Tim Stuart

Regulatory element modules as universal features for single-cell chromatin analysis

The paper introduces REMO, a set of DNA regulatory element modules for single-cell chromatin analysis, improving cell state separation and annotation.

Dictionary learning for integrative, multimodal, and scalable single-cell analysis

Dictionary learning enables assumption-free cross-modality single-cell mapping via multi-omic bridge datasets and scales single-modality integration to millions of cells in under an hour via atomic sketching.

Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro

The paper introduces scCUT&Tag-pro and scChromHMM to analyze chromatin states in single cells, showing their ability to characterize dynamic changes and regulatory priming across immune cell types.

Nanobody-tethered transposition allows for multifactorial chromatin profiling at single-cell resolution

This paper introduces NTT-seq, a method to measure multiple chromatin features at single-cell resolution, and demonstrates its application in immune cells.

Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants

The paper develops a multi-omic single-nucleus sequencing method and framework to analyze regulatory genome diversity in human cortical cells and link it to disease risk variants.

geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq.

geneBasis selects an optimal gene panel from scRNA-seq data by iteratively adding genes that maximize manifold distance, outperforming existing methods in resolving cell types and states.

Single-cell chromatin state analysis with Signac

Signac extends Seurat with a ChromatinAssay for single-cell chromatin and multimodal analysis, adds modified TF-IDF weighting, peak-gene linkage and mitochondrial-variant clonotyping, and scales to 733,526 cells.

Integrated analysis of multimodal single-cell data

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.

A single cell transcriptional roadmap for cardiopharyngeal fate diversification

This study uses single-cell genomics in Ciona to map cardiopharyngeal fate decisions, revealing FGF-MAPK signaling's role in maintaining multipotency and the Tbx1/10-Dach pathway's role in suppressing the first heart lineage program.

Comprehensive integration of single cell data

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.