A5066509741- Rheumatoid Arthritis Research and Therapies
- Bioinformatics and Genomic Networks
- Metabolomics and Mass Spectrometry Studies
- Systemic Lupus Erythematosus Research
- RNA Research and Splicing
- Microbial Metabolic Engineering and Bioproduction
- interferon and immune responses
- Photosynthetic Processes and Mechanisms
- Monoclonal and Polyclonal Antibodies Research
- Genomics and Phylogenetic Studies
- Viral Infections and Immunology Research
- Histone Deacetylase Inhibitors Research
- Lymphoma Diagnosis and Treatment
- Image and Video Quality Assessment
- Microbial Community Ecology and Physiology
- Chromosomal and Genetic Variations
- Plant Reproductive Biology
- Protein Degradation and Inhibitors
- Plant and animal studies
- Cancer, Hypoxia, and Metabolism
- Plant Molecular Biology Research
- Mycotoxins in Agriculture and Food
- Machine Learning in Bioinformatics
- Cytokine Signaling Pathways and Interactions
- Wheat and Barley Genetics and Pathology
Medical University of Vienna
2017-2022
Center for Rheumatology
2019
Austrian Academy of Sciences
2013-2018
Gregor Mendel Institute of Molecular Plant Biology
2012-2018
Vienna Biocenter
2016-2017
University of Vienna
2007-2016
Forschungszentrum Telekommunikation Wien
2011
University Medical Center Freiburg
2010
University of Potsdam
2009
Max Planck Institute of Molecular Plant Physiology
2009
Protein secretion systems play a key role in the interaction of bacteria and hosts. EffectiveDB (http://effectivedb.org) contains pre-calculated predictions bacterial secreted proteins intact systems. Here we describe major update database, which was previously featured NAR Database Issue. bundles various tools to recognize Type III signals, conserved binding sites chaperones, IV peptides, eukaryotic-like domains subcellular targeting signals host. Beyond analysis arbitrary protein sequence...
In plants, gametogenesis occurs late in development, and somatic mutations can therefore be transmitted to the next generation. Longer periods of growth are believed result an increase number cell divisions before gametogenesis, with a concomitant arising due replication errors. However, there is little experimental evidence addressing how many occur gametogenesis. Here, we measured loss telomeric DNA accumulation errors Arabidopsis short long life spans determine replications lineages...
Recent evidence suggests that metabolic changes play a pivotal role in the biology of cancer and particular renal cell carcinoma (RCC). Here, global metabolite profiling approach was applied to characterize pool RCC normal tissue. Advanced decision tree models were signature explore features metastasized tumours. The findings validated second independent dataset. Vitamin E derivates metabolites glucose, fatty acid, inositol phosphate metabolism determined profile RCC. α-tocopherol, hippuric...
Abstract Background Analyzing differential-gene-expression data in the context of protein-interaction networks (PINs) yields information on functional cellular status. PINs can be formally represented as graphs, and approximating undirected graphs allows network properties to characterized using well-established graph measures. This paper outlines features derived from 29 studies differential gene expression cancer. For each study number differentially regulated genes was determined used a...
Quality of Experience (QoE) has gained enormous attention during the recent years. So far, most existing QoE research focused on audio and video streaming applications, although HTTP traffic carries majority in residential broadband Internet. However, models for this domain do not consider temporal dynamics or historical experiences user's satisfaction while consuming a certain service. This psychological influence factor past experience is referred to as memory effect. The first...
Single Nucleotide Polymorphisms (SNPs) are one of the largest sources new data in biology. In most papers, SNPs between individuals visualized with Principal Component Analysis (PCA), an older method for this purpose.
Anti-citrullinated protein antibodies (ACPA) and rheumatoid factor (RF) are the most commonly used diagnostic markers of arthritis (RA). These predominantly IgM or IgG isotype. Other subtypes both – particularly IgA isotypes- other autoantibodies such as RA33 have been repeatedly reported but their value has still not fully elucidated. Here, we investigated prevalence IgA, RF, ACPA in patients with RA. To determine specificity sensitivity sera from 290 RA (165 early 125 established disease),...
Rheumatoid arthritis (RA) is an autoimmune disease characterized by persistent synovial inflammation. The major drivers of inflammation are cytokines and chemokines. Among these molecules, TNF activates fibroblast-like synoviocytes (FLSs), which leads to the production inflammatory mediators. Here, we show that regulates expression transcription factor interferon regulatory 1 (IRF1) in human FLSs as well a transgenic mouse model. Transcriptomic analyses IRF1-deficient, TNF-stimulated define...
Although the transition to selfing in model plant Arabidopsis thaliana involved loss of self-incompatibility (SI) system, it clearly did not occur due fixation a single inactivating mutation at locus determining specificities SI (the S-locus). At least three groups divergent haplotypes (haplogroups), corresponding ancient functional S-alleles, have been maintained this locus, and extensive studies shown that all carry distinct mutations. However, historical process is well understood,...
Mycotoxins are secondary metabolites produced by certain fungi, posing significant health risks to humans and animals through contaminated food feed. These consequently the mycotoxins which they produce, strongly influenced weather, this shifts over time due climate change, leading more frequent severe events, such as heat waves, storms, heavy rainfall. This study investigates how long-term weather trends climatic factors impacted mycotoxin levels in corn samples a 17-year period (2006-2022)...
Due to the accelerating uptake of mobile broadband services, Quality Experience (QoE) assessment and optimization for wireless networks has become a topic vital importance. In this field, subjective quality evaluation methods based on MOS (Mean Opinion Score) are most widely used approaches understanding measuring perceived performance. However, while these have been proven reliably quantify users' degrees satisfaction, they do not sufficiently address following important question: "Which...
Experimental high-throughput analysis of molecular networks is a central approach to characterize the adaptation plant metabolism environment. However, recent studies have demonstrated that it hardly possible predict in situ metabolic phenotypes from experiments under controlled conditions, such as growth chambers or greenhouses. This particularly due high variance samples induced by environmental fluctuations. An functional metabolome interpretation field would be desirable order able...
Transposable elements (TEs) are common mobile DNA present in nearly all genomes. Since the movement of TEs within a genome can sometimes have phenotypic consequences, an accurate report TE actions is desirable. To this end, we developed TE-Locate, computational tool that uses paired-end reads to identify novel locations known TEs. TE-Locate utilize either database sequences, or annotated reference sequence interest. This makes useful search for any sequence, including retrotransposed gene...
TNF-induced activation of fibroblast-like synoviocytes (FLS) is a critical determinant for synovial inflammation and joint destruction in RA. The detrimental role TNF-receptor 1 (TNFR1) has thoroughly been characterized. contributions TNFR2, however, are largely unknown. This study was performed to delineate the TNFR2 human FLS activation.TNFR2 expression tissue samples determined by immunohistochemistry. Expression silenced using RNAi or CRISPR/Cas9 technologies. Global transcriptional...
Abstract Objectives To develop and test the reliability of a new semiquantitative scoring system for assessment cartilage changes by ultrasound in web-based exercise as well patient patients with RA. Methods A taskforce Outcome Measures Rheumatology Ultrasound Working Group performed systematic literature review on US RA, followed Delphi survey system, finally exercise. For exercise, members scored dataset anonymized static images MCP joints RA healthy controls, which also contained...
Abstract Metagenomics provides quantitative measurements for microbial species over time. To obtain a global overview of an experiment and to explore the full potential given dataset, intuitive interactive visualization tools are needed. Therefore, we established BioSankey visualize in microbiome studies time as Sankey diagram. These diagrams embedded into project-specific webpage which depends only on JavaScript Google API allow searches interesting without requiring web server or...
The era of next-generation sequencing has mounted the foundation many gene expression studies. In rheumatoid arthritis research, this led to discovery important candidate genes which offered novel insights into mechanisms and their possible roles in cure disease. last years, data generation outstripped analysis while studies focused on specific aspects disease, a global picture disease is not yet accomplished. Here, we analyzed compared collection information from healthy individuals...
Abstract Motivation: The rapidly growing number of available prokaryotic genome sequences requires fully automated and high-quality software solutions for their initial re-annotation. Here we present ConsPred, a annotation framework that performs intrinsic gene predictions, homology searches, predictions non-coding genes as well CRISPR repeats integrates all evidence into consensus annotation. ConsPred achieves comprehensive, annotations based on rules priorities, similar to decision-making...
Wheat represents one of the most widely consumed cereals worldwide. Cultivated in winter and spring, it is vulnerable to an array different pathogens, including fungi, which are managed largely through in-field application fungicides. During this study, a 4-year field investigation (2018–2021) was performed France, aiming assess efficacy fungicide treatment reduce mycotoxin contamination common durum wheat. Several commercially available fungicides were applied via sprayers. Concentrations...
Identification of trajectories radiographic damage in rheumatoid arthritis (RA) by clustering patients according to the shape their curve Sharp-van der Heijde scores (SHSs) over time. Developing models predict progression cluster from baseline characteristics.Patient-level data a 2-year period five large randomised controlled trials on tumour necrosis factor inhibitors RA were used. SHSs clustered shape-respecting manner identify distinct clusters progression. Characteristics within...