Marlon Stoeckius

This paper introduces SPOTS, a method for integrating spatial transcriptome and proteome data, and shows it reveals biological processes in spleen and breast cancer samples.

Weighted-nearest neighbor (WNN) analysis in Seurat v4 learns per-cell modality weights to define cell states, enabling a 228-antibody human PBMC CITE-seq reference for RNA-only query mapping.

The paper identifies cis-regulatory elements and trans-factors governing mRNA stability during zebrafish MZT and develops a model to predict mRNA stability.

Seurat v3 finds scored mutual-nearest-neighbor anchors in canonical correlation space to integrate scRNA-seq batches and transfer labels, protein levels and transcriptome-wide expression across modalities.

The paper introduces cell hashing using barcoded antibodies to enable multiplexing and doublet detection in single-cell genomics, demonstrating its effectiveness with human PBMC samples.

The paper introduces ECCITE-seq, a method that simultaneously captures transcriptomes, immune clonotypes, surface markers, sample identity, and CRISPR perturbations from single cells.

The paper introduces a method to simultaneously measure epitopes and transcriptomes in single cells using oligonucleotide-labeled antibodies.