| Reversed graph embedding resolves complex single-cell trajectories X Qiu, Q Mao, Y Tang, L Wang, R Chawla, HA Pliner, C Trapnell Nature methods 14 (10), 979-982, 2017 | 2943 | 2017 |
| The single-cell transcriptional landscape of mammalian organogenesis J Cao, M Spielmann, X Qiu, X Huang, DM Ibrahim, AJ Hill, F Zhang, ... Nature 566 (7745), 496-502, 2019 | 2501 | 2019 |
| Single-cell mRNA quantification and differential analysis with Census X Qiu, A Hill, J Packer, D Lin, YA Ma, C Trapnell Nature methods 14 (3), 309-315, 2017 | 1271 | 2017 |
| Comprehensive single-cell transcriptional profiling of a multicellular organism J Cao, JS Packer, V Ramani, DA Cusanovich, C Huynh, R Daza, X Qiu, ... Science 357 (6352), 661-667, 2017 | 1261 | 2017 |
| Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data HA Pliner, JS Packer, JL McFaline-Figueroa, DA Cusanovich, RM Daza, ... Molecular cell 71 (5), 858-871. e8, 2018 | 586 | 2018 |
| Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays A Chen, S Liao, M Cheng, K Ma, L Wu, Y Lai, X Qiu, J Yang, J Xu, S Hao, ... Cell 185 (10), 1777-1792. e21, 2022 | 549 | 2022 |
| The cis-regulatory dynamics of embryonic development at single-cell resolution DA Cusanovich, JP Reddington, DA Garfield, RM Daza, D Aghamirzaie, ... Nature 555 (7697), 538-542, 2018 | 338 | 2018 |
| Mapping transcriptomic vector fields of single cells X Qiu, Y Zhang, JD Martin-Rufino, C Weng, S Hosseinzadeh, D Yang, ... Cell 185 (4), 690-711. e45, 2022 | 222* | 2022 |
| Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis NK Hanchate, K Kondoh, Z Lu, D Kuang, X Ye, X Qiu, L Pachter, ... Science 350 (6265), 1251-1255, 2015 | 222 | 2015 |
| A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition JL McFaline-Figueroa, AJ Hill, X Qiu, D Jackson, J Shendure, C Trapnell Nature genetics 51 (9), 1389-1398, 2019 | 152 | 2019 |
| Inferring causal gene regulatory networks from coupled single-cell expression dynamics using scribe X Qiu, A Rahimzamani, L Wang, B Ren, Q Mao, T Durham, ... Cell systems 10 (3), 265-274. e11, 2020 | 150* | 2020 |
| Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution D Yang, MG Jones, S Naranjo, WM Rideout, KHJ Min, R Ho, W Wu, ... Cell 185 (11), 1905-1923. e25, 2022 | 130 | 2022 |
| Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq Q Qiu, P Hu, X Qiu, KW Govek, PG Cámara, H Wu Nature methods 17 (10), 991-1001, 2020 | 116 | 2020 |
| Thyroid hormone regulates distinct paths to maturation in pigment cell lineages LM Saunders, AK Mishra, AJ Aman, VM Lewis, MB Toomey, JS Packer, ... Elife 8, e45181, 2019 | 106 | 2019 |
| Single-cell Stereo-seq reveals induced progenitor cells involved in axolotl brain regeneration X Wei, S Fu, H Li, Y Liu, S Wang, W Feng, Y Yang, X Liu, YY Zeng, ... Science 377 (6610), eabp9444, 2022 | 105 | 2022 |
| Aligning single-cell developmental and reprogramming trajectories identifies molecular determinants of myogenic reprogramming outcome D Cacchiarelli, X Qiu, S Srivatsan, A Manfredi, M Ziller, E Overbey, ... Cell Systems 7 (3), 258-268. e3, 2018 | 72 | 2018 |
| Massively parallel base editing to map variant effects in human hematopoiesis JD Martin-Rufino, N Castano, M Pang, EI Grody, S Joubran, A Caulier, ... Cell 186 (11), 2456-2474. e24, 2023 | 35 | 2023 |
| From understanding the development landscape of the canonical fate-switch pair to constructing a dynamic landscape for two-step neural differentiation X Qiu, S Ding, T Shi PloS one 7 (12), e49271, 2012 | 33 | 2012 |
| HCCNet: an integrated network database of hepatocellular carcinoma B He, X Qiu, P Li, L Wang, Q Lv, T Shi Cell Research 20 (6), 732-734, 2010 | 33 | 2010 |
| A transcriptional dynamic network during Arabidopsis thaliana pollen development J Wang, X Qiu, Y Li, Y Deng, T Shi BMC Systems Biology 5, 1-11, 2011 | 22 | 2011 |
Cole TrapnellAssociate Professor, Dept. of Genome Sciences, University of WashingtonVerified email at uw.edu
