Johannes Griss

Johannes Griss
Medical University of Vienna | MedUni Vienna · Division of Immunology, Allergy and Infectious Skin Diseases

MD, Ph.D.

About

109
Publications
16,072
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
13,423
Citations
Introduction
Johannes Griss currently works at the Division of Immunology, Allergy and Infectious Skin Diseases, Medical University of Vienna. Johannes research focuses on algorithms for MS/MS based proteomics data analysis (spectrum clustering) and the integration of multi-omics biomedical datasets.

Publications

Publications (109)
Article
Full-text available
Spectrum clustering is a powerful strategy to minimize redundant mass spectra by grouping them based on similarity, with the aim of forming groups of mass spectra from the same repeatedly measured analytes. Each such group of near-identical spectra can be represented by its so-called consensus spectrum for downstream processing. Although several al...
Preprint
Full-text available
Spectrum clustering is a powerful strategy to minimize redundant mass spectral data by grouping highly similar mass spectra corresponding to repeatedly measured analytes. Based on spectrum similarity, near-identical spectra are grouped in clusters, after which each cluster can be represented by its so-called consensus spectrum for downstream proces...
Article
Full-text available
Background Automatic cell type identification is essential to alleviate a key bottleneck in scRNA-seq data analysis. While most existing classification tools show good sensitivity and specificity, they often fail to adequately not-classify cells that are missing in the used reference. Additionally, many tools do not scale to the continuously increa...
Article
Full-text available
The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics...
Article
Full-text available
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 and acquired disease processes. The processes are annotated as an ordered network of molecular transformations in a s...
Article
Background NSAID-exacerbated respiratory disease (N-ERD) comprises the triad of chronic rhinosinusitis with nasal polyps (CRSwNP), asthma and intolerance to inhibitors of the cyclooxygenase-1-enzyme. The impact of omalizumab on prevention of aspirin–induced hypersensitivity in N-ERD patients with and without atopic sensitization has not been thorou...
Article
We report the case of a female, 77 year old patient with multi‐localized skin infarctions following vaccination with mRNA‐1273 (Moderna). This phenomenon is to our knowledge otherwise only seen in infection‐associated purpura fulminans ‐ which was thoroughly ruled out in our patient. This report demonstrates that we need to be vigilant of a wider a...
Article
Full-text available
Background While ample knowledge exists about phenotype and function of cutaneous T lymphocytes, much less is known about the lymphocytic components of the skin‘s innate immune system. Objective To better understand the biologic role of cutaneous innate lymphoid cells (ILCs), we investigated their phenotypic and molecular features under physiologi...
Article
Full-text available
Activated antigen-experienced B cells play an unexpected complex role in anti-tumor immunity in human melanoma patients. However, correlative studies between B cell infiltration and tumor progression are limited by the lack of distinction between functional B cell subtypes. In this study, we examined a series of 59 primary and metastatic human cuta...
Chapter
Isobaric labeling has become an essential method for quantitative mass spectrometry based experiments. This technique allows high-throughput proteomics while providing reasonable coverage of protein measurements across multiple samples. Here, the analysis of isobarically labeled mass spectrometry data with a special focus on quality control and pot...
Article
Full-text available
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 of TLS phenotypes, density and spatial distribution at different disease stages is la...
Preprint
Full-text available
The amount of public proteomics data is increasing at an extraordinary rate. Hundreds of datasets are submitted each month to ProteomeXchange repositories, representing many types of proteomics studies, focusing on different aspects such as quantitative experiments, post-translational modifications, protein-protein interactions, or subcellular loca...
Article
Full-text available
Background: The role of tumor-associated B cells in human cancer is only starting to emerge. B cells typically undergo a series of developmental changes in phenotype and function, however, data on the composition of the B cell population in human melanoma are largely absent including changes during tumor progression and their potential clinical sig...
Article
Spectral similarity calculation is widely used in protein identification tools and mass spectra clustering algorithms while comparing theoretical or experimental spectra. The performance of the spectral similarity calculation plays an important role in these tools and algorithms especially in the analysis of large-scale datasets. Recently, deep lea...
Article
Full-text available
Atopic dermatitis (AD) typically starts in infancy or early childhood, showing spontaneous remission in a subset of patients, while others develop lifelong disease. Despite an increased understanding of AD, factors guiding its natural course are only insufficiently elucidated. We thus performed suction blistering in skin of adult patients with stab...
Article
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 of treatment. To better understand tissue-resident immune memory in human disease, we investigated patients with atopic dermati...
Article
Full-text available
Anti-PD-1 therapy is used as a front-line treatment for many cancers, but mechanistic insight into this therapy resistance is still lacking. Here we generate a humanized (Hu)-mouse melanoma model by injecting fetal liver-derived CD34 ⁺ cells and implanting autologous thymus in immune-deficient NOD- scid IL2Rγ null (NSG) mice. Reconstituted Hu-mice...
Preprint
Full-text available
Motivation Automatic cell type identification in scRNA-seq datasets is an essential method to alleviate a key bottleneck in scRNA-seq data analysis. While most existing tools show good sensitivity and specificity in classifying cell types, they often fail to adequately not-classify cells that are not present in the used reference. Results scTypeR...
Article
Full-text available
Pathway analyses are key methods to analyze 'omics experiments. Nevertheless, integrating data from different 'omics technologies and different species still requires considerable bioinformatics knowledge. Here we present the novel ReactomeGSA resource for comparative pathway analyses of multi-omics datasets. ReactomeGSA can be used through Reactom...
Preprint
Full-text available
Pathway analyses are key methods to analyse ‘omics experiments. Nevertheless, integrating data from different ‘omics technologies and different species still requires considerable bioinformatics knowledge. Here we present the novel ReactomeGSA resource for comparative pathway analyses of multi-omics datasets. ReactomeGSA can be used through Reactom...
Article
Full-text available
Prostate cancer (PCa) has a broad spectrum of clinical behavior; hence, biomarkers are urgently needed for risk stratification. Here, we aim to find potential biomarkers for risk stratification, by utilizing a gene co-expression network of transcriptomics data in addition to laser-microdissected proteomics from human and murine prostate FFPE sample...
Preprint
Full-text available
Motivation Spectrum clustering has been used to enhance proteomics data analysis: some originally unidentified spectra can potentially be identified and individual peptides can be evaluated to find potential mis-identifications by using clusters of identified spectra. The Phoenix Enhancer provides an infrastructure to analyze tandem mass spectra an...
Preprint
Full-text available
Prostate cancer (PCa) has a broad spectrum of clinical behaviour, hence biomarkers are urgently needed for risk stratification. We previously described the protective effect of STAT3 in a prostate cancer mouse model. By utilizing a gene co-expression network in addition to laser microdissected proteomics from human and murine prostate FFPE samples,...
Article
Full-text available
Tumor associated inflammation predicts response to immune checkpoint blockade in human melanoma. Current theories on regulation of inflammation center on anti-tumor T cell responses. Here we show that tumor associated B cells are vital to melanoma associated inflammation. Human B cells express pro- and anti-inflammatory factors and differentiate in...
Article
The order of enzymatic activity across Golgi cisternae is essential for complex molecule biosynthesis. However, an inability to separate Golgi cisternae has meant that the cisternal distribution of most resident proteins, and their underlying localization mechanisms, are unknown. Here, we exploit differences in surface charge of intact cisternae to...
Article
Full-text available
Label-free quantification has become a common-practice in many mass spectrometry-based proteomics experiments. In recent years, we and others have shown that spectral clustering can considerably improve the analysis of (primarily large-scale) proteomics datasets. We show that spectral clustering can also be used to infer additional peptide-spectrum...
Article
Full-text available
Reproducibility has become a major concern in biomedical research. In proteomics, bioinformatic workflows can quickly consist of multiple software tools each with its own set of parameters. Their usage involves the definition of often hundreds of parameters as well as data operations to ensure tool interoperability. Hence a manuscript’s methods sec...
Preprint
Full-text available
Tumor associated inflammation is one of important predictors of response to immune checkpoint blockade. Understanding molecular processes that regulate tumor inflammation is key to improve the efficacy of checkpoint blockade. Established mechanisms that underlie therapy response and resistance have centered on anti-tumor T cell responses. We show t...
Article
Full-text available
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 is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous...
Preprint
Full-text available
Mass spectrometry coupled with isobaric labelling provides fast large-scale comparison of protein abundances over multiple conditions. To date, no one-stop-shop software solution exists that enables non-bioinformatics experts to carry out the full analysis of the acquired raw data with minimal intervention. Mostly, pipelines for such analyses are b...
Article
The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further...
Poster
Full-text available
Introduction There is an increasing demand for approaches to integrate proteomics data with other ‘omics’ data types, especially genomics. In fact, current resources to integrate proteomics in a genome context are insufficient for large-scale studies. To bring the genomics and proteomics results into coherence, novel resources must be developed th...
Article
Full-text available
In this Viewpoint article, we discuss current and future applications of spectral clustering in the context of mass spectrometry‐based proteomics approaches. First of all, we are introducing the main algorithms and tools that can currently be used to perform spectral clustering. In addition, we explain its main applications and their use in current...
Article
Full-text available
In the recent benchmarking article entitled “Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra”, Rieder et al. compared several different approaches to cluster MS/MS spectra. While we certainly recognize the value of the manuscript, here, we report some shortcomings detected in the original analyses. For most analyses, the...
Article
Aims Immune checkpoint inhibitors have become a successful treatment in metastatic melanoma. The high response rates in a subset of patients suggest that a sensitive companion diagnostic test is required. The predictive value of programmed death ligand 1 (PD‐L1) staining in melanoma has been questioned due to inconsistent correlation with clinical...
Article
Full-text available
In melanoma, therapies with inhibitors to oncogenic BRAFV600E are highly effective but responses are often short-lived due to the emergence of drug-resistant tumor subpopulations. We describe here a mechanism of acquired drug resistance through the tumor microenvironment, which is mediated by human tumor-associated B cells. Human melanoma cells con...
Article
Background: Intravascular large B-cell lymphoma (IVLBCL) is a rare type of extranodal large B-cell lymphoma. It is characterized by the proliferation of tumour cells exclusively intraluminally in small blood vessels of different organs. The clinical manifestation depends on the type of organ affected, additionally, a haemophagocytic syndrome can b...
Article
Motivation: BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful ana...
Article
Full-text available
The authors wish to correct the affiliation of one of the authors. GerhardMayer's only affiliation should be ³Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany. He does NOT have a second affiliation at: ¹European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Camp...
Article
Mass spectrometry (MS) is the main technology used in proteomics approaches. However, on average, 75% of spectra analyzed in an MS experiment remain unidentified. We propose to use spectrum clustering at a large scale to shed light on these unidentified spectra. The Proteomics Identifications (PRIDE) Database Archive is one of the largest MS proteo...
Article
B cells often infiltrate the microenvironment of human tumors. B cells can both positively and negatively regulate anti-tumor immune responses. In several human cancers, higher numbers of CD20(+) tumor associated B cells (TAB) are associated with a favorable prognosis, whereas in human primary melanomas this association is contentious. In this stud...
Article
Full-text available
Chemically modified trypsin is a standard reagent in proteomics experiments but is usually not considered in database searches. Modification of trypsin is supposed to protect the protease against autolysis and the resulting loss of activity. Here we show that modified trypsin is still subject to self-digestion and as a result modified trypsin deriv...
Article
Spectral library searching has become a mature method to identify tandem mass spectra in proteomics data analysis. This review provides a comprehensive overview of available spectral library search engines and highlights their distinct features. Additionally, resources providing spectral libraries are summarized and tools presented that extend expe...
Article
Full-text available
The original PRIDE Inspector tool was developed as an open source standalone tool to enable the visualization and validation of mass-spectrometry (MS)-based proteomics data before data submission or already publicly available in the Proteomics Identifications (PRIDE) database. The initial implementation of the tool focused on visualizing PRIDE data...
Article
Full-text available
The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories of mass spectrometry (MS)-based proteomics data. Since the beginning of 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) is the new PRIDE archival system, replacing the original PRIDE database. Here we summarize the developments in PRIDE resources...
Article
Dermatitis herpetiformis (DH) is a highly pruritic, symmetric, papulo-vesicular dermatosis with lesions most predominantly found on the extensor surfaces of the extremities. It is currently the only dermatosis characterized by granular IgA deposits in the papillary dermis as visualized by direct immunofluorescence (IF) microscopy from perilesional...