Leon Bichmann
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View article: Longitudinal single cell multi-omic profiling of Nicaraguan children reveals trajectories of pediatric immune development and variation 2840
Longitudinal single cell multi-omic profiling of Nicaraguan children reveals trajectories of pediatric immune development and variation 2840 Open
Description The state of the immune system varies widely within individuals over time and between populations. These variations make it difficult to predict the response to infection, vaccination, and other stimuli. Recent studies have beg…
View article: MHCquant2 refines immunopeptidomics tumor antigen discovery
MHCquant2 refines immunopeptidomics tumor antigen discovery Open
Confident identification of human leukocyte antigen (HLA)-presented peptides is crucial for advancing cancer immunotherapy. We present MHCquant2, a scalable and modular Nextflow pipeline integrated into nf-core as a reproducible, portable,…
View article: Fetal and maternal immune cells exhibit tandem maturation across gestation and dysregulation in preterm birth
Fetal and maternal immune cells exhibit tandem maturation across gestation and dysregulation in preterm birth Open
Immune cells are crucially important for the development and function of many organ systems including the maternal-fetal interface during pregnancy: the placenta and fetal membranes. While maternal uterine NK cells have been studied in pre…
View article: HLA Ligand Atlas DIA: extending the benign immunopeptidomics resource with increased sensitivity through data-independent acquisition mass spectrometry
HLA Ligand Atlas DIA: extending the benign immunopeptidomics resource with increased sensitivity through data-independent acquisition mass spectrometry Open
The human leukocyte antigen (HLA)-presented peptide repertoire, termed immunopeptidome, plays a crucial role for T-cell mediated immune reactions. Previously, the human immunopeptidome of non-malignant tissues has been mapped in a large-sc…
View article: The immunopeptidomic landscape of ependymomas provides actionable antigens for T-cell-based immunotherapy
The immunopeptidomic landscape of ependymomas provides actionable antigens for T-cell-based immunotherapy Open
Background Ependymoma are primary tumors of the nervous system. Due to their growth pattern, many ependymomas can be managed with neurosurgical resection alone. A substantial proportion of these tumors recurs or displays infiltrative growt…
View article: MHCquant2 refines immunopeptidomics tumor antigen discovery
MHCquant2 refines immunopeptidomics tumor antigen discovery Open
The identification of human leukocyte antigen (HLA)-presented peptides as targets of anti-cancer T cell response is pivotal for the development of novel immunotherapies. Mass spectrometry (MS)-based immunopeptidomics enables the detection …
View article: OpenMS 3 expands the frontiers of open-source computational mass spectrometry
OpenMS 3 expands the frontiers of open-source computational mass spectrometry Open
Mass spectrometry has become an indispensable tool in the life sciences. The new major version 3 of the computational framework OpenMS provides significant advancements regarding open, scalable, and reproducible high-throughput workflows f…
View article: Understanding the constitutive presentation of MHC class I immunopeptidomes in primary tissues
Understanding the constitutive presentation of MHC class I immunopeptidomes in primary tissues Open
Understanding the molecular principles that govern the composition of the MHC-I immunopeptidome across different primary tissues is fundamentally important to predict how T cells respond in different contexts in vivo. Here, we performed a …
View article: Mass spectrometry guided immunoinformatics
Mass spectrometry guided immunoinformatics Open
A key task of the human immune system is the recognition and surveillance of peptides presented by the HLA complex on the surface of body cells. In this way, abnormalities can be discovered rapidly to elicit targeted immune responses. The …
View article: DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics
DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics Open
Data-independent acquisition (DIA) is becoming a leading analysis method in biomedical mass spectrometry. The main advantages include greater reproducibility and sensitivity and a greater dynamic range compared with data-dependent acquisit…
View article: Tumor-exclusive peptides from shared and individual antigens in the HLA-ligandome of oropharyngeal squamous cell carcinoma
Tumor-exclusive peptides from shared and individual antigens in the HLA-ligandome of oropharyngeal squamous cell carcinoma Open
Introduction Cancer-antigens are presented to the immune system via Human leucocyte antigens (HLA). The HLA-ligandome in oropharyngeal squamous cell carcinoma (OPSCC) has not been described previously.
View article: HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy
HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy Open
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 the benign HLA ligand repertoire is a pre…
View article: The Impact of Biomaterial Cell Contact on the Immunopeptidome
The Impact of Biomaterial Cell Contact on the Immunopeptidome Open
Biomaterials play an increasing role in clinical applications and regenerative medicine. A perfectly designed biomaterial should restore the function of damaged tissue without triggering an undesirable immune response, initiate self-regene…
View article: DIAproteomics: A multi-functional data analysis pipeline for data-independent-acquisition proteomics and peptidomics
DIAproteomics: A multi-functional data analysis pipeline for data-independent-acquisition proteomics and peptidomics Open
Data-independent acquisition (DIA) is becoming a leading analysis method in biomedical mass spectrometry. Main advantages include greater reproducibility, sensitivity and dynamic range compared to data-dependent acquisition (DDA). However,…
View article: Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison
Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison Open
Here we present the Universal Spectrum Explorer (USE), a web-based tool based on IPSA for cross-resource (peptide) spectrum visualization and comparison ( https://www.proteomicsdb.org/use/ ). Mass spectra under investigation can either be …
View article: An innovative approach for HLA typing, molecular tumor testing and the validation of tumor exclusive antigens
An innovative approach for HLA typing, molecular tumor testing and the validation of tumor exclusive antigens Open
Disclaimer This manuscript has been withdrawn by the corresponding author, as it was submitted and made public in bioRxiv without knowledge and the full consent of all the authors listed. The co-authors are therefore not responsible for th…
View article: Identification of HCMV-derived T cell epitopes in seropositive individuals through viral deletion models
Identification of HCMV-derived T cell epitopes in seropositive individuals through viral deletion models Open
In healthy individuals, immune control of persistent human cytomegalovirus (HCMV) infection is effectively mediated by virus-specific CD4+ and CD8+ T cells. However, identifying the repertoire of T cell specificities for HCMV is hampered b…
View article: IMMU-08. THE ANTIGENIC LANDSCAPE OF GLIOBLASTOMA - REFINING THE TARGETS FOR IMMUNOTHERAPY
IMMU-08. THE ANTIGENIC LANDSCAPE OF GLIOBLASTOMA - REFINING THE TARGETS FOR IMMUNOTHERAPY Open
We provide a comprehensive analysis of the antigenic landscape of glioblastoma using a multi-omics approach including ligandome mapping of the Human Leukocyte Antigen (HLA) ligandome, next generation sequencing (NGS) as well as an in-depth…
View article: The HLA Ligand Atlas - A resource of natural HLA ligands presented on benign tissues
The HLA Ligand Atlas - A resource of natural HLA ligands presented on benign tissues Open
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 the HLA Ligand Atlas, an extensive collection of…
View article: The HLA ligandome landscape of chronic myeloid leukemia delineates novel T-cell epitopes for immunotherapy
The HLA ligandome landscape of chronic myeloid leukemia delineates novel T-cell epitopes for immunotherapy Open
Antileukemia immunity plays an important role in disease control and maintenance of tyrosine kinase inhibitor (TKI)-free remission in chronic myeloid leukemia (CML). Thus, antigen-specific immunotherapy holds promise for strengthening immu…