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1.

Integrated analysis of multimodal single-cell data.

Hao, Yuhan; Hao, Stephanie; Andersen-Nissen, Erica; Mauck, William M; Zheng, Shiwei; Butler, Andrew; Lee, Maddie J; Wilk, Aaron J; Darby, Charlotte; Zager, Michael; Hoffman, Paul; Stoeckius, Marlon; Papalexi, Efthymia; Mimitou, Eleni P; Jain, Jaison; Srivastava, Avi; Stuart, Tim; Fleming, Lamar M; Yeung, Bertrand; Rogers, Angela J; McElrath, Juliana M; Blish, Catherine A; Gottardo, Raphael; Smibert, Peter; Satija, Rahul.

Cell ; 184(13): 3573-3587.e29, 2021 06 24.

Article in English | MEDLINE | ID: mdl-34062119

2.

Comprehensive Integration of Single-Cell Data.

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

Cell ; 177(7): 1888-1902.e21, 2019 06 13.

Article in English | MEDLINE | ID: mdl-31178118

3.

Toward a Common Coordinate Framework for the Human Body.

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

Cell ; 179(7): 1455-1467, 2019 12 12.

Article in English | MEDLINE | ID: mdl-31835027

4.

Integrative single-cell analysis.

Stuart, Tim; Satija, Rahul.

Nat Rev Genet ; 20(5): 257-272, 2019 05.

Article in English | MEDLINE | ID: mdl-30696980

5.

Single-cell chromatin state analysis with Signac.

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

Nat Methods ; 18(11): 1333-1341, 2021 11.

Article in English | MEDLINE | ID: mdl-34725479

6.

Author Correction: Single-cell chromatin state analysis with Signac.

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

Nat Methods ; 19(2): 257, 2022 Feb.

Article in English | MEDLINE | ID: mdl-34997233

7.

DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity.

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

Genome Res ; 26(11): 1520-1531, 2016 11.

Article in English | MEDLINE | ID: mdl-27613611

8.

Dictionary learning for integrative, multimodal and scalable single-cell analysis.

Hao, Yuhan; Stuart, Tim; Kowalski, Madeline H; Choudhary, Saket; Hoffman, Paul; Hartman, Austin; Srivastava, Avi; Molla, Gesmira; Madad, Shaista; Fernandez-Granda, Carlos; Satija, Rahul.

Nat Biotechnol ; 42(2): 293-304, 2024 Feb.

Article in English | MEDLINE | ID: mdl-37231261

9.

Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution.

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

Nat Biotechnol ; 41(6): 806-812, 2023 06.

Article in English | MEDLINE | ID: mdl-36536150

10.

Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro.

Zhang, Bingjie; Srivastava, Avi; Mimitou, Eleni; Stuart, Tim; Raimondi, Ivan; Hao, Yuhan; Smibert, Peter; Satija, Rahul.

Nat Biotechnol ; 40(8): 1220-1230, 2022 08.

Article in English | MEDLINE | ID: mdl-35332340

11.

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

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

Cell Genom ; 2(3)2022 Mar 09.

Article in English | MEDLINE | ID: mdl-35419551

12.

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

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

Genome Biol ; 22(1): 333, 2021 12 06.

Article in English | MEDLINE | ID: mdl-34872616

13.

A single-cell transcriptional roadmap for cardiopharyngeal fate diversification.

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

Nat Cell Biol ; 21(6): 674-686, 2019 06.

Article in English | MEDLINE | ID: mdl-31160712

14.

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

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

Plant Direct ; 3(5): e00138, 2019 May.

Article in English | MEDLINE | ID: mdl-31276082

15.

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

Stuart, Tim; Buckberry, Sam; Lister, Ryan.

Methods Mol Biol ; 1767: 299-310, 2018.

Article in English | MEDLINE | ID: mdl-29524143

16.

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

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

Elife ; 52016 12 02.

Article in English | MEDLINE | ID: mdl-27911260

17.

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

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

Nat Plants ; 2(5): 16058, 2016 04 29.

Article in English | MEDLINE | ID: mdl-27243651

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