Author: Bjoern Peters

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Preprints

RNA-seq preprocessing and sample size considerations for gene network inference

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Immunological memory to SARS-CoV-2 assessed for up to eight months after infection

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Negligible impact of SARS-CoV-2 variants on CD4+ and CD8+ T cell reactivity in COVID-19 exposed donors and vaccinees.

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NetTCR: sequence-based prediction of TCR binding to peptide-MHC complexes using convolutional neural networks

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Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV): sequence homology- and bioinformatic-based predictions

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Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases

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NetMHCpan 4.0: Improved peptide-MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data

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MOGSA: integrative single sample gene-set analysis of multiple omics data

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Improved prediction of MHC II antigen presentation through integration and motif deconvolution of mass spectrometry MHC eluted ligand data

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No cell is an island: circulating T cell:monocyte complexes are markers of immune perturbations

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A Modified Injector and Sample Acquisition Protocol Can Improve Data Quality and Reduce Inter-Instrument Variability of the Helios Mass Cytometer

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Benchmarking predictions of MHC class I restricted T cell epitopes

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BepiPred-3.0: Improved B-cell epitope prediction using protein language models

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Footprints of antigen processing boost MHC class II natural ligand binding predictions

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The challenge of distinguishing cell-cell complexes from singlet cells in non-imaging flow cytometry and single-cell sorting

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DAFi: A Directed Recursive Filtering and Clustering Approach to Data-Driven Identification of Cell Populations from Polychromatic Flow Cytometry Data

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TCRMatch: Predicting T-cell receptor specificity based on sequence similarity to previously characterized receptors

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A curated collection of human vaccination response signatures

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Gene Regulatory Cross Networks: Inferring Gene Level Cell-to-Cell Communications of Immune Cells

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Transcriptional analysis of peripheral memory T cells reveals Parkinson's disease-specific gene signatures

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A system-view of B. pertussis booster vaccine responses in adults primed with whole-cell vs. acellular vaccine in infancy

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Combined assessment of MHC binding and antigen expression improves T cell epitope predictions

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Predictive performance and clinical application of COV50, a urinary proteomic biomarker in early COVID-19 infection: a cohort study

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Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: results from the IMPACC study

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Uncovering the cell type specificity of blood sample derived gene signatures using RNA expression data

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Transcriptomics of acute DENV-specific CD8+ T cells does not support qualitative differences as drivers of disease severity.

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OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies

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Disruption of Mitochondrial Quality Control Genes Promotes Caspase-Resistant Cell Survival Following Apoptotic Stimuli

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Comparison of HLA ligand elution data and binding predictions reveals varying prediction performance for the multiple motifs recognized by HLA-DQ2.5

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CD4+CCR6+ T cells dominate the BCG-induced transcriptional signature

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Towards the prediction of non-peptidic epitopes

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Expression of specific HLA class II alleles is associated with an increased risk for active tuberculosis and a distinct gene expression profile

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Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome by accurate and comprehensive HLA-DQ antigen presentation prediction

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High-resolution African HLA resource uncovers HLA-DRB1 expression effects underlying vaccine response

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