2024

2023

Mammalian olfactory cortex neurons retain molecular signatures of ancestral cell types
S. Zeppilli, A. Ortega Gurrola, P. Demetci, D. H. Brann, R. Attey, N. Zilkha, T. Kimchi, S. R. Datta, R. Singh, M. A. Tosches, A. Crombach, A. Fleischmann
bioRxiv, 2023

Single-cell DNA replication dynamics in genomically unstable cancers
Adam C. Weiner, Marc J. Williams, Hongyu Shi, Ignacio Vázquez-García, Sohrab Salehi, Nicole Rusk, Samuel Aparicio, Sohrab P. Shah, Andrew McPherson
bioRxiv, 2023

Exploiting allele-specific transcriptional effects of subclonal copy number alterations for genotype-phenotype mapping in cancer cell populations
Hongyu Shi, Marc J. Williams, Gryte Satas, Adam C. Weiner, Andrew McPherson, Sohrab P. Shah
bioRxiv, 2023

Spatial host-microbiome sequencing reveals niches in the mouse gut
Britta Lötstedt, Martin Stražar, Ramnik Xavier, Aviv Regev & Sanja Vickovic
Nat Biotechnology, 2023

A global view of aging and Alzheimer’s pathogenesis-associated cell population dynamics and molecular signatures in human and mouse brains
Andras Sziraki, Ziyu Lu, Jasper Lee, Gabor Banyai, Sonya Anderson, Abdulraouf Abdulraouf, Eli Metzner, Andrew Liao, Jason Banfelder, Alexander Epstein, Chloe Schaefer, Zihan Xu, Zehao Zhang, Li Gan, Peter T. Nelson, Wei Zhou & Junyue Cao
Nature Genetics, 2023
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Breast Cancer Macrophage Heterogeneity and Self-renewal are Determined by Spatial Localization
Nir Ben-Chetrit, Xiang Niu, Jesus Sotelo, Ariel D. Swett, Vinagolu K. Rajasekhar, Maria S. Jiao, Caitlin M. Stewart, Priya Bhardwaj, Sanjay Kottapalli, Saravanan Ganesan, Pierre-Louis Loyher, Catherine Potenski, Assaf Hannuna, Kristy A. Brown, Neil M. Iyengar, Dilip D. Giri, Scott W. Lowe, John H. Healey, Frederic Geissmann, Irit Sagi, Johanna A. Joyce, Dan A. Landau
bioRxiv, 2023
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Tracking cell-type-specific temporal dynamics in human and mouse brains
Ziyu Lu, Melissa Zhang, Jasper Lee, Andras Sziraki, Sonya Anderson, Zehao Zhang, Zihan Xu, Weirong Jiang, Shaoyu Ge, Peter T. Nelson, Wei Zhou, Junyue Cao
Cell, 2023
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Multimodal single-cell datasets characterize antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection
Bingjie Zhang, Rabi Upadhyay, Yuhan Hao, Marie I. Samanovic, Ramin S. Herati, John D. Blair, Jordan Axelrad, Mark J. Mulligan, Dan R. Littman & Rahul Satija
Nature Immunology, 2023
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Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths
Mariela Cortés-López, Paulina Chamely, Allegra G. Hawkins, Robert F. Stanley, Ariel D. Swett, Saravanan Ganesan, Tarek H. Mouhieddine, Xiaoguang Dai, Lloyd Kluegel, Celine Chen, Kiran Batta, Nili Furer, Rahul S. Vedula, John Beaulaurier , Alexander W. Drong, Scott Hickey , Neville Dusaj, Gavriel Mullokandov, Adam M. Stasiw, Jiayu Su, Dan A. Landau
Cell Stem Cell, 2023
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Dictionary learning for integrative, multimodal, and scalable single-cell analysis
Yuhan Hao, Tim Stuart, Madeline Kowalski, Saket Choudhary, Paul Hoffman, Austin Hartman, Avi Srivastava, Gesmira Molla, Shaista Madad, Carlos Fernandez-Granda, Rahul Satija
Nature Biotechnology, 2023
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Phospho-seq: Integrated, multi-modal profiling of intracellular protein dynamics in single cells
John D. Blair, Austin Hartman, Fides Zenk, Carol Dalgarno, Barbara Treutlein, Rahul Satija
bioRxiv, 2023
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CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators
Madeline H. Kowalski, Hans-Hermann Wessels, Johannes Linder, Saket Choudhary, Austin Hartman, Yuhan Hao, Isabella Mascio, Carol Dalgarno, Anshul Kundaje, Rahul Satija
bioRxiv, 2023
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Defining ancestry, heritability and plasticity of cellular phenotypes in somatic evolution
Joshua S. Schiffman, Andrew R. D’Avino, Tamara Prieto, Catherine Potenski, Yilin Fan, Toshiro Hara, Mario L. Suvà, Dan A. Landau
bioRxiv, 2023
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2022

Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq
Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Yuhan Hao, Efthymia Papalexi, William M. Mauck III, Lu Lu, John A. Morris, Eleni P. Mimitou, Peter Smibert, Neville E. Sanjana & Rahul Satija
Nature Methods, 2022
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Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution
Tim Stuart, Stephanie Hao, Bingjie Zhang, Levan Mekerishvili, Dan A. Landau, Silas Maniatis, Rahul Satija & Ivan Raimondi
Nature Biotechnology, 2022
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Ovarian cancer mutational processes drive site-specific immune evasion
Ignacio Vázquez-García, Florian Uhlitz, Nicholas Ceglia, Jamie L. P. Lim, Michelle Wu, Neeman Mohibullah, Juliana Niyazov, Arvin Eric B. Ruiz, Kevin M. Boehm, Viktoria Bojilova, Christopher J. Fong, Tyler Funnell, Diljot Grewal, Eliyahu Havasov, Samantha Leung, Arfath Pasha, Druv M. Patel, Maryam Pourmaleki, Nicole Rusk, Hongyu Shi, Rami Vanguri, Marc J. Williams, Allen W. Zhang, Vance Broach, …Sohrab P. Shah
Nature, 2022

Cell type profiling in salamanders identifies innovations in vertebrate forebrain evolution
Jamie Woych, Alonso Ortega Gurrola, Astrid Deryckere, Eliza C. B. Jaeger, Elias Gumnit, Gianluca Merello, Jiacheng Gu, Alberto Joven Araus, Nicholas D. Leigh, Maximina Yun, András Simon, Maria Antonietta Tosches
Science, 2022
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Glutamatergic neuron types in the amygdala of the urodele amphibian Pleurodeles waltl
Astrid Deryckere, Jamie Woych, Eliza C. B. Jaeger, Maria Antonietta Tosches
bioRxiv, 2022

Integrated Single-Cell Genotyping and Chromatin Accessibility Charts JAK2V617F Human Hematopoietic Differentiation
Robert M. Myers, Franco Izzo, Sanjay Kottapalli, Tamara Prieto, Andrew Dunbar, Robert L. Bowman, Eleni P. Mimitou, Maximilian Stahl, Sebastian El Ghaity-Beckley, JoAnn Arandela, Ramya Raviram, Saravanan Ganesan, Levan Mekerishvili, Ronald Hoffman, Ronan Chaligné, Omar Abdel-Wahab, Peter Smibert, Bridget Marcellino, Ross L. Levine, Dan Avi Landau
bioRxiv, 2022
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Integrated protein and transcriptome high-throughput spatial profiling
Nir Ben Chetrit, Xiang Niu, Ariel D. Swett, Jesus Sotelo, Maria S. Jiao, Patrick Roelli, Marlon Stoeckius, Dan Avi Landau
bioRxiv, 2022

Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation
Anna S. Nam, Neville Dusaj, Franco Izzo, Rekha Murali, Robert M. Myers, Tarek Mouhieddine, Jesus Sotelo, Salima Benbarche, Michael Waarts, Federico Gaiti, Sabrin Tahri, Ross Levine, Omar Abdel-Wahab, Lucy A. Godley, Ronan Chaligne, Irene Ghobrial, Dan A. Landau
Nature Genetics, 2022
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Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro
Bingjie Zhang, Avi Srivastava, Eleni Mimitou, Tim Stuart, Ivan Raimondi, Yuhan Hao, Peter Smibert, Rahul Satija
Nature Biotechnology, 2022
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PySeq2500: An open source toolkit for repurposing HiSeq 2500 sequencing systems as versatile fluidics and imaging platforms
Kunal Pandit, Joana Petrescu, Miguel Cuevas, William Stephenson, Peter Smibert, Hemali Phatnani, Silas Maniatis
Scientific Reports, 2022
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Comparison and evaluation of statistical error models for scRNA-seq
Saket Choudhary, Rahul Satija
Genome Biology, 2022

2021

Multimodal single-cell chromatin analysis with Signac
Tim Stuart, Avi Srivastava, Shaista Madad, Caleb Lareau, Rahul Satija
Nature Methods, 2021

Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states
Ronan Chaligne, Federico Gaiti, Dana Silverbush, Joshua S. Schiffman, Hannah R. Weisman, Lloyd Kluegel, Simon Gritsch, Sunil D. Deochand, L. Nicolas Gonzalez Castro, Alyssa R. Richman, Johanna Klughammer, Tommaso Biancalani, Christoph Muus, Caroline Sheridan, Alicia Alonso, Franco Izzo, Jane Park, Orit Rozenblatt-Rosen, Aviv Regev, Mario L. Suvà & Dan A. Landau
Nature Genetics, 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
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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
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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
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