2021

Clonal fitness inferred from time-series modelling of single-cell cancer genomes
Sohrab Salehi, Farhia Kabeer, Nicholas Ceglia, Mirela Andronescu, Marc J. Williams, Kieran R. Campbell, Tehmina Masud, Beixi Wang, Justina Biele, Jazmine Brimhall, David Gee, Hakwoo Lee, Jerome Ting, Allen W. Zhang, Hoa Tran, Ciara O’Flanagan, Fatemeh Dorri, Nicole Rusk, Teresa Ruiz de Algara, So Ra Lee, Brian Yu Chieh Cheng, Peter Eirew, Takako Kono, Jenifer Pham, Diljot Grewal, Daniel Lai, Richard Moore, Andrew J. Mungall, Marco A. Marra, IMAXT Consortium, Andrew McPherson, Alexandre Bouchard-Côté, Samuel Aparicio & Sohrab P. Shah
Nature, 2021

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells
Eleni P. Mimitou, Caleb A. Lareau, Kelvin Y. Chen, Andre L. Zorzetto-Fernandes, Yuhan Hao, Yusuke Takeshima, Wendy Luo, Tse-Shun Huang, Bertrand Z. Yeung, Efthymia Papalexi, Pratiksha I. Thakore, Tatsuya Kibayashi, James Badger Wing, Mayu Hata, Rahul Satija, Kristopher L. Nazor, Shimon Sakaguchi, Leif S. Ludwig, Vijay G. Sankaran, Aviv Regev, Peter Smibert
Nature Biotechnology, 2021

Integrated analysis of multimodal single-cell data
Yuhan Hao*, Stephanie Hao*, Erica Andersen-Nissen, William M. Mauck, Shiwei Zheng, Andrew Butler, Maddie Jane Lee, Aaron J. Wilk, Charlotte Darby, Michael Zagar, Paul Hoffman, Marlon Stoeckius, Efthymia Papalexi, Eleni P. Mimitou, Jaison Jain, Avi Srivastava, Tim Stuart, Lamar B. Fleming, Bertrand Yeung, Angela J. Rogers, Juliana M. McElrath, Catherine A. Blish, Raphael Gottardo, Peter Smibert*, Rahul Satija*
Cell, 2021

Characterizing the molecular regulation of inhibitory immune checkpoints with multi-modal single-cell screens
Efthymia Papalexi, Eleni Mimitou, Andrew W. Butler, Samantha Foster, Bernadette Bracken, William M. Mauck III, Hans-Hermann Wessels, Bertrand Z. Yeung, Peter Smibert, Rahul Satija
Nature Genetics, 2021

2020

Multimodal single-cell chromatin analysis with Signac
Tim Stuart, Avi Srivastava, Caleb Lareau, Rahul Satija
bioRxiv, 2020