Simon Steiger

Disagreement between demultiplexing methods reveals structured cell quality gradients in multiplexed single-cell data

This paper introduces Split-flow, a pipeline that uses concordance between demultiplexing methods to classify cell quality in multiplexed single-cell data, revealing structured quality gradients.

Conserved programs and specificities of T cells targeting hematological malignancies

This study identifies rare tumor-reactive T cells and conserved antigen repertoires in multiple myeloma and acute myeloid leukemia, developing a TCR fitness model to predict immunotherapy response.

pheno-seq - linking morphological features to gene expression in 3D cell culture systems

The paper introduces pheno-seq, a method that links morphological features to gene expression in 3D cell cultures, showing its ability to identify morphology-specific genes and regulatory states not captured by scRNA-seq.