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. BMC Bioinformatics (2024).

A review of single-cell transcriptomics and epigenomics studies in maternal and child health

• Chang Shu, Kelly Street, Carrie V. Breton, Theresa M. Bastain, Melissa L. Wilson. Epigenomics (2024).

Spatially resolved immune exhaustion within the alloreactive microenvironment predicts liver transplant rejection

• Arianna Barbetta, Brittany Rocque, Sarah Bangerth, Kelly Street, Carly Weaver, Shefali Chopra, Janet Kim, Linda Sher, Brice Gaudilliere, Omid Akbari, Rohit Kohli, Juliet Emamaullee. Science Advances (2024).

Trajectory inference across multiple conditions with condiments

• Hector Roux de Bézieux, Koen Van den Berge, Kelly Street*, Sandrine Dudoit*. Nature Communications (2024).

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

• Isabella N. Grabski, Kelly Street, Rafael A. Irizarry. Nature Methods (2023).

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. Cell Reports Methods (2022).

Book chapter: A guide to trajectory inference and RNA velocity

Philipp Weiler, Koen Van den Berge, Kelly Street*, Simone Tiberi*. Single Cell Transcriptomics: Methods and Protocols. Springer US (2022).

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

Epigenetic Conservation Infers That Colorectal Cancer Progenitors Retain The Phenotypic Plasticity Of Normal Colon

• Kelly Street, Kimberly Siegmund, Darryl Shibata. Research Square (2023).