| Comprehensive integration of single-cell data T Stuart, A Butler, P Hoffman, C Hafemeister, E Papalexi, WM Mauck, ... cell 177 (7), 1888-1902. e21, 2019 | 10349 | 2019 |
| Integrated analysis of multimodal single-cell data Y Hao, S Hao, E Andersen-Nissen, WM Mauck, S Zheng, A Butler, MJ Lee, ... Cell 184 (13), 3573-3587. e29, 2021 | 6641 | 2021 |
| Integrative single-cell analysis T Stuart, R Satija Nature reviews genetics 20 (5), 257-272, 2019 | 1087 | 2019 |
| Single-cell chromatin state analysis with Signac T Stuart, A Srivastava, S Madad, CA Lareau, R Satija Nature methods 18 (11), 1333-1341, 2021 | 622 | 2021 |
| The human body at cellular resolution: the NIH Human Biomolecular Atlas Program Caltech-UW TMC Cai Long lcai@ caltech. edu 21 b Shendure Jay 9 Trapnell Cole ... Nature 574 (7777), 187-192, 2019 | 375 | 2019 |
| Dictionary learning for integrative, multimodal and scalable single-cell analysis Y Hao, T Stuart, MH Kowalski, S Choudhary, P Hoffman, A Hartman, ... Nature biotechnology 42 (2), 293-304, 2024 | 201 | 2024 |
| Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation T Stuart, SR Eichten, J Cahn, YV Karpievitch, JO Borevitz, R Lister elife 5, e20777, 2016 | 191 | 2016 |
| Unique cell-type-specific patterns of DNA methylation in the root meristem T Kawakatsu, T Stuart, M Valdes, N Breakfield, RJ Schmitz, JR Nery, ... Nature plants 2 (5), 1-8, 2016 | 179 | 2016 |
| Multimodal single-cell chromatin analysis with Signac T Stuart, A Srivastava, C Lareau, R Satija BioRxiv, 2020.11. 09.373613, 2020 | 138 | 2020 |
| Toward a common coordinate framework for the human body JE Rood, T Stuart, S Ghazanfar, T Biancalani, E Fisher, A Butler, ... Cell 179 (7), 1455-1467, 2019 | 86 | 2019 |
| A single-cell transcriptional roadmap for cardiopharyngeal fate diversification W Wang, X Niu, T Stuart, E Jullian, WM Mauck III, RG Kelly, R Satija, ... Nature cell biology 21 (6), 674-686, 2019 | 75 | 2019 |
| Single nucleus multi-omics identifies human cortical cell regulatory genome diversity C Luo, H Liu, F Xie, EJ Armand, K Siletti, TE Bakken, R Fang, WI Doyle, ... Cell genomics 2 (3), 2022 | 67 | 2022 |
| Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro B Zhang, A Srivastava, E Mimitou, T Stuart, I Raimondi, Y Hao, P Smibert, ... Nature biotechnology 40 (8), 1220-1230, 2022 | 54 | 2022 |
| DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity SR Eichten, T Stuart, A Srivastava, R Lister, JO Borevitz Genome research 26 (11), 1520-1531, 2016 | 39 | 2016 |
| Comprehensive integration of single cell data. bioRxiv: 460147 T Stuart, A Butler, P Hoffman, C Hafemeister, E Papalexi, WM Mauck, ... | 33 | 2018 |
| Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution T Stuart, S Hao, B Zhang, L Mekerishvili, DA Landau, S Maniatis, R Satija, ... Nature biotechnology 41 (6), 806-812, 2023 | 30 | 2023 |
| A Genome‐Wide Association Study of Non‐Photochemical Quenching in response to local seasonal climates in Arabidopsis thaliana T Rungrat, AA Almonte, R Cheng, PJ Gollan, T Stuart, EM Aro, JO Borevitz, ... Plant Direct 3 (5), e00138, 2019 | 22 | 2019 |
| geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq A Missarova, J Jain, A Butler, S Ghazanfar, T Stuart, M Brusko, ... Genome biology 22, 1-22, 2021 | 18 | 2021 |
| An environmentally responsive transcriptional state modulates cell identities during root development M Oliva, T Stuart, D Tang, J Pflueger, D Poppe, JS Jabbari, S Gigante, ... bioRxiv, 2022.03. 04.483008, 2022 | 7 | 2022 |
| Approaches for the analysis and interpretation of whole genome bisulfite sequencing data T Stuart, S Buckberry, R Lister Epigenome Editing: Methods and Protocols, 299-310, 2018 | 7 | 2018 |
