A5001448895- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Mass Spectrometry Techniques and Applications
- Cancer Immunotherapy and Biomarkers
- Immunotherapy and Immune Responses
- Cutaneous lymphoproliferative disorders research
- Autoimmune Bullous Skin Diseases
- Dermatology and Skin Diseases
- T-cell and B-cell Immunology
- Lymphoma Diagnosis and Treatment
- CAR-T cell therapy research
- Immune Cell Function and Interaction
- Bioinformatics and Genomic Networks
- IL-33, ST2, and ILC Pathways
- Gene expression and cancer classification
- Advanced Biosensing Techniques and Applications
- Hair Growth and Disorders
- Scientific Computing and Data Management
- Biomedical Text Mining and Ontologies
- Asthma and respiratory diseases
- Urticaria and Related Conditions
- Machine Learning in Bioinformatics
- Nail Diseases and Treatments
- Genomics and Phylogenetic Studies
- Fungal Infections and Studies
Medical University of Vienna
2015-2024
European Bioinformatics Institute
2015-2024
Universitätszahnklinik Wien
2021-2024
Vienna General Hospital
2011-2021
Wellcome Trust
2011-2020
University Dermatology
2020
National Institute of Allergy and Infectious Diseases
2015
Austrian Academy of Sciences
2012
Centro de Ingeniería Genética y Biotecnología
2012
CeMM Research Center for Molecular Medicine
2012
The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data, and one founding members global ProteomeXchange (PX) consortium. In this manuscript, we summarize developments in PRIDE resources related tools since previous update manuscript was published Nucleic Acids Research 2016. last 3 years, public sharing through (as part PX) has definitely become norm field. parallel, re-use increased...
The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories mass spectrometry (MS)-based proteomics data. Since beginning 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) new archival system, replacing original database. Here we summarize developments in resources and related tools since previous update manuscript Database Issue 2013. constitutes a complete redevelopment PRIDE, comprising storage backend, submission system web interface, among other...
The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of most prominent data repositories mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in PRIDE and related tools. First, provide up-to-date statistics content, splitting figures by groups organisms species, including peptide protein identifications, post-translational modifications. We then describe tools that are part submission...
The Reactome Knowledgebase (https://reactome.org), an Elixir core resource, provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans, including both hereditary acquired disease processes. are annotated as ordered network transformations single consistent data model. thus functions digital archive human tool for discovering functional relationships such gene expression profiles or somatic mutation catalogs from tumor...
BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. allows labs of all sizes to easily install software, maintain multiple versions the same software combine tools into powerful analysis pipelines. based on popular projects Docker rkt frameworks, that allow be installed executed under isolated controlled environment. Also, it infrastructure basic guidelines create, manage...
The Reactome Knowledgebase (https://reactome.org), an Elixir and GCBR core biological data resource, provides manually curated molecular details of a broad range normal disease-related processes. Processes are annotated as ordered network transformations in single consistent model. thus functions both digital archive human processes tool for discovering functional relationships such gene expression profiles or somatic mutation catalogs from tumor cells. Here we review progress towards...
Abstract Tumor associated inflammation predicts response to immune checkpoint blockade in human melanoma. Current theories on regulation of center anti-tumor T cell responses. Here we show that tumor B cells are vital melanoma inflammation. Human express pro- and anti-inflammatory factors differentiate into plasmablast-like when exposed autologous secretomes vitro. This phenotype can be reconciled melanomas where also cell-recruiting chemokines CCL3, CCL4, CCL5. Depletion patients by...
Pathway analyses are key methods to analyze 'omics experiments. Nevertheless, integrating data from different technologies and species still requires considerable bioinformatics knowledge.Here we present the novel ReactomeGSA resource for comparative pathway of multi-omics datasets. can be used through Reactome's existing web interface R Bioconductor package with explicit support scRNA-seq data. Data is automatically mapped a common space. Public ExpressionAtlas Single Cell directly...
Anti-PD-1 therapy is used as a front-line treatment for many cancers, but mechanistic insight into this resistance still lacking. Here we generate humanized (Hu)-mouse melanoma model by injecting fetal liver-derived CD34+ cells and implanting autologous thymus in immune-deficient NOD-scid IL2Rγnull (NSG) mice. Reconstituted Hu-mice are challenged with HLA-matched melanomas treated anti-PD-1, which results restricted tumor growth not complete regression. Tumor RNA-seq, multiplexed imaging...
Therapeutic options for autoimmune diseases typically consist of broad and targeted immunosuppressive agents. However, sustained clinical benefit is rarely achieved, as the disease phenotype usually returns after cessation treatment. To better understand tissue-resident immune memory in human disease, we investigated patients with atopic dermatitis (AD) who underwent short-term or long-term treatment IL-4Rα blocker dupilumab. Using multi-omics profiling single-cell RNA sequencing multiplex...
We report the release of mzIdentML, an exchange standard for peptide and protein identification data, designed by Proteomics Standards Initiative. The format was developed Initiative in collaboration with instrument software vendors, developers major open-source projects proteomics. Software implementations have been to enable conversion from most popular proprietary formats, mzIdentML will soon be supported public repositories. These developments proteomics scientists start working...
The original PRIDE Inspector tool was developed as an open source standalone to enable the visualization and validation of mass-spectrometry (MS)-based proteomics data before submission or already publicly available in Proteomics Identifications (PRIDE) database. initial implementation focused on visualizing by supporting XML format a direct access private (password protected) public experiments PRIDE.The ProteomeXchange (PX) Consortium has been set up better integration existing...
The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate sharing in mass spectrometry (MS)-based proteomics. These allow researchers report their complete results a unified way. However, at present, there is no format describe the final qualitative and quantitative for proteomics metabolomics experiments simple tabular format. Many downstream analysis use cases are only concerned with of an experiment require easily accessible format, compatible...
Abstract In melanoma, therapies with inhibitors to oncogenic BRAF V600E are highly effective but responses often short-lived due the emergence of drug-resistant tumor subpopulations. We describe here a mechanism acquired drug resistance through microenvironment, which is mediated by human tumor-associated B cells. Human melanoma cells constitutively produce growth factor FGF-2, activates tumor-infiltrating IGF-1. B-cell-derived IGF-1 critical for melanomas and MEK heterogeneous...
The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to database. However, after much user feedback, it was noted that had some limitations and could not handle several requirements were now becoming commonplace. This prompted us design implement a whole new suite tools would build on successes allow users generate submission-ready, well-annotated XML files. 2 allows convert search result files into (the format needed for...
BackgroundAlthough ample knowledge exists about phenotype and function of cutaneous T lymphocytes, much less is known the lymphocytic components skin's innate immune system.ObjectiveTo better understand biologic role lymphoid cells (ILCs), we investigated their phenotypic molecular features under physiologic (normal human skin [NHS]) pathologic (lesional patients with atopic dermatitis [AD]) conditions.MethodsSkin punch biopsies reduction sheets as well blood specimens were obtained from...
There is increasing evidence that tertiary lymphoid structures (TLS) control not only local adaptive B cell responses at melanoma tumor sites but also the cellular composition and function of other immune cells. In human melanoma, however, a comprehensive analysis TLS phenotypes, density spatial distribution different disease stages lacking. Here we used 7-color multiplex immunostaining whole tissue sections from 103 samples to characterize phenotypes along expression established...
Abstract Pathway databases provide descriptions of the roles proteins, nucleic acids, lipids, carbohydrates, and other molecular entities within their biological cellular contexts. Pathway‐centric views these may allow for discovery unexpected functional relationships in data such as gene expression profiles somatic mutation catalogues from tumor cells. For this reason, there is a high demand high‐quality pathway associated tools. The Reactome project (a collaboration between Ontario...
Abstract Dupilumab, an IL4R-blocking antibody, has shown clinical efficacy for atopic dermatitis (AD) treatment. In addition to conjunctivitis/blepharitis, the de novo appearance of head/neck is now recognized as a distinct side effect, occurring in up 10% patients. Histopathological features from AD suggest drug but exact underlying mechanisms remain unknown. We profiled punch biopsies dupilumab-associated head and neck (DAHND) by using single-cell RNA sequencing compared data with...