David Gfeller
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View article: Engineered CD4 TCR T cells with conserved high-affinity TCRs targeting NY-ESO-1 for advanced cellular therapies in cancer
Engineered CD4 TCR T cells with conserved high-affinity TCRs targeting NY-ESO-1 for advanced cellular therapies in cancer Open
While cancer immunotherapy has primarily focused on CD8 T cells, CD4 T cells are increasingly recognized for their role in antitumor immunity. The HLA-DRB3*02:02 allele is found in 50% of Caucasians. In this study, we screened HLA-DRB3*02:…
View article: Phage display enables machine learning discovery of cancer antigen–specific TCRs
Phage display enables machine learning discovery of cancer antigen–specific TCRs Open
T cells targeting epitopes in infectious diseases or cancer play a central role in spontaneous and therapy-induced immune responses. Epitope recognition is mediated by the binding of the T cell receptor (TCR), and TCRs recognizing clinical…
View article: Predicting MHC-I ligands across alleles and species: how far can we go?
Predicting MHC-I ligands across alleles and species: how far can we go? Open
Our work provides a valuable tool for predicting antigen presentation across all human and mouse MHC-I alleles. MixMHCpred3.0 tool is available at https://github.com/GfellerLab/MixMHCpred .
View article: Donor HLA-DQ genetic and functional divergence affect the control of BK polyoma virus infection after kidney transplantation
Donor HLA-DQ genetic and functional divergence affect the control of BK polyoma virus infection after kidney transplantation Open
BK polyomavirus (BKPyV) infection remains a major concern after kidney transplantation, increasing the risk of graft loss in the absence of specific antiviral agent now available. Here, we investigated the impact of HLA diversity on the co…
View article: SuperSpot: coarse graining spatial transcriptomics data into metaspots
SuperSpot: coarse graining spatial transcriptomics data into metaspots Open
Summary Spatial Transcriptomics is revolutionizing our ability to phenotypically characterize complex biological tissues and decipher cellular niches. With current technologies such as VisiumHD, thousands of genes can be detected across mi…
View article: A comprehensive proteogenomic pipeline for neoantigen discovery to advance personalized cancer immunotherapy
A comprehensive proteogenomic pipeline for neoantigen discovery to advance personalized cancer immunotherapy Open
The accurate identification and prioritization of antigenic peptides is crucial for the development of personalized cancer immunotherapies. Publicly available pipelines to predict clinical neoantigens do not allow direct integration of mas…
View article: Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data
Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data Open
Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq) is a widely used technique to explore gene regulatory mechanisms. For most ATAC-Seq data from healthy and diseased tissues such as tumors, chromatin accessibility measurement…
View article: Lessons learned from the IMMREP23 TCR-epitope prediction challenge
Lessons learned from the IMMREP23 TCR-epitope prediction challenge Open
International audience
View article: Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data
Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data Open
Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq) is a widely used technique to explore gene regulatory mechanisms. For most ATAC-Seq data from healthy and diseased tissues such as tumors, chromatin accessibility measurement…
View article: Community assessment of methods to deconvolve cellular composition from bulk gene expression
Community assessment of methods to deconvolve cellular composition from bulk gene expression Open
We evaluate deconvolution methods, which infer levels of immune infiltration from bulk expression of tumor samples, through a community-wide DREAM Challenge. We assess six published and 22 community-contributed methods using in vitro and i…
View article: Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data
Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data Open
Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq) is a widely used technique to explore gene regulatory mechanisms. For most ATAC-Seq data from healthy and diseased tissues such as tumors, chromatin accessibility measurement…
View article: Author response: Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data
Author response: Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data Open
Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq) is a widely used technique to explore gene regulatory mechanisms. For most ATAC-Seq data from healthy and diseased tissues such as tumors, chromatin accessibility measurement…
View article: Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.
Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data. Open
Bulk ATAC-seq data of tumour samples result in an averaged signal across different cell-types (cancer, stromal, vascular and immune cells). We propose a deconvolution framework called EPIC-ATAC (https://doi.org/10.7554/eLife.94833.1), whic…
View article: SuperSpot: Coarse Graining Spatial Transcriptomic Data into Metaspots
SuperSpot: Coarse Graining Spatial Transcriptomic Data into Metaspots Open
Summary Spatial Transcriptomics is revolutionizing our ability to phenotypically characterize complex biological tissues and decipher cellular niches. As of today, thousands of genes can be detected across hundreds of thousands of spots. A…
View article: Predicting MHC-I ligands across alleles and species: How far can we go?
Predicting MHC-I ligands across alleles and species: How far can we go? Open
CD8 + T-cell activation is initiated by the recognition of epitopes presented on class I major histocompatibility complex (MHC-I) molecules. Identifying such epitopes is useful for molecular understanding of cellular immune responses and c…
View article: Reviewer #2 (Public Review): Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data
Reviewer #2 (Public Review): Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data Open
Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq) is a widely used technique to explore gene regulatory mechanisms. For most ATAC-Seq data from healthy and diseased tissues such as tumors, chromatin accessibility measurement…
View article: Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data
Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data Open
Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq) is a widely used technique to explore gene regulatory mechanisms. For most ATAC-Seq data from healthy and diseased tissues such as tumors, chromatin accessibility measurement…
View article: Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data
Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data Open
Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq) is a widely used technique to explore gene regulatory mechanisms. For most ATAC-Seq data from healthy and diseased tissues such as tumors, chromatin accessibility measurement…
View article: Building and analyzing metacells in single-cell genomics data
Building and analyzing metacells in single-cell genomics data Open
The advent of high-throughput single-cell genomics technologies has fundamentally transformed biological sciences. Currently, millions of cells from complex biological tissues can be phenotypically profiled across multiple modalities. The …
View article: Semi-supervised integration of single-cell transcriptomics data
Semi-supervised integration of single-cell transcriptomics data Open
Batch effects in single-cell RNA-seq data pose a significant challenge for comparative analyses across samples, individuals, and conditions. Although batch effect correction methods are routinely applied, data integration often leads to ov…
View article: How to predict binding specificity and ligands for new MHC-II alleles with MixMHC2pred
How to predict binding specificity and ligands for new MHC-II alleles with MixMHC2pred Open
MHC-II molecules are key mediators of antigen presentation in vertebrate species and bind to their ligands with high specificity. The very high polymorphism of MHC-II genes within species and the fast-evolving nature of these genes across …
View article: Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data
Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data Open
Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq) is a widely used technique to explore gene regulatory mechanisms. For most ATAC-Seq data from healthy and diseased tissues such as tumors, chromatin accessibility measurement…