Publications & Preprints

Cellular mechanisms of epithelial stem cell self‐renewal and differentiation during homeostasis and repair

WIREs Developmental Biology, August 2019

Epithelia in adult mammals exhibit remarkable regenerative capacities owing to the presence of adult stem cells. Signaling pathways such as WNT, bone morphogenetic protein, and Sonic Hedgehog play critical roles in stem cell maintenance and cell fate decisions across diverse epithelia and conditions, suggesting that conserved mechanisms underlie the regenerative capacity of adult epithelial structures. Read more

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets

PLOS Computational Biology, September 2018

With the increasing popularity of single-cell transcriptome sequencing, many experiments are creating large gene expression datasets with the goal of detecting previously unknown heterogeneity within cells. We introduce a Bioconductor R package, clusterExperiment, that implements a general and flexible clustering strategy we entitle Resampling-based Sequential Ensemble Clustering (RSEC). Read more

Deconstructing Olfactory Stem Cell Trajectories at Single Cell Resolution

Cell Stem Cell, June 2017

The olfactory epithelium is a site of active neurogenesis. We combine single-cell transcriptomics and clonal lineage analysis to trace cell fates from the multipotent olfactory stem cell and identify multiple mechanisms controlling cell fate, including direct conversion of quiescent stem cells into support cells without cell division. Read more