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). 📄