Selected Publications

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

A review of single-cell transcriptomics and epigenomics studies in maternal and child health

Spatially resolved immune exhaustion within the alloreactive microenvironment predicts liver transplant rejection

Trajectory inference across multiple conditions with condiments

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

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

Book chapter: A guide to trajectory inference and RNA velocity

Philipp Weiler, Koen Van den Berge, Kelly Street*, Simone Tiberi*. Single Cell Transcriptomics: Methods and Protocols. Springer US (2022).

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


Epigenetic Conservation Infers That Colorectal Cancer Progenitors Retain The Phenotypic Plasticity Of Normal Colon