enhancing efficacy reducing toxicity. However, the exponential increase combinatorial possibilities constrains ability to identify validate effective combinations. In this context, we have developed Onko_DrugCombScreen, innovative tool aiming at advancing precision medicine based on identifying significant combination candidates target...
Abstract Identifying essential genes on a genome scale is resource intensive and has been performed for only few eukaryotes. For less studied organisms essentiality might be predicted by gene homology. However, this approach cannot applied to non-conserved genes. Additionally, divergent information obtained from studying single cells or whole, multi-cellular organisms, particularly when derived human cell line screens population studies. We employed machine learning across six model...
Dealing with sequence coordinates in different formats and reference genomes is challenging genetic research. This complexity arises from the need to convert harmonize datasets of sources using alternating nomenclatures. Since manual processing time-consuming requires specialized knowledge, Sequence Conversion Analysis Toolbox (SeqCAT) was developed for daily work datasets. Our tool provides a range functions designed standardize gene variant based on various types. Its user-friendly web...
Abstract Formation of the mammalian primitive streak appears to rely on cell proliferation a minor extent only, but compensating movements have not yet been directly observed. This study analyses individual migration and simultaneously, using multiphoton differential interference contrast time‐lapse microscopy late pregastrulation rabbit blastocysts. Epiblast cells in posterior gastrula extension area accumulated medially displayed complex planar including U‐turns novel type processional...
In a morphological ontology the expert's knowledge is represented in terms, which describe structures and how these relate to each other. With assistance of ontologies this expert made processable by machines, through formal standardized representation terms their relations The red flour beetle Tribolium castaneum, representative most species rich animal taxon on earth (the Coleoptera), an emerging model organism for development, evolution, physiology, pest control. order foster research, we...
The semantic web depends on the use of ontologies to let electronic systems interpret contextual information. Optimally, handling and access should be completely transparent user. As a means this end, we have developed service that attempts bridge gap between experts in certain knowledge domain, ontologists, application developers. ontology-based answers (OBA) introduced here can embedded into custom applications grant classes their relations as most important structural features well...
In multicellular organisms, an intercellular signaling network communicates information from the environment or distant tissues to defined target cells. Intercellular (mostly mediated by hormones) can affect metabolic state and gene expression program of cells, thereby coordinating development, homeostasis organism its reactions external stimuli. Knowledge components (specifically: endocrine) their relations is important, though so far a largely neglected part systems biology. EndoNet...
Introduction: Precision oncology and biomedical cancer research increasingly rely on tools to select optimal drugs targeting specific genetic alterations in cancer. A major challenge for bioinformatic supporting drug selection is standardize different annotations (substance, name, class) a common level, typically the class. While manual classification time-consuming potentially biased, existing resources often lack completeness, granularity, or mix up classes targets. structured,...
Abstract BACKGROUND An increasing human population, the emergence of resistances against pesticides and their potential impact on environment call for development new eco‐friendly pest control strategies. RNA interference (RNAi)‐based have emerged as a option with first products entering market. Essentially, double‐stranded RNAs targeting essential genes pests are either expressed in plants or sprayed surface. Upon feeding, mount an RNAi response die. However, it has remained unclear whether...
Next-generation sequencing methods continuously provide clinicians and researchers in precision oncology with growing numbers of genomic variants found cancer. However, manually interpreting the list to identify reliable targets is an inefficient cumbersome process that does not scale increasing number cases. Support by computer systems needed for analysis large experiments clinical studies new therapies, user-friendly applications are molecular tumor boards support their decision-making...
EndoNet is an information resource about intercellular regulatory communication. It provides hormones, hormone receptors, the sources (i.e. cells, tissues and organs) where hormones are synthesized secreted, respective receptors expressed. The database focuses on relations between them. An elementary communication displayed as a causal link from cell that secretes particular to those cells which express corresponding receptor respond hormone. Whenever expression, synthesis and/or secretion...
Chronic kidney disease (CKD), a major public health problem with differing etiologies, leads to complications, comorbidities, polypharmacy, and mortality. Monitoring progression personalized treatment efforts are crucial for long-term patient outcomes. Physicians need integrate different data levels, e.g., clinical parameters, biomarkers, drug information, medical knowledge. Clinical decision support systems (CDSS) can tackle these issues improve management. Knowledge about the awareness...
Abstract Background: The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, ecological evolutionary genomics, pest control a plethora other topics. RNA interference (RNAi), transgenesis genome editing are well established resources genome-wide RNAi screening have become available this model. All these techniques depend on high quality assembly precise models. However, first version was generated by...
High-throughput methods for measuring transcript abundance, like SAGE or microarrays, are widely used determining differences in gene expression between different tissue types, dignities (normal/malignant) time points. Further analysis of such data frequently aims at the identification interaction networks that form causal basis observed properties systems under examination. To this end, it is usually not sufficient to rely on measured levels alone; rather, additional biological knowledge...