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

• BRAIN Initiative Cell Census Network (BICCN). Nature (2021).

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

• Zizhen Yao*, Hanqing Liu*, Fangming Xie*, Stephan Fischer*, et al. Nature (2021).

Progressive immune dysfunction with advancing disease stage in renal cell carcinoma

• David A Braun*, Kelly Street*, Kelly P Burke, David L Cookmeyer, Thomas Denize, Christina B Pedersen, Satyen H Gohil, Nicholas Schindler, Lucas Pomerance, Laure Hirsch, Ziad Bakouny, Yue Hou, Juliet Forman, Teddy Huang, Shuqiang Li, Ang Cui, Derin B Keskin, John Steinharter, Gabrielle Bouchard, Maxine Sun, Erica M Pimenta, Wenxin Xu, Kathleen M Mahoney, Bradley A McGregor, Michelle S Hirsch, Steven L Chang, Kenneth J Livak, David F McDermott, Sachet A Shukla, Lars R Olsen, Sabina Signoretti, Arlene H Sharpe, Rafael A Irizarry, Toni K Choueiri**, Catherine J Wu**. Cancer Cell (2021).

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

Significance Analysis for Clustering with Single-Cell RNA-Sequencing Data

• Isabella N. Grabski, Kelly Street, Rafael A. Irizarry. bioRxiv (2022).

Book chapter: A guide to trajectory inference and RNA velocity

Philipp Weiler, Koen Van den Berge, Kelly Street*, Simone Tiberi*. bioRxiv (2021).

Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression

• Hector Roux de Bézieux, Koen Van den Berge, Kelly Street*, Sandrine Dudoit*. bioRxiv (2021).

Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects

• Koen Van den Berge, Hsin-Jung Chou, Hector Roux de Bézieux, Kelly Street, Davide Risso, John Ngai, Sandrine Dudoit. bioRxiv (2021).

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).