A5016549644- Genomics and Phylogenetic Studies
- Protein Structure and Dynamics
- Genetic Mapping and Diversity in Plants and Animals
- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- Circular RNAs in diseases
- Enzyme Structure and Function
- Epigenetics and DNA Methylation
- Bioinformatics and Genomic Networks
- Gut microbiota and health
- Dermatology and Skin Diseases
- Machine Learning in Bioinformatics
- Genetic Associations and Epidemiology
- Molecular Biology Techniques and Applications
- Advanced Proteomics Techniques and Applications
- RNA regulation and disease
- Genomics and Rare Diseases
- Human-Animal Interaction Studies
- Bacteriophages and microbial interactions
- Forensic and Genetic Research
- Digestive system and related health
- Cancer Genomics and Diagnostics
- Sarcoma Diagnosis and Treatment
- Polyamine Metabolism and Applications
- Metabolism and Genetic Disorders
University of Lübeck
2015-2025
Research Center Borstel - Leibniz Lung Center
2023-2025
University of Duisburg-Essen
2012-2024
Institute for Integrative and Experimental Genomics
2015-2022
Centrum Wiskunde & Informatica
2009-2013
Max Planck Institute for Informatics
2010
Charité - Universitätsmedizin Berlin
2009
Abstract Introduction Genome‐wide association studies have led to numerous genetic loci associated with Alzheimer's disease (AD). Whole‐genome sequencing (WGS) now permits genome‐wide analyses identify rare variants contributing AD risk. Methods We performed single‐variant and spatial clustering–based testing on (minor allele frequency [MAF] ≤1%) in a family‐based WGS‐based study of 2247 subjects from 605 multiplex families, followed by replication 1669 unrelated individuals. Results...
Abstract We present Bioconda ( https://bioconda.github.io ), a distribution of bioinformatics software for the lightweight, multiplatform and language-agnostic package manager Conda. Currently, offers collection over 3000 packages, which is continuously maintained, updated, extended by growing global community more than 200 contributors. improves analysis reproducibility allowing users to define isolated environments with defined versions, all are easily installed managed without...
Like its human counterpart, canine atopic dermatitis (cAD) is a chronic relapsing condition; thus, most cAD-affected dogs will require lifelong treatment to maintain an acceptable quality of life. A potential intervention modulation the composition gut microbiota, and in fact, probiotic has been proposed tried (AD) patients. Since are currently receiving intensive medical care, this be same option for dogs, while evidence dysbiosis cAD still missing, although skin microbial profiling...
The pathogenesis of T-cell large granular lymphocytic leukemia (T-LGL) is poorly understood, as STAT3 mutations are the only known frequent genetic lesions. Here, we identified non-synonymous alterations in TNFAIP3 tumor suppressor gene 3 39 T-LGL. In two cases these were somatic mutations, one case origin was likely. A further harbored a SNP that risk allele for autoimmune diseases and B cell lymphomas. Thus, represent recurrent lesions T-LGL affect about 8% cases, likely contributing to...
<h3>Objective</h3> A recent large-scale study in multiple sclerosis (MS) using the ImmunoChip platform reported on 11 loci that showed suggestive genetic association with MS. Additional data sufficiently sized and independent sets are needed to assess whether these represent genuine MS risk factors. <h3>Methods</h3> The lead SNPs of all were genotyped 10 796 cases 793 controls from Germany, Spain, France, Netherlands, Austria Russia, previously cohorts. Association analyses performed...
Abstract Exploration of genetic variant-to-gene relationships by quantitative trait loci such as expression QTLs is a frequently used tool in genome-wide association studies. However, the wide range public QTL databases and lack batch annotation features complicate comprehensive GWAS results. In this work, we introduce “Qtlizer” for annotating lists variants human with associated changes gene protein abundance using an integrated database published QTLs. Features include incorporation...
A small number of de novo assembled human genomes have been reported to date, and few complemented with population-based genetic variation, which is particularly important for North Africa, a region underrepresented in current genome-wide references. Here, we combine long- short-read whole-genome sequencing data recent assembly approaches into an Egyptian genome. The demonstrates well-balanced quality metrics variant phasing via linked reads haploblocks, associate gene expression changes...
Visceral leishmaniasis (VL) is a fatal parasitic disease if untreated. Treatment options of VL diminish due to emerging drug resistance. Although the principal host cells for multiplication Leishmania are macrophages, neutrophils first infected with parasites rapidly after parasite inoculation. can survive in despite potent antimicrobial effector functions that eliminate parasites. Recently, growing field immunometabolism provided strong evidence therapeutic potential targeting metabolic...
Background: X-linked dystonia-parkinsonism (XDP) is an adult-onset neurodegenerative disorder characterized by progressive dystonia and parkinsonism. It caused a SINE-VNTR-Alu (SVA) retrotransposon insertion in the TAF1 gene with polymorphic (CCCTCT)n domain that acts as genetic modifier of disease onset expressivity. Methods: Herein, we used Nanopore sequencing to investigate SVA variability methylation. We blood-derived DNA from 96 XDP patients for amplicon-based deep validated it fragment...
Mycobacterium tuberculosis is well adapted to survive and persist in the infected host, escaping host's immune response. Since polyamines such as spermine, which are synthesized by macrophages, able inhibit growth of M. tuberculosis, pathogen needs strategies cope with these toxic metabolites. The actinomycete Streptomyces coelicolor, a close relative makes use gamma-glutamylation pathway functionally neutralize spermine. We therefore considered whether similar would be functional...
Abstract Introduction Risk stratification of children with ependymomas the posterior fossa in current therapeutic protocols is mainly based on clinical criteria. We aimed to identify independent outcome predictors for this disease entity by a systematic integrated analysis clinical, histological and genetic information defined cohort patients treated according German HIT protocols. Methods Tumor samples 134 aged 0.2–15.9 years between 1999 2010 were analyzed features including mitotic...
Abstract Motivation: Structural alignments of proteins are important for identification structural similarities, homology detection and functional annotation. The alignment problem is well studied computationally difficult. Many different scoring schemes similarity as many algorithms finding high-scoring have been proposed. Algorithms using contact map overlap (CMO) function currently the only practical able to compute provably optimal alignments. Results: We propose a new mathematical model...
CSA is a web server for the computation, evaluation and comprehensive comparison of pairwise protein structure alignments.Its exact alignment engine computes either optimal, top-scoring alignments or heuristic with quality guarantee inter-residue distance-based scorings contact map overlap, PAUL, DALI MATRAS.These additional, uploaded are compared using number measures intuitive visualizations.CSA brings new insight into structural relationship pairs under investigation valuable tool...
We present a mathematical model and exact algorithm for optimally aligning protein structures using the DALI scoring model. This is based on comparing interresidue distance matrices of proteins used in popular software tool, heuristic method structure alignment. Our extend an integer linear programming approach that has been previously applied related, but simpler, contact map overlap problem. To this end, we introduce novel type constraint handles negative score values relax it Lagrangian...
ABSTRACT Mycobacterium tuberculosis is well adapted to survive and persist in the infected host, escaping host immune response. Since polyamines, which are synthesized by macrophages able inhibit growth of M. , pathogen needs strategies cope with toxic spermine. The actinomycete Streptomyces coelicolor closely related makes use a gamma-glutamylation pathway functionally neutralize We therefore considered whether similar would be functional . In current study we demonstrated that was...