A5012388687- Immunotherapy and Immune Responses
- vaccines and immunoinformatics approaches
- Metabolomics and Mass Spectrometry Studies
- Monoclonal and Polyclonal Antibodies Research
- Peptidase Inhibition and Analysis
- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- CAR-T cell therapy research
- T-cell and B-cell Immunology
- Cancer Immunotherapy and Biomarkers
- Microbial Metabolic Engineering and Bioproduction
- Antimicrobial Peptides and Activities
- Cytomegalovirus and herpesvirus research
- Autoimmune and Inflammatory Disorders Research
- Chromatin Remodeling and Cancer
- Cancer Mechanisms and Therapy
- Bacteriophages and microbial interactions
- Chronic Myeloid Leukemia Treatments
- Inflammasome and immune disorders
- Immune Cell Function and Interaction
- Genomics and Phylogenetic Studies
- Erythrocyte Function and Pathophysiology
- Biomedical Text Mining and Ontologies
- Gut microbiota and health
- Cardiac tumors and thrombi
University of Tübingen
2018-2023
University of Alberta
2015-2023
University of Würzburg
2015
Spitalul Clinic Județean de Urgență Cluj-Napoca
1969
DrugBank (www.drugbank.ca) is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, interactions and targets. First described in 2006, has continued to evolve over the past 12 years response marked improvements web standards changing needs for drug research development. This year's update, 5.0, represents most significant upgrade more than 10 years. In many cases, existing data content grown by 100% or last update. For instance, total number of...
PHASTER (PHAge Search Tool – Enhanced Release) is a significant upgrade to the popular PHAST web server for rapid identification and annotation of prophage sequences within bacterial genomes plasmids. Although steps in phage pipeline remain largely same as original PHAST, numerous software improvements hardware enhancements have now made faster, more efficient, visually appealing much user friendly. In particular, 4.3× faster than when analyzing typical genome. More specifically,...
The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the now considered standard resource for studies. Over past decade has continued to grow evolve response emerging needs metabolomics researchers continuing changes web...
Heatmapper is a freely available web server that allows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface. Unlike existing non-commercial map packages, which either lack interfaces or are specialized for only one two kinds maps, versatile tool easily create wide variety many different types and applications. More specifically, generate, cluster visualize: (i) expression-based from transcriptomic, proteomic metabolomic experiments;...
Background The human leucocyte antigen (HLA) complex controls adaptive immunity by presenting defined fractions of the intracellular and extracellular protein content to immune cells. Understanding benign HLA ligand repertoire is a prerequisite define safe T-cell-based immunotherapies against cancer. Due poor availability tissues, if available, normal tissue adjacent tumor has been used as surrogate when defining tumor-associated antigens. However, this comparison proven be insufficient even...
YMDB or the Yeast Metabolome Database (http://www.ymdb.ca/) is a comprehensive database containing extensive information on genome and metabolome of Saccharomyces cerevisiae Initially released in 2012, has gone through significant expansion number improvements over past 4 years. This manuscript describes most recent version (YMDB 2.0). More specifically, it provides an updated description that was previously described 2012 NAR Issue details many additions made to time. Some important changes...
ECMDB or the Escherichia coli Metabolome Database (http://www.ecmdb.ca) is a comprehensive database containing detailed information about genome and metabolome of E. (K-12). First released in 2012, has undergone substantial expansion many modifications over past 4 years. This manuscript describes most recent version (ECMDB 2.0). In particular, it provides update that was previously described 2013 NAR Issue details additions improvements made to time. Some important significant enhancements...
PathBank (www.pathbank.org) is a new, comprehensive, visually rich pathway database containing more than 110 000 machine-readable pathways found in 10 model organisms (Homo sapiens, Bos taurus, Rattus norvegicus, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae, Escherichia coli and Pseudomonas aeruginosa). aims to provide for every protein map metabolite. This resource designed specifically support elucidation discovery...
Autophagy participates in innate immunity by eliminating intracellular pathogens. Consequently, numerous microorganisms have developed strategies to impair the autophagic machinery phagocytes. In current study, interactions between Leishmania major (L. m.) and of bone marrow-derived macrophages (BMDM) were analyzed. BMDM generated from BALB/c mice, cells infected with L. m. promastigotes. Transmission electron microscopy (TEM) tomography used investigate ultrastructure parasites. Affymetrix®...
Activity of the NLRP3 inflammasome, a critical mediator inflammation, is controlled by accessory proteins, posttranslational modifications, cellular localization, and oligomerization. How these factors relate unclear. We show that well-established drug target, Bruton’s tyrosine kinase (BTK), affects several levels regulation. BTK directly interacts with in immune cells phosphorylates four conserved residues upon inflammasome activation, vitro vivo. Furthermore, promotes relocalization,...
The broad application of precision cancer immunotherapies is limited by the number validated neoepitopes that are common among patients or tumor types. To expand known repertoire shared neoantigen-human leukocyte antigen (HLA) complexes, we developed a high-throughput platform coupled an in vitro peptide-HLA binding assay with engineered cellular models expressing individual HLA alleles combination concatenated transgene harboring 47 neoantigens. From more than 24,000 possible neoepitope-HLA...
Abstract PathBank (https://pathbank.org) and its predecessor database, the Small Molecule Pathway Database (SMPDB), have been providing comprehensive metabolite pathway information for metabolomics community since 2010. Over past 14 years, these databases grown evolved significantly to meet needs of respond continuing changes in computing technology. This year's update, 2.0, brings a number important improvements upgrades that should make database more useful appealing larger cross-section...
The Pseudomonas aeruginosaMetabolome Database (PAMDB, http://pseudomonas.umaryland.edu) is a searchable, richly annotated metabolite database specific to P. aeruginosa. aeruginosa soil organism and significant opportunistic pathogen that adapts its environment through versatile energy metabolism network. Furthermore, model for the study of biofilm formation, quorum sensing, bioremediation processes, each which are dependent on unique pathways metabolites. PAMDB modelled Escherichia coli...
NMR is a widely used analytical technique with growing number of repositories available. As result, demands for vendor-agnostic, open data format long-term archiving have emerged the aim to ease and encourage sharing, comparison, reuse data. Here we present nmrML, an XML-based exchange storage spectral The nmrML intended be fully compatible existing chemical, biochemical, metabolomics experiments. can capture raw data, acquisition parameters, where available metadata, such as chemical...
Antigen-specific immunotherapies, in particular peptide vaccines, depend on the recognition of naturally presented antigens derived from mutated and unmutated gene products human leukocyte antigens, represent a promising low-side-effect concept for cancer treatment. So far, broad application vaccines patients is hampered by challenges time- cost-intensive personalized vaccine design, lack neoepitopes tumor-specific mutations, especially low-mutational burden malignancies. In this study, we...
Cancer treatment with immune checkpoint blockade (ICB) often induces immune-related adverse events (irAEs). We hypothesized that proteins coexpressed in tumors and normal cells could be antigenic targets irAEs herein described DITAS (discovery of tumor-associated self-antigens) for their identification. computed transcriptional similarity between lung healthy tissue based on single-sample gene set enrichment analysis. This identified 10 tissue–specific genes highly expressed the tumors....
Tapasin and TAPBPR are known to perform peptide editing on major histocompatibility complex class I (MHC I) molecules; however, the precise molecular mechanism(s) involved in this process remain largely enigmatic. Here, using immunopeptidomics combination with novel cell-based assays that assess TAPBPR-mediated exchange, we reveal a critical role for K22-D35 loop of mediating exchange MHC I. We identify specific leucine within enables facilitate dissociation from Moreover, delineate features...
For more than two decades naturally presented, human leukocyte antigen (HLA)-restricted peptides (immunopeptidome) have been eluted and sequenced using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Since, identified disease-associated HLA ligands characterized evaluated as potential active substances. Treatments based on HLA-presented shown promising results in clinical application personalized T cell-based immunotherapy. Peptide vaccination cocktails are produced...
ABSTRACT The human leukocyte antigen (HLA) complex controls adaptive immunity by presenting defined fractions of the intracellular and extracellular protein content to immune cells. Here, we describe HLA Ligand Atlas, an extensive collection mostly matched HLA-I -II ligandomes from 225 benign samples (29 tissues, 21 subjects). initial release covers 51 86 HLA-II allotypes 89,853 HLA-I- 140,861 ligands. We observe that immunopeptidomes differ considerably between tissues individuals on both...