Publications

Asterisk indicates co-first authorship.


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

BMC Genomics, June 2018

Stable 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

Kelly Street, Davide Risso, Russell B. Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, and Sandrine Dudoit. (2018). Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19, 477. https://doi.org/10.1186/s12864-018-4772-0


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

bioRxiv, March 2018

Clustering of genes and/or samples is a common task in gene expression analysis. 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. It is common in the detection of novel subtypes to run many clustering algorithms, as well as rely on subsampling and ensemble methods to improve robustness. We introduce a Bioconductor R package, clusterExperiment, that implements a general and flexible strategy we entitle Resampling-based Sequential Ensemble Clustering (RSEC). Read more

Davide Risso, Liam Purvis, Russell Fletcher, Diya Das, John Ngai, Sandrine Dudoit, and Elizabeth Purdom. (2018). clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets. BioRxiv 280545. https://doi.org/10.1101/280545


Injury Activates Transient Olfactory Stem Cell States With Diverse Lineage Capacities

Cell Stem Cell, December 2017

We 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

Levi Gadye*, Diya Das*, Michael A. Sanchez*, Kelly Street, Davide Risso, Ariane Baudhuin, Michael B. Cole, Allon Wagner, Yoon Gi Choi, Elizabeth Purdom, Sandrine Dudoit, Nir Yosef, John Ngai, and Russell B. Fletcher. (2017). Injury Activates Transient Olfactory Stem Cell States With Diverse Lineage Capacities. Cell Stem Cell 21, 775-790.e9. https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(17)30452-6


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

Russell B. Fletcher*, Diya Das*, Levi Gadye, Kelly N. Street, Ariane Baudhuin, Allon Wagner, Michael B. Cole, Quetzal Flores, Yoon Gi Choi, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit, Davide Risso and John Ngai. (2017). Deconstructing Olfactory Stem Cell Trajectories at Single Cell Resolution. Cell Stem Cell 20, 817-830.e8. http://www.cell.com/cell-stem-cell/fulltext/S1934-5909(17)30127-3