Selected Publications

A multimodal cell census and atlas of the mammalian primary motor cortex

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Progressive immune dysfunction with advancing disease stage in renal cell carcinoma

Trajectory-based differential expression analysis for single-cell sequencing data

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities

Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution

Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference

Preprints

Significance Analysis for Clustering with Single-Cell RNA-Sequencing Data

Book chapter: A guide to trajectory inference and RNA velocity

Philipp Weiler, Koen Van den Berge, Kelly Street*, Simone Tiberi*. bioRxiv (2021).

Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression

Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects

Improving replicability in single-cell RNA-Seq cell type discovery with Dune