| A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information Y Luo, X Zhao, J Zhou, J Yang, Y Zhang, W Kuang, J Peng, L Chen, ... Nature communications 8 (1), 573, 2017 | 957 | 2017 |
| Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex C Luo, CL Keown, L Kurihara, J Zhou, Y He, J Li, R Castanon, J Lucero, ... Science 357 (6351), 600-604, 2017 | 589 | 2017 |
| A multimodal cell census and atlas of the mammalian primary motor cortex Principal manuscript editors, Analysis coordination, ... Nature 598 (7879), 86-102, 2021 | 461 | 2021 |
| Simultaneous profiling of 3D genome structure and DNA methylation in single human cells DS Lee, C Luo, J Zhou, S Chandran, A Rivkin, A Bartlett, JR Nery, ... Nature methods 16 (10), 999-1006, 2019 | 368 | 2019 |
| A deep learning framework for modeling structural features of RNA-binding protein targets S Zhang, J Zhou, H Hu, H Gong, L Chen, C Cheng, J Zeng Nucleic acids research 44 (4), e32-e32, 2016 | 326 | 2016 |
| DNA methylation atlas of the mouse brain at single-cell resolution H Liu, J Zhou, W Tian, C Luo, A Bartlett, A Aldridge, J Lucero, JK Osteen, ... Nature 598 (7879), 120-128, 2021 | 278 | 2021 |
| Robust single-cell DNA methylome profiling with snmC-seq2 C Luo, A Rivkin, J Zhou, JP Sandoval, L Kurihara, J Lucero, R Castanon, ... Nature communications 9 (1), 3824, 2018 | 199 | 2018 |
| Robust single-cell Hi-C clustering by convolution-and random-walk–based imputation J Zhou, J Ma, Y Chen, C Cheng, B Bao, J Peng, TJ Sejnowski, JR Dixon, ... Proceedings of the National Academy of Sciences 116 (28), 14011-14018, 2019 | 197 | 2019 |
| Modeling gene regulatory networks using neural network architectures H Shu, J Zhou, Q Lian, H Li, D Zhao, J Zeng, J Ma Nature Computational Science 1 (7), 491-501, 2021 | 194 | 2021 |
| 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 | 166* | 2022 |
| Single-cell DNA methylation and 3D genome architecture in the human brain W Tian, J Zhou, A Bartlett, Q Zeng, H Liu, RG Castanon, M Kenworthy, ... Science 382 (6667), eadf5357, 2023 | 141* | 2023 |
| Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain H Liu, Q Zeng, J Zhou, A Bartlett, BA Wang, P Berube, W Tian, ... Nature 624 (7991), 366-377, 2023 | 123 | 2023 |
| A rare PRIMER cell state in plant immunity T Nobori, A Monell, TA Lee, Y Sakata, S Shirahama, J Zhou, JR Nery, ... Nature 638 (8049), 197-205, 2025 | 103* | 2025 |
| Conserved and divergent gene regulatory programs of the mammalian neocortex NR Zemke, EJ Armand, W Wang, S Lee, J Zhou, YE Li, H Liu, W Tian, ... Nature 624 (7991), 390-402, 2023 | 90 | 2023 |
| Analysis of ribosome stalling and translation elongation dynamics by deep learning S Zhang, H Hu, J Zhou, X He, T Jiang, J Zeng Cell systems 5 (3), 212-220. e6, 2017 | 90* | 2017 |
| Single-cell analysis of chromatin accessibility in the adult mouse brain S Zu, YE Li, K Wang, EJ Armand, S Mamde, ML Amaral, Y Wang, A Chu, ... Nature 624 (7991), 378-389, 2023 | 80 | 2023 |
| Epigenomic diversity of cortical projection neurons in the mouse brain Z Zhang, J Zhou, P Tan, Y Pang, AC Rivkin, MA Kirchgessner, E Williams, ... Nature 598 (7879), 167-173, 2021 | 77 | 2021 |
| Biomni: A general-purpose biomedical ai agent K Huang, S Zhang, H Wang, Y Qu, Y Lu, Y Roohani, R Li, L Qiu, G Li, ... biorxiv, 2025 | 72 | 2025 |
| Brain-wide correspondence of neuronal epigenomics and distant projections J Zhou, Z Zhang, M Wu, H Liu, Y Pang, A Bartlett, Z Peng, W Ding, ... Nature 624 (7991), 355-365, 2023 | 48 | 2023 |
| Temporally distinct 3D multi-omic dynamics in the developing human brain MG Heffel, J Zhou, Y Zhang, DS Lee, K Hou, O Pastor-Alonso, ... Nature 635 (8038), 481-489, 2024 | 43* | 2024 |
