Publications

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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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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