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

• Koen Van den Berge, Hector Roux de Bézieux, Kelly Street, Wouter Saelens, Robrecht Cannoodt, Yvan Saeys, Sandrine Dudoit, Lieven Clement. Nature Communications (2020).

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

• Kelly Street, Davide Risso, Russell B Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit. BMC Genomics (2018).

Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities

• Levi Gadye, Diya Das, Michael A Sanchez, Kelly Street, Ariane Baudhuin, Allon Wagner, Michael B Cole,Yoon Gi Choi, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit, Davide Risso, John Ngai, Russell B Fletcher. Cell Stem Cell (2017).

Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution

• Russell B Fletcher, Diya Das, Levi Gadye, Kelly Street, Ariane Baudhuin, Allon Wagner, Michael B Cole, Quetzal Flores, Yoon Gi Choi, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit, Davide Risso, John Ngai. Cell Stem Cell (2017).

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

• Fanny Perraudeau, Davide Risso, Kelly Street, Elizabeth Purdom, Sandrine Dudoit. F1000 Research (2017).

Preprints

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

• Hector Roux de Bézieux, Kelly Street, Stephan Fischer, Koen Van den Berge, Rebecca Chance, Davide Risso, Jesse Gillis, John Ngai, Elizabeth Purdom, Sandrine Dudoit. bioRxiv (2020).

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

• Zizhen Yao, Hanqing Liu, Fangming Xie, Stephan Fischer, et al. bioRxiv (2020).

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

• BRAIN Initiative Cell Census Network (BICCN). bioRxiv (2020).