A5100706958- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- vaccines and immunoinformatics approaches
- Quantum Computing Algorithms and Architecture
- Peptidase Inhibition and Analysis
- Antibiotics Pharmacokinetics and Efficacy
- Quantum Information and Cryptography
- Advanced Fluorescence Microscopy Techniques
- Immunotherapy and Immune Responses
- Monoclonal and Polyclonal Antibodies Research
- Speech Recognition and Synthesis
- Infrared Target Detection Methodologies
- Music and Audio Processing
- Radiation Detection and Scintillator Technologies
- Reproductive Biology and Fertility
- Ubiquitin and proteasome pathways
- Bacterial Identification and Susceptibility Testing
- Optical Coherence Tomography Applications
- Speech and Audio Processing
- Biosimilars and Bioanalytical Methods
- RNA Interference and Gene Delivery
- Advanced Image and Video Retrieval Techniques
- Pharmacological Effects and Toxicity Studies
- Gene expression and cancer classification
Radiation Monitoring Devices (United States)
2023-2024
University of Lausanne
2019-2024
University Hospital of Lausanne
2023-2024
SIB Swiss Institute of Bioinformatics
2014-2023
Ludwig Cancer Research
2021-2023
Bielefeld University
2022-2023
Cornell University
2023
Medical University of Vienna
2006-2022
Federal Ministry for the Interior
2022
Amazon (United States)
2022
Receiver operating characteristic (ROC) curves are useful tools to evaluate classifiers in biomedical and bioinformatics applications. However, conclusions often reached through inconsistent use or insufficient statistical analysis. To support researchers their ROC analysis we developed pROC, a package for R S+ that contains set of displaying, analyzing, smoothing comparing user-friendly, object-oriented flexible interface. With data previously imported into the environment, pROC builds...
Therapeutic drug monitoring (TDM), i. e., the quantification of serum or plasma concentrations medications for dose optimization, has proven a valuable tool patient-matched psychopharmacotherapy. Uncertain adherence, suboptimal tolerability, non-response at therapeutic doses, pharmacokinetic drug-drug interactions are typical situations when measurement medication is helpful. Patient populations that may predominantly benefit from TDM in psychiatry children, pregnant women, elderly patients,...
The history of phenothiazines, from methylene blue via chlorpromazine to recently synthesized isomeric derivatives various neuroleptics, is reviewed in the light their antimicrobial activity and Paul Ehrlich's receptor concept. latter clearly line with most modern theories concerning drug action stereo-isomeric compounds.
Abstract Label‐free quantification of high mass resolution LC‐MS data has emerged as a promising technology for proteome analysis. Computational methods are required the accurate extraction peptide signals from and tracking these features across measurements different samples. We present here an open source software tool, SuperHirn , that comprises set modules to process acquired on spectrometer. The program includes newly developed functionalities analyze such feature quantification,...
Abstract Efforts to precisely identify tumor human leukocyte antigen (HLA) bound peptides capable of mediating T cell-based rejection still face important challenges. Recent studies suggest that non-canonical tumor-specific HLA derived from annotated non-coding regions could elicit anti-tumor immune responses. However, sensitive and accurate mass spectrometry (MS)-based proteogenomics approaches are required robustly these peptides. We present an MS-based analytical approach characterizes...
Comprehensive knowledge of the human leukocyte antigen (HLA) class-I and class-II peptides presented to T-cells is crucial for designing innovative therapeutics against cancer other diseases. However methodologies their purification mass-spectrometry analysis have been a major limitation. We designed novel high-throughput, reproducible sensitive method sequential immuno-affinity HLA-I -II from up 96 samples in plate format, suitable both cell lines tissues. Our methodology drastically...
Abstract One key barrier to improving efficacy of personalized cancer immunotherapies that are dependent on the tumor antigenic landscape remains patient stratification. Although patients with CD3 + CD8 T cell-inflamed tumors typically show better response immune checkpoint inhibitors, it is still unknown whether immunopeptidome repertoire presented in highly inflamed and noninflamed substantially different. We surveyed 61 regions adjacent nonmalignant lung tissues from 8 performed deep...
Circular RNAs (circRNAs) are covalently closed non-coding lacking the 5' cap and poly-A tail. Nevertheless, it has been demonstrated that certain circRNAs can undergo active translation. Therefore, aberrantly expressed in human cancers could be an unexplored source of tumor-specific antigens, potentially mediating anti-tumor T cell responses. This study presents immunopeptidomics workflow with a specific focus on generating circRNA-specific protein fasta reference. The main goal this is to...
Spliced peptides are short protein fragments spliced together in the proteasome by peptide bond formation. True estimation of contribution proteasome-spliced (PSPs) to global human leukocyte antigen (HLA) ligandome is critical. A recent study suggested that PSPs contribute up 30% HLA ligandome. We performed a thorough reanalysis reported results using multiple computational tools and various validation steps concluded only fraction proposed passes quality filters. To better estimate actual...
The remarkable clinical efficacy of the immune checkpoint blockade therapies has motivated researchers to discover immunogenic epitopes and exploit them for personalized vaccines. HLA binding peptides derived from processing presentation mutated proteins are one leading targets T-cell recognition cancer cells. Currently, most studies attempt identify neoantigens based on predicted affinity molecules, but performance such prediction algorithms is rather poor rare class I alleles II. Direct...
Mass spectrometry (MS) is the state-of-the-art methodology for capturing breadth and depth of immunopeptidome across human leukocyte antigen (HLA) allotypes cell types. The majority studies in immunopeptidomics field are discovery driven. Hence, data-dependent tandem MS (MS/MS) acquisition (DDA) widely used, as it generates high-quality references peptide fingerprints. However, DDA suffers from stochastic selection abundant ions that impairs sensitivity reproducibility. In contrast,...
The accurate selection of neoantigens that bind to class I human leukocyte antigen (HLA) and are recognized by autologous T cells is a crucial step in many cancer immunotherapy pipelines. We reprocessed whole-exome sequencing RNA (RNA-seq) data from 120 patients two external large-scale neoantigen immunogenicity screening assays combined with an in-house dataset 11 identified 46,017 somatic single-nucleotide variant mutations 1,781,445 neo-peptides, which 212 178 neo-peptides were...
We have developed a new algorithm to identify proteins by means of peptide mass fingerprinting. Starting from the matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) spectra and environmental data such as species, isoelectric point molecular weight, well chemical modifications or number missed cleavages protein, program performs fully automated identification protein. The first step is peak detection algorithm, which allows precise fast determination masses, even if peaks...
Protein complexes have largely been studied by immunoaffinity purification and (mass spectrometric) analysis. Although this approach has widely successfully used it is limited because difficulties reliably discriminating true from false protein complex components, identifying post-translational modifications, detecting quantitative changes in composition or state of modification components. We developed a protocol that enables us to determine, single LC-MALDI-TOF/TOF analysis, the...
The presentation of peptides on class I human leukocyte antigen (HLA-I) molecules plays a central role in immune recognition infected or malignant cells. In cancer, non-self HLA-I ligands can arise from many different alterations, including non-synonymous mutations, gene fusion, cancer-specific alternative mRNA splicing aberrant post-translational modifications. Identifying remains challenging task that requires either heavy experimental work for vivo identification optimized bioinformatics...
The accurate identification and prioritization of antigenic peptides is crucial for the development personalized cancer immunotherapies. Publicly available pipelines to predict clinical neoantigens do not allow direct integration mass spectrometry immunopeptidomics data, which can uncover derived from various canonical noncanonical sources. To address this, we present an end-to-end proteogenomic pipeline, called NeoDisc, that combines state-of-the-art publicly in-house software...
Identification and characterization of all proteins expressed by a genome in biological samples represent major challenges proteomics. Today's commonly used high-throughput approaches combine two-dimensional electrophoresis (2-DE) with peptide mass fingerprinting (PMF) analysis. Although automation is often possible, number limitations still adversely affect the rate protein identification annotation 2-DE databases: sequential excision process pieces gel containing protein; enzymatic...