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Articles by Jonas Scheid
github.com/nf-core/mhcquant
Published May 22, 2025 | Version 3.0.0 Software Open No description specified https://dockstore.org/aliases/workflow-versions/10.5281-zenodo.15492449 (URL) https://dockstore.org/workflows/github.com/nf-core/mhcquant:3.0.0 (URL) https://dockstore.org/api/ga4gh/trs/v2/tools/%23workflow%2Fgithub.com%2Fnf-core%2Fmhcquant/versions/3.0.0/PLAIN-NFL/descriptor/nextflow.config (URL)
github.com/nf-core/epitopeprediction
Published May 9, 2025 | Version 3.0.0 Software Open A fully reproducible and state of the art epitope prediction pipeline. Usage: The typical command for running the pipeline is as follows: nextflow run nf-core/epitopeprediction -profile --input "*.vcf.gz" Mandatory arguments: --input Path to input data (must be surrounded with quotes) --alleles Path to the file containing the MHC alleles -profile Configuration profile to use.
TIMS2Rescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MS2Rescore
Introduction Click to copy section linkSection link copied! Proteomics is an invaluable tool for understanding human biology, facilitating the discovery of new disease biomarkers, identifying potential therapeutic targets, and exploring interactions with pathogens or microorganisms. (1−4) Various proteomics subfields have emerged that address specific challenges.
TIMS2Rescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MS2Rescore
Introduction Click to copy section linkSection link copied! Proteomics is an invaluable tool for understanding human biology, facilitating the discovery of new disease biomarkers, identifying potential therapeutic targets, and exploring interactions with pathogens or microorganisms. (1−4) Various proteomics subfields have emerged that address specific challenges.
Mapping naturally presented T cell antigens in medulloblastoma based on integrative multi-omics - Nature Communications
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Abstract Medulloblastoma is the most frequent malignant primary brain tumor in children. Despite recent advances in integrated genomics, the prognosis in children with high-risk medulloblastoma remains devastating, and new tumor-specific therapeutic approaches are needed. Here, we present an atlas of naturally presented T cell antigens in medulloblastoma.
By Julia Velz, Gioele Medici, Marissa L. Dubbelaar, Malte Mohme, David R. Ghasemi, Jonas Scheid, Daniel Kowalewski, Matthias Eyrich, Beat M. Frey, Martin Sill, Sven Nahnsen, Tobias Weiss, Hans-Georg Wirsching, Niklaus Krayenbühl, Luca Regli, Hans-Georg Rammensee, Elisabeth Rushing, Felix Sahm, Juliane S. Walz, Michael Weller, Lena K. Freudenmann, Marie Gauder
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Nature
Verified
TIMS2Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS2Rescore
Abstract The high throughput analysis of proteins with mass spectrometry (MS) is highly valuable for understanding human biology, discovering disease biomarkers, identifying therapeutic targets, and exploring pathogen interactions. To achieve these goals, specialized proteomics subfields - such as plasma proteomics, immunopeptidomics, and metaproteomics - must tackle specific analytical challenges, such as an increased identification ambiguity compared to routine proteomics experiments.
TOFIMS mass spectrometry-based immunopeptidomics refines tumor antigen identification - Nature Communications
Abstract T cell recognition of human leukocyte antigen (HLA)-presented tumor-associated peptides is central for cancer immune surveillance. Mass spectrometry (MS)-based immunopeptidomics represents the only unbiased method for the direct identification and characterization of naturally presented tumor-associated peptides, a key prerequisite for the development of T cell-based immunotherapies.
DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts - Nature Communications
Abstract Immunotherapies targeting cancer-specific neoantigens have revolutionized the treatment of cancer patients. Recent evidence suggests that epigenetic therapies synergize with immunotherapies, mediated by the de-repression of endogenous retroviral element (ERV)-encoded promoters, and the initiation of transcription.
Phase I/II trial of a peptide-based COVID-19 T-cell activator in patients with B-cell deficiency - Nature Communications
Abstract T-cell immunity is central for control of COVID-19, particularly in patients incapable of mounting antibody responses. CoVac-1 is a peptide-based T-cell activator composed of SARS-CoV-2 epitopes with documented favorable safety profile and efficacy in terms of SARS-CoV-2-specific T-cell response. We here report a Phase I/II open-label trial (NCT04954469) in 54 patients with congenital or acquired B-cell deficiency receiving one subcutaneous CoVac-1 dose.
The oncogenic fusion protein DNAJB1-PRKACA can be specifically targeted by peptide-based immunotherapy in fibrolamellar hepatocellular carcinoma - Nature Communications
Abstract The DNAJB1-PRKACA fusion transcript is the oncogenic driver in fibrolamellar hepatocellular carcinoma, a lethal disease lacking specific therapies. This study reports on the identification, characterization, and immunotherapeutic application of HLA-presented neoantigens specific for the DNAJB1-PRKACA fusion transcript in fibrolamellar hepatocellular carcinoma.
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