Implementation of The FAIR Data Principles for Exploratory Biomarker Data from Clinical Trials
Data Intelligence, July 2021This paper describes our use of the FAIR data principles to manage clinical trial data. Read more
Publications & Preprints
Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia
Science Advances, July 2020This paper addresses how SARS-CoV2 infection may lead to anosmia in COVID-19 patients. Read more
Cellular mechanisms of epithelial stem cell self‐renewal and differentiation during homeostasis and repair
WIREs Developmental Biology, August 2019Epithelia 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
Best Practices for Managing Turnover in Data Science Groups, Teams, and Labs
SocArXiv, March 2019We discuss the challenges of personnel turnover and some potential practices for helping manage it, particularly for computational- and data-intensive research teams and projects. Read more
Best Practices for Fostering Diversity and Inclusion in Data Science: Report from the BIDS Best Practices in Data Science Series
SocArXiv, February 2019We discuss concrete actions that we can take to foster diverse and inclusive workplaces in fields around data science. 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 2018With 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
Creating Lineage Trajectory Maps Via Integration of Single-Cell RNA-Sequencing and Lineage Tracing
BioEssays, June 2018Integrating transgenic lineage tracing and single‐cell RNA‐sequencing is a robust approach for mapping developmental lineage trajectories and cell fate changes. Read more
Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics
BMC Genomics, June 2018Stable and accurate inference of branching trajectories is an important problem in single-cell genomics. We provide a quantitative comparison of existing methods and introduce a more modular novel method, Slingshot. Read more
Career Paths and Prospects in Academic Data Science: Report of the Moore-Sloan Data Science Environments Survey
SocArXiv, June 2018We take an in-depth look at career prospects in academic data science through a survey of members and affiliates at three institutes dedicated to data science at major U.S. universities. Read more
Injury Activates Transient Olfactory Stem Cell States With Diverse Lineage Capacities
Cell Stem Cell, December 2017We use multiple single-cell techniques to identify the cell state transitions underlying the stem cell self-renewal and differentiation during injury-induced regeneration of the olfactory epithelium. Olfactory stem cells shift en masse to a transient cell state unique to regeneration in which diverse fates are specified. Read more
Deconstructing Olfactory Stem Cell Trajectories at Single Cell Resolution
Cell Stem Cell, June 2017The 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