| Inference and analysis of cell-cell communication using CellChat S Jin, CF Guerrero-Juarez, L Zhang, I Chang, R Ramos, CH Kuan, ... Nature communications 12 (1), 1088, 2021 | 4356 | 2021 |
| Differentialequations. jl–a performant and feature-rich ecosystem for solving differential equations in julia C Rackauckas, Q Nie Journal of open research software 5 (1), 15-15, 2017 | 1716 | 2017 |
| Do morphogen gradients arise by diffusion? AD Lander, Q Nie, FYM Wan Developmental cell 2 (6), 785-796, 2002 | 526 | 2002 |
| Single-cell analysis reveals fibroblast heterogeneity and myeloid-derived adipocyte progenitors in murine skin wounds CF Guerrero-Juarez, PH Dedhia, S Jin, R Ruiz-Vega, D Ma, Y Liu, ... Nature communications 10 (1), 650, 2019 | 485 | 2019 |
| Nonlinear simulation of tumor growth V Cristini, J Lowengrub, Q Nie Journal of mathematical biology 46, 191-224, 2003 | 385 | 2003 |
| Cell lineages and the logic of proliferative control AD Lander, KK Gokoffski, FYM Wan, Q Nie, AL Calof PLoS biology 7 (1), e1000015, 2009 | 365 | 2009 |
| Inferring spatial and signaling relationships between cells from single cell transcriptomic data Z Cang, Q Nie Nature communications 11 (1), 2084, 2020 | 323 | 2020 |
| An Ovol2-Zeb1 mutual inhibitory circuit governs bidirectional and multi-step transition between epithelial and mesenchymal states T Hong, K Watanabe, CH Ta, A Villarreal-Ponce, Q Nie, X Dai PLoS computational biology 11 (11), e1004569, 2015 | 296 | 2015 |
| Complex Regulation of cyp26a1 Creates a Robust Retinoic Acid Gradient in the Zebrafish Embryo RJ White, Q Nie, AD Lander, TF Schilling PLoS biology 5 (11), e304, 2007 | 268 | 2007 |
| Inference and analysis of cell-cell communication using CellChat. Nat. Commun. 12, 1088 S Jin, CF Guerrero-Juarez, L Zhang, I Chang, R Ramos, CH Kuan, ... | 240 | 2021 |
| Screening cell–cell communication in spatial transcriptomics via collective optimal transport Z Cang, Y Zhao, AA Almet, A Stabell, R Ramos, MV Plikus, SX Atwood, ... Nature methods 20 (2), 218-228, 2023 | 229 | 2023 |
| Formation of the BMP activity gradient in the Drosophila embryo CM Mizutani, Q Nie, FYM Wan, YT Zhang, P Vilmos, R Sousa-Neves, ... Developmental cell 8 (6), 915-924, 2005 | 202 | 2005 |
| Defining epidermal basal cell states during skin homeostasis and wound healing using single-cell transcriptomics D Haensel, S Jin, P Sun, R Cinco, M Dragan, Q Nguyen, Z Cang, Y Gong, ... Cell reports 30 (11), 3932-3947. e6, 2020 | 192 | 2020 |
| UFold: fast and accurate RNA secondary structure prediction with deep learning L Fu, Y Cao, J Wu, Q Peng, Q Nie, X Xie Nucleic acids research 50 (3), e14-e14, 2022 | 184 | 2022 |
| Free extracellular diffusion creates the Dpp morphogen gradient of the Drosophila wing disc S Zhou, WC Lo, JL Suhalim, MA Digman, E Gratton, Q Nie, AD Lander Current Biology 22 (8), 668-675, 2012 | 172 | 2012 |
| Cell lineage and communication network inference via optimization for single-cell transcriptomics S Wang, M Karikomi, AL MacLean, Q Nie Nucleic acids research 47 (11), e66-e66, 2019 | 166 | 2019 |
| Single cell transcriptomics of human epidermis identifies basal stem cell transition states S Wang, ML Drummond, CF Guerrero-Juarez, E Tarapore, AL MacLean, ... Nature communications 11 (1), 4239, 2020 | 165 | 2020 |
| The landscape of cell–cell communication through single-cell transcriptomics AA Almet, Z Cang, S Jin, Q Nie Current opinion in systems biology 26, 12-23, 2021 | 163 | 2021 |
| scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles S Jin, L Zhang, Q Nie Genome biology 21, 1-19, 2020 | 149 | 2020 |
| CellChat for systematic analysis of cell–cell communication from single-cell transcriptomics S Jin, MV Plikus, Q Nie Nature Protocols 20 (1), 180-219, 2025 | 148 | 2025 |