Publications

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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

PDF DOI bioRxiv

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Nanobody-tethered transposition allows for multifactorial chromatin profiling at single-cell resolution

Tim Stuart, Stephanie Hao, Bingjie Zhang, Levan Mekerishvili, Dan Landau, Silas Maniatis, Rahul Satija, Ivan Raimondi

bioRxiv. 2022

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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, and Rahul Satija

bioRxiv. 2022

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An environmentally-responsive transcriptional state modulates cell identities during root development

Marina Oliva, Tim Stuart, Dave Tang, Jahnvi Pflueger, Daniel Poppe, Jafar S. Jabbari, Scott Gigante, Jonathan Michael Dragwidge, James Whelan, Mathew G. Lewsey, Ryan Lister

bioRxiv. 2022

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Single nucleus multi-omics identifies human cortical cell regulatory genome diversity

Chongyuan Luo*, Hanqing Liu*, Fangming Xie*, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, Wayne I. Doyle, Tim Stuart, Rebecca D. Hodge, Lijuan Hu, Bang-An Wang, Zhuzhu Zhang, Sebastian Preissl, Dong-Sung Lee, Jingtian Zhou, Sheng-Yong Niu, Rosa Castanon, Anna Bartlett, Angeline Rivkin, Xinxin Wang, Jacinta Lucero, Joseph R. Nery, David A. Davis, Deborah C. Mash, Rahul Satija, Jesse R. Dixon, Sten Linnarsson, Ed Lein, M. Margarita Behrens, Bing Ren, Eran A. Mukamel, and Joseph R. Ecker

Cell Genomics. 2022

PDF DOI bioRxiv

2021

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Single-cell chromatin state analysis with Signac

Tim Stuart, Avi Srivastava, Shaista Madad, Caleb Lareau, and Rahul Satija.

Nature Methods. 2021

PDF DOI bioRxiv

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geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq

Alsu Missarova, Jaison Jain, Andrew Butler, Shila Ghazanfar, Tim Stuart, Maigan Brusko, Clive Wasserfall, Harry Nick, Todd Brusko, Mark Atkinson, Rahul Satija, John Marioni

Genome Biology. 2021

PDF DOI bioRxiv

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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, Jaisin Jain, Avi Srivastava, Tim Stuart , Lamar B Fleming, Bertrand Yeung, Angela J Rogers, Juliana M McElrath, Catherine A Blish, Raphael Gottardo, Peter Smibert, and Rahul Satija

Cell. 2021

PDF DOI bioRxiv

2019

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Comprehensive integration of single-cell data

Tim Stuart*, Andrew Butler*, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M. Mauck III, Yuhan Hao, Marlon Stoeckius, Peter Smibert, and Rahul Satija.

Cell. 2019

PDF DOI bioRxiv

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Integrative single-cell analysis

Tim Stuart and Rahul Satija.

Nature Reviews Genetics. 2019

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Toward a Common Coordinate Framework for the Human Body

Jennifer E. Rood, Tim Stuart*, Shila Ghazanfar*, Tommaso Biancalani*, Eyal Fisher, Andrew Butler, Anna Hupalowska, Leslie Gaffney, William Mauck, Gökçen Eraslan, John C. Marioni, Aviv Regev, Rahul Satija

Cell. 2019

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The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

HuBMAP consortium

Nature. 2019

PDF DOI arXiv

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A single cell transcriptional roadmap for cardiopharyngeal fate diversification

Wei Wang*, Xiang Niu*, Tim Stuart, Estelle Jullian, William Mauck, Robert G. Kelly, Rahul Satija, Lionel Christiaen

Nature Cell Biology. 2019

PDF DOI bioRxiv

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A Genome-Wide Association Study of Non-Photochemical Quenching in response to local seasonal climates in Arabidopsis thaliana

Tepsuda Rungrat*, Andrew Allan Almonte*, Riyan Cheng, Peter J. Gollan, Tim Stuart, Eva-Mari Aro, Justin O. Borevitz, Barry Pogson, Pip B. Wilson

Plant Direct. 2019

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2018

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Approaches for the Analysis and Interpretation of Whole Genome Bisulfite Sequencing Data

Tim Stuart, Sam Buckberry, and Ryan Lister

Epigenome Editing: Methods and Protocols. Methods in Molecular Biology, 2018

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2016

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Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

Tim Stuart, Steven R Eichten, Jonathan Cahn, Yuliya V Karpievitch, Justin O Borevitz, and Ryan Lister

eLife. 2016

PDF DOI bioRxiv

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DNA Methylation profiles of diverse Brachypodium distachyon aligns with underlying genetic diversity

Steven R. Eichten, Tim Stuart, Akanksha Srivastava, Ryan Lister, and Justin O. Borevitz

Genome Research. 2016

PDF DOI bioRxiv

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Unique cell-type-specific patterns of DNA methylation in the root meristem

Taiji Kawakatsu*, Tim Stuart*, Manuel Valdes*, Natalie Breakfield, Robert J. Schmitz, Joseph R. Nery, Mark A. Urich, Xinwei Han, Ryan Lister, Philip N. Benfey, and Joseph R. Ecker

Nature Plants. 2016

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* denotes equal contribution