D. Gfeller

How to predict binding specificity and ligands for new MHC-II alleles with MixMHC2pred

This paper describes using MixMHC2pred to predict MHC-II binding specificity and ligands from amino acid sequences across species.

Rapid BCMA downmodulation on myeloma cells upon CAR T cell contact is mediated by trogocytosis and BCMA internalization

This study designs APRIL-based dual-antigen CAR T cells for multiple myeloma and finds rapid BCMA downmodulation on tumor cells through trogocytosis and internalization, independent of binding moiety.

Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes

The paper predicts MHC-II epitope specificities using machine learning, revealing a reverse binding mode in ligands across multiple species.

Deciphering the landscape of phosphorylated HLA-II ligands

The paper identifies 1,113 unique phosphorylated HLA-II ligands and develops a predictor for their presentation on HLA-II molecules.

Mass spectrometry based immunopeptidomics leads to robust predictions of phosphorylated HLA class I ligands

The paper curates phosphorylated HLA-I ligands and develops a predictor for their interaction with HLA-I molecules.

Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq

This study identifies four CD8 TIL states in B16 melanoma tumors using single-cell RNA-seq and finds anti-PD-1 treatment expands EM-like cells.

Deep motif deconvolution of HLA-II peptidomes for robust class II epitope predictions

The paper improves HLA-II epitope prediction by combining mass spectrometry data with a new motif deconvolution algorithm, enhancing motif definition and prediction accuracy.

The length distribution and multiple specificity of naturally presented HLA-I ligands

The paper analyzes HLA-I ligand length distribution and multiple specificity using HLA peptidomics data from human meningioma samples, improving predictions of naturally presented ligands.

The C-terminal extension landscape of naturally presented HLA-I ligands

The paper identifies frequent C-terminal extensions in HLA-I ligands across multiple alleles and demonstrates their recognition by CD8+ T cells.

Simultaneous Enumeration Of Cancer And Immune Cell Types From Bulk Tumor Gene Expression Data

The paper presents an algorithm to estimate cancer and immune cell fractions from bulk tumor gene expression data, validated with multiple experimental methods.