A5041475009- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Bacteriophages and microbial interactions
- RNA Research and Splicing
- MicroRNA in disease regulation
- Plant Virus Research Studies
- interferon and immune responses
- Cancer-related molecular mechanisms research
- Viral gastroenteritis research and epidemiology
- Viral Infections and Vectors
- Viral Infections and Outbreaks Research
- Microbial Community Ecology and Physiology
- Animal Virus Infections Studies
- SARS-CoV-2 and COVID-19 Research
- Machine Learning in Bioinformatics
- Extracellular vesicles in disease
- Pregnancy and preeclampsia studies
- Plant Pathogenic Bacteria Studies
- Reproductive tract infections research
- vaccines and immunoinformatics approaches
- Influenza Virus Research Studies
- Chromosomal and Genetic Variations
- Microbial infections and disease research
- RNA regulation and disease
Friedrich Schiller University Jena
2016-2025
Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
2015-2025
Bioinformatics Institute
2018-2024
German Centre for Integrative Biodiversity Research
2016-2024
Ernst Abbe University of Applied Sciences Jena
2015-2024
Leibniz Association
2015-2024
Max Planck Institute for the Science of Human History
2024
Schiller International University
2023
InfectoGnostics Research Campus Jena
2022
Heinrich Heine University Düsseldorf
2021
Orthology analysis is an important part of data in many areas bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood sequence data, hence the rapidly increasing number genomes that can be compared simultaneously, calls for efficient software tools brute-force approaches with quadratic memory requirements become infeasible practise. rapid pace at which new available, furthermore, makes it desirable to compute genome-wide orthology relations a given...
Abstract Rfam is a database of RNA families where each the 3444 represented by multiple sequence alignment known sequences and covariance model that can be used to search for additional members family. Recent developments have involved expert collaborations improve quality coverage data, focusing on microRNAs, viral bacterial RNAs. We completed first phase synchronising microRNA in miRBase, creating 356 new updating 40. established procedure comprehensive annotation starting with Flavivirus...
A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided cost-effective assembly the genome sequence domestic turkey (Meleagris gallopavo). Heterozygosity sequenced source allowed discovery more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, current (∼1.1 Gb) includes 917 Mb assigned to specific chromosomes. Annotation identified nearly 16,000 genes, 15,093 recognized as protein...
Ning Li and colleagues report the whole-genome sequence of duck, Anas platyrhynchos, a natural host avian influenza viruses. They examine response to infection by comparing lung transcriptomes ducks that were infected with A The duck (Anas platyrhynchos) is one principal hosts We present genome perform deep transcriptome analyses investigate immune-related genes. Our data indicate possesses contractive immune gene repertoire, as in chicken zebra finch, this repertoire has been shaped through...
Sequence analyses of RNA virus genomes remain challenging owing to the exceptional genetic plasticity these viruses. Because high mutation and recombination rates, genome replication by viral RNA-dependent polymerases leads populations closely related viruses, so-called "quasispecies." Standard (short-read) sequencing technologies are ill-suited reconstruct large numbers full-length haplotypes (1) (2) subgenome-length (sg) RNAs composed noncontiguous regions. Here, we used a full-length,...
In recent years, massively parallel complementary DNA sequencing (RNA [RNA-Seq]) has emerged as a fast, cost-effective, and robust technology to study entire transcriptomes in various manners. particular, for non-model organisms the absence of an appropriate reference genome, RNA-Seq is used reconstruct transcriptome de novo. Although novo assembly been on rise recently new tools are frequently developing, there still knowledge gap about which software should be build comprehensive...
Despite the demonstrated functional importance of gut microbes, our understanding how animals regulate their metabolism in response to nutritionally beneficial symbionts remains limited. Here, we elucidate African cotton stainer's (Dysdercus fasciatus) association with two actinobacterial and subsequently examine insect's transcriptional following symbiont elimination. In line bioassays demonstrating symbionts' contribution towards host fitness through supplementation B vitamins, comparative...
Near-surface groundwaters are prone to receive (in)organic matter input from their recharge areas and known harbor autotrophic microbial communities linked nitrogen sulfur metabolism. Here, we use multi-omic profiling gain holistic insights into the turnover of inorganic compounds, carbon fixation processes, organic processing in groundwater. We sampled biomass two superimposed aquifers via monitoring wells that follow groundwater flow its area through differences hydrogeochemical settings...
The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate in response environmental drivers or host organisms. Their mechanisms employed cope with oxidative stress largely unknown. Here, we utilized genome-resolved metagenomics investigate the adaptive genome repertoire oxic anoxic groundwaters, infer putative ranges.Within six groundwater wells, was most dominant (up 79%)...
Abstract The terrestrial subsurface contains nearly all of Earth’s freshwater reserves and harbours the majority our planet’s total prokaryotic biomass. Although genetic surveys suggest these organisms rely on in situ carbon fixation, rather than photosynthetically derived organic transported from surface environments, direct measurements fixation are absent. Using an ultra-low level 14 C-labelling technique, we estimate rates a carbonate aquifer. We find similar to those measured...
Taxonomic classification, that is, the assignment to biological clades with shared ancestry, is a common task in genetics, mainly based on genome similarity search of large databases. The classification quality depends heavily database, since representative relatives must be present. Many genomic sequences cannot classified at all or only high misclassification rate. Here we present BERTax, deep neural network program natural language processing precisely classify superkingdom and phylum DNA...
The Rfam database, a widely used repository of non-coding RNA families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion Rfamseq to 26 106 genomes, 76% increase, incorporating latest UniProt reference proteomes and additional viral genomes. Sixty-five families were enhanced using experimentally determined 3D structures, improving accuracy consensus secondary structures annotations. R-scape covariation analysis was refine...
Lichtheimia species are the second most important cause of mucormycosis in Europe. To provide broader insights into molecular basis pathogenicity-associated traits basal Mucorales, we report full genome sequence L. corymbifera and compared it to Rhizopus oryzae, common worldwide. The assembly encompasses 33.6 MB 12,379 protein-coding genes. This study reveals four major differences R. oryzae: (i) presence an highly elevated number gene duplications which unlike oryzae not due whole...
Telomerase is a ribonucleoprotein with an intrinsic telomerase RNA (TER) component. Within yeasts, TER remarkably large and presents little similarity in secondary structure to vertebrate or ciliate TERs. To better understand the evolution of fungal telomerase, we identified 74 TERs from Pezizomycotina Taphrinomycotina subphyla, sister clades budding yeasts. We initially Neurospora crassa using novel deep-sequencing–based approach, homologous sequences available genome databases by...
Abstract Many disciplines, from human genetics and oncology to plant breeding, microbiology virology, commonly face the challenge of analyzing rapidly increasing numbers genomes. In case Homo sapiens , number sequenced genomes will approach hundreds thousands in next few years. Simply scaling up established bioinformatics pipelines not be sufficient for leveraging full potential such rich genomic datasets. Instead, novel, qualitatively different computational methods paradigms are needed. We...
Abstract Candida glabrata is the second most common pathogenic species and has emerged as a leading cause of nosocomial fungal infections. Its reduced susceptibility to antifungal drugs its close relationship Saccharomyces cerevisiae make it an interesting research focus. Although genome sequence was published in 2004, little known about transcriptional dynamics. Here, we provide detailed RNA-Seq-based analysis transcriptomic landscape C. nutrient-rich media, well under nitrosative stress...
Organism aging is characterized by increased inflammation and decreased stem cell function, yet the relationship between these factors remains incompletely understood. This study shows that aged hematopoietic progenitor cells (HSPCs) exhibit ground-stage NF-κB activity, which enhances their responsiveness to undergo differentiation loss of self-renewal in response inflammation. The identifies Rad21/cohesin as a critical mediator signaling, increases chromatin accessibility vicinity target...
Zika virus (ZIKV) is an arthropod-borne emerging pathogen causing febrile illness. ZIKV associated Guillain-Barré syndrome and other neurological complications. Infection during pregnancy with complications developmental abnormalities collectively defined as congenital syndrome. There still no vaccine or specific treatment for infection. To identify host factors that can rescue cells from infection, we used a genome-scale CRISPR activation screen. Our highly ranking hits included short list...
ABSTRACT Bats serve as a reservoir for various, often zoonotic viruses, including significant human pathogens such Ebola and influenza viruses. However, unknown reasons, viral infections rarely cause clinical symptoms in bats. A tight control of replication by the host innate immune defense might contribute to this phenomenon. Transcriptomic studies revealed presence interferon-induced antiviral myxovirus resistance (Mx) proteins bats, but detailed functional aspects have not been assessed....