Publications by authors named "Tim Stuart"

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Regulatory element modules as universal features for single-cell chromatin analysis.
Chrysania Lim, Javen Tan Yih Ruay, Tim Stuart

bioRxiv· December 2025

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Cis-regulatory elements at cellular resolution.
Yi Xiang See, Tim Stuart, Jay W Shin

Nat Rev Genet· October 2025

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Establishment of single-cell transcriptional states during seed germination.
Lim Chee Liew, Yue You, Lucas Auroux, Marina Oliva, Marta Peirats-Llobet, Tim Stuart

Nat Plants· September 2024

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Progress in multifactorial single-cell chromatin profiling methods.
Tim Stuart

Biochem Soc Trans· August 2024

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Approaches for the Analysis and Interpretation of Whole-Genome Bisulfite Sequencing Data.
Tim Stuart, Sam Buckberry, Trung Viet Nguyen, Ryan Lister

Methods Mol Biol· July 2024

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Dictionary learning for integrative, multimodal and scalable single-cell analysis.
Yuhan Hao, Tim Stuart, Madeline H Kowalski, Saket Choudhary, Paul Hoffman

Nat Biotechnol· February 2024

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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

Nat Biotechnol· June 2023

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Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro.
Bingjie Zhang, Avi Srivastava, Eleni Mimitou, Tim Stuart, Ivan Raimondi

Nat Biotechnol· August 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, Tim Stuart

Cell Genom· March 2022

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Author Correction: Single-cell chromatin state analysis with Signac.
Tim Stuart, Avi Srivastava, Shaista Madad, Caleb A Lareau, Rahul Satija

Nat Methods· February 2022

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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

Genome Biol· December 2021

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Single-cell chromatin state analysis with Signac.
Tim Stuart, Avi Srivastava, Shaista Madad, Caleb A Lareau, Rahul Satija

Nat Methods· November 2021

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Integrated analysis of multimodal single-cell data.
Yuhan Hao, Stephanie Hao, Erica Andersen-Nissen, William M Mauck, Shiwei Zheng, Tim Stuart

Cell· June 2021

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Toward a Common Coordinate Framework for the Human Body.
Jennifer E Rood, Tim Stuart, Shila Ghazanfar, Tommaso Biancalani, Eyal Fisher

Cell· December 2019

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A single-cell transcriptional roadmap for cardiopharyngeal fate diversification.
Wei Wang, Xiang Niu, Tim Stuart, Estelle Jullian, William M Mauck

Nat Cell Biol· June 2019

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Comprehensive Integration of Single-Cell Data.
Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi

Cell· June 2019

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Integrative single-cell analysis.
Tim Stuart, Rahul Satija

Nat Rev Genet· May 2019

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A Genome-Wide Association Study of Non-Photochemical Quenching in response to local seasonal climates in .
Tepsuda Rungrat, Andrew A Almonte, Riyan Cheng, Peter J Gollan, Tim Stuart

Plant Direct· May 2019

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Approaches for the Analysis and Interpretation of Whole Genome Bisulfite Sequencing Data.
Tim Stuart, Sam Buckberry, Ryan Lister

Methods Mol Biol· February 2019

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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

Elife· December 2016

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DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity.
Steven R Eichten, Tim Stuart, Akanksha Srivastava, Ryan Lister, Justin O Borevitz

Genome Res· November 2016

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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

Nat Plants· April 2016

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