A5065931843- Cancer Genomics and Diagnostics
- Head and Neck Cancer Studies
- Chromatin Remodeling and Cancer
- Gut microbiota and health
- Genetic diversity and population structure
- Dermatology and Skin Diseases
- Lymphoma Diagnosis and Treatment
- Pancreatic and Hepatic Oncology Research
- Cutaneous lymphoproliferative disorders research
- Genomics and Phylogenetic Studies
- Diet and metabolism studies
- Cancer-related molecular mechanisms research
- Chromosomal and Genetic Variations
- Viral-associated cancers and disorders
- Autoimmune Bullous Skin Diseases
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Animal Behavior and Reproduction
- CAR-T cell therapy research
- Fungal Infections and Studies
- Cancer Cells and Metastasis
- RNA modifications and cancer
- Urticaria and Related Conditions
- Clostridium difficile and Clostridium perfringens research
- Probiotics and Fermented Foods
- Genetic factors in colorectal cancer
University of Lübeck
2016-2025
University Hospital Schleswig-Holstein
2021-2025
Institute for Integrative and Experimental Genomics
2019-2023
HistoGenetics (United States)
2022
Max Planck Institute for Evolutionary Biology
2014-2017
Uppsala University
2009-2016
Max Planck Institute for Developmental Biology
2012-2016
Max Planck Society
2012-2013
The genome of the zebra finch — a songbird and model for study vertebrate brain, behaviour evolution has been sequenced. Its comparison with chicken genome, only other bird available, shows that genes neural function implicated in cognitive processing song have rapidly evolving lineage. also vocal communication engages much brain transcriptome identifies potential integrator microRNA signals linked to communication. studying Comparison are Moreover, brain. is an important organism several...
Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied are important avian speciation models that show pre- as well postzygotic isolation. We sequenced assembled 1.1-Gb genome, physically mapped assembly chromosomes using a low-density linkage map re-sequenced population samples each species. Here we species differentiation highly heterogeneous with approximately 50 'divergence islands'...
During the last few years, DNA and RNA sequencing have started to play an increasingly important role in biological medical applications, especially due greater amount of data yielded from new machines enormous decrease costs. Particularly, Illumina/Solexa has had increasing impact on gathering model non-model organisms. However, accurate easy use tools for quality filtering not yet been established. We present ConDeTri, a method content dependent read trimming next generation using scores...
Transcriptome Shotgun Sequencing (RNA-seq) has been readily embraced by geneticists and molecular ecologists alike. As with all high-throughput technologies, it is critical to understand which analytic strategies are best suited parameters may bias the interpretation of data. Here we use a comprehensive simulation approach explore how various features transcriptome (complexity, degree polymorphism π, alternative splicing), technological processing (sequencing error ε, library normalization)...
Abstract Background Obtaining a draft genome sequence of the zebra finch ( Taeniopygia guttata ), second bird to be sequenced, provides necessary resource for whole-genome comparative analysis gene evolution in non-mammalian vertebrate lineage. To analyze basic molecular evolutionary processes during avian evolution, and contrast these with situation mammals, we aligned protein-coding sequences 8,384 1:1 orthologs chicken, finch, lizard three mammalian species. Results We found clear...
IL-17A has been identified as key regulatory molecule in several autoimmune and chronic inflammatory diseases followed by the successful use of anti-IL-17 therapy, e.g. ankylosing spondylitis psoriasis. Bullous pemphigoid (BP) is most frequent blistering disease with a high need for more specific, effective safe treatment options. The aim this study was to clarify pathophysiological importance BP. We found elevated numbers IL-17A+ CD4+ lymphocytes peripheral blood BP patients CD3+ cells...
For over a century, the live bearing guppy, Poecilia reticulata, has been used to study sexual selection as well local adaptation. Natural guppy populations differ in many traits that are of intuitively adaptive significance such ornamentation, age at maturity, brood size and body shape. Water depth, light supply, food resources predation regime shape these traits, barrier waterfalls often separate contrasting environments same river. We have assembled annotated genome an inbred single...
Significance Increasing evidence suggests a role for the gut microbiome in autoimmune diseases, including multiple sclerosis. However, impact of natural genetic variation mammalian host and other underlying mechanisms has been largely overlooked. We used mouse model diversity to explore interactions between microbiome. Our results demonstrate complex interplay genotype microbiota disease, identify single commensal species capable modifying disease susceptibility genetically susceptible host....
Selection modulates gene sequence evolution in different ways by constraining potential changes of amino acid sequences (purifying selection) or favoring new and adaptive genetic variants (positive selection). The number nonsynonymous differences a pair protein-coding can be used to quantify the mode strength selection. To control for regional variation substitution rates, proportionate (dN) is divided synonymous (dS). resulting ratio (dN/dS) widely indicator functional divergence identify...
Next-generation sequencing technology provides an attractive means to obtain large-scale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across avian genome, we performed brain transcriptome using Roche 454 10 different non-model species. Contigs from de novo assemblies were aligned two available reference genomes, chicken zebra finch. In total, identified 6499 genes all species, with approximately 1000...
Resolving the phylogenetic relationships among birds is a classical problem in systematics, and this particularly so when it comes to understanding Neoaves. Previous inference of has been limited mitochondrial genomes or few nuclear genes. Here, we apply deep brain transcriptome sequencing nine bird species (several passerines, hummingbirds, dove, parrot, emu), using next-generation technology understand features evolution how affects inference, combine with data from two first generation...
Sexually dimorphic phenotypes are generally associated with differential gene expression between the sexes. The study of molecular evolution and genomic location these differentially expressed, or sex-biased, genes is important for understanding inter-sexual divergence under sex-specific selection pressures. Teleost fish provide a unique opportunity to examine this in presence variable sex-determination mechanisms recent origin. guppy, Poecilia reticulata, displays sexual dimorphism size,...
Abstract Convergent evolution represents one of the best lines evidence for adaptation, but few cases phenotypic convergence are understood at genetic level. Guppies inhabiting Northern Mountain Range Trinidad provide a classic example convergent evolution, where adaptation to low or high predation environments has been found variety traits. A major advantage this system is possibility long‐term experimental studies in nature, including transplantation from sites. We used genome scans...
Endogenous circadian clocks regulate 24-h rhythms of physiology and behavior. Circadian rhythm disruption (CRD) is suggested as a risk factor for inflammatory bowel disease. However, the underlying molecular mechanisms remain unknown. Intestinal biopsies from Per1/2 mutant wild-type (WT) mice were investigated by electron microscopy, immunohistochemistry, bromodeoxyuridine pulse-chase experiments. TNF-α was injected intraperitoneally, with or without necrostatin-1, into rhythmic externally...
Relatively little is known about the character of gene expression evolution as species diverge. It for instance unclear if generally evolves in a clock-like manner (by stabilizing selection or neutral evolution) there are frequent episodes directional selection. To gain insights into evolutionary divergence expression, we sequenced and compared transcriptomes multiple organs from population samples collared (Ficedula albicollis) pied flycatchers (F. hypoleuca), two which diverged less than...
Abstract Epstein–Barr virus (EBV)-associated diffuse large B-cell lymphoma not otherwise specified (DLBCL NOS) constitute a distinct clinicopathological entity in the current World Health Organization (WHO) classification. However, its genomic features remain sparsely characterized. Here, we combine whole-genome sequencing (WGS), targeted amplicon (tNGS), and fluorescence situ hybridization (FISH) from 47 EBV + DLBCL (NOS) cases to delineate landscape of this rare disease. Integrated WGS...
Human telomere biology disorders (TBD)/short syndromes (STS) are heterogeneous caused by inherited loss-of-function mutations in telomere-associated genes. Here, we identify 3 germline heterozygous missense variants the RPA1 gene 4 unrelated probands presenting with short telomeres and varying clinical features of TBD/STS, including bone marrow failure, myelodysplastic syndrome, T- B-cell lymphopenia, pulmonary fibrosis, or skin manifestations. All cluster to DNA-binding domain A protein. is...
Sex chromosome divergence, which follows the cessation of recombination and degeneration sex-limited chromosome, can cause a reduction in expression level for sex-linked genes heterozygous sex, unless some mechanisms dosage compensation develops to counter gene dose. Because large-scale perturbations levels arising from changes dose might have strong deleterious effects, evolutionary response should be strong. However, birds at least other female heterogametic organisms, wholesale sex does...
Gut microbial communities are key mediators of health and disease have the capacity to drive pathogenesis diverse complex diseases including metabolic chronic inflammatory as well aging. Host genetics is also a major determinant phenotypes, whereby two different genomes play role, nuclear (nDNA)- mitochondrial genome (mtDNA). We investigated impact mutations in mtDNA on gut microbiota using conplastic mouse strains exhibiting distinct their an identical nDNA. Each three strain tested harbors...
Non-alcoholic fatty liver disease (NAFLD) is the most common chronic and associated with an enhanced risk for cardiovascular diseases mortality. NAFLD can progress from simple hepatic steatosis to non-alcoholic steatohepatitis (NASH). However, mechanisms predisposing this progression remain undefined. Notably, mitochondrial dysfunction a finding in patients NASH. Due lack of appropriate experimental animal models, it has not been evaluated whether plays causative role development To...
Experimental models of neuroendocrine tumor disease are scarce, with only a few existing cell lines pancreatic origin (panNET). Their molecular characterization has so far focused on the phenotype and cancer-related mutations, while transcription-based assessment their developmental malignant potential is lacking. In this study, we performed immunoblotting qPCR analysis neuroendocrine, epithelial, endocrine-related genes as well next-generation sequencing (NGS) microRNAs (miRs) three panNET...
Abstract Blastic plasmacytoid dendritic cell neoplasm (BPDCN) constitutes a rare and aggressive malignancy originating from cells (pDCs) with primarily cutaneous tropism followed by dissemination to the bone marrow other organs. We conducted genome-wide analysis of tumor methylome in an extended cohort 45 BPDCN patients supplemented WES RNA-seq as well ATAC-seq on selected cases. determined DNA methylation profile observed dramatic loss during malignant transformation early mature DCs...
Desmoglein 1 (DSG1) and desmoglein 3 (DSG3) are adhesion molecules that maintain intercellular connections between epidermal, hair follicle, mucosal keratinocytes. Autoantibodies (AAbs) targeting these ultimately lead to the blister formation characteristic of pemphigus vulgaris (PV) or foliaceus (PF). To investigate molecular events following autoantibody binding up 48 hours, we quantified transcriptome proteome dynamics during split in a human skin organ culture (HSOC) model for PV 2D...
Abstract In classic Hodgkin-lymphoma (cHL), only a few cases recur, and limited fraction of patients is primary-refractory to standard-polychemotherapy. Underlying genomic features unfavorable clinical courses remain sparsely characterized. Here, we investigated the characteristics primary-refractory/relapsed cHL in contrast with responders. Therefore, ultra-deep next-generation panel-sequencing was performed on total 59 FFPE-samples (20 responders, 26 relapsed (rHL: 11 initial-diagnosis, 15...