Qing Nie

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 66

Top Topics

Basal Cell Carcinoma

High Throughput

Top Venues

Nature communications

PLoS computational biology

Science advances

This page only lists publications with an associated author ORCID identifier.

Publications

Tae-Yun Kang, Federico Bocci, Qing Nie, José Nelson Onuchic, Andre Levchenko
Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification. eLife 12 (2024)
Peijie Zhou, Federico Bocci, Tiejun Li, Qing Nie
Spatial transition tensor of single cells. Nature methods 21 (6) (2024)
Suoqin Jin, Maksim V Plikus, Qing Nie
CellChat for systematic analysis of cell-cell communication from single-cell transcriptomics. Nature protocols (2024)
Kevin G Johnston, Steven F Grieco, Qing Nie, Fabian Joachim Theis, Xiangmin Xu
Small data methods in omics: the power of one. Nature methods (2024)
Peijie Zhou, Federico Bocci, Tiejun Li, Qing Nie
Spatial transition tensor of single cells. Nature methods 21 (6) (2024)
Axel A Almet, Yuan-Chen Tsai, Momoko Watanabe, Qing Nie
Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics. Nature methods (2024)
Peijie Zhou, Federico Bocci, Tiejun Li, Qing Nie
Spatial transition tensor of single cells. Nature methods 21 (6) (2024)
Peijie Zhou, Federico Bocci, Tiejun Li, Qing Nie
Spatial transition tensor of single cells. Nature methods 21 (6) (2024)
Peijie Zhou, Federico Bocci, Tiejun Li, Qing Nie
Spatial transition tensor of single cells. Nature methods (2024)
Tae-Yun Kang, Federico Bocci, Qing Nie, José Nelson Onuchic, Andre Levchenko
Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification. eLife 12 (2024)
Tae-Yun Kang, Federico Bocci, Qing Nie, José Nelson Onuchic, Andre Levchenko
Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification. eLife 12 (2024)
Peijie Zhou, Federico Bocci, Tiejun Li, Qing Nie
Spatial transition tensor of single cells. Nature methods (2024)
Tae-Yun Kang, Federico Bocci, Qing Nie, José Nelson Onuchic, Andre Levchenko
Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification. eLife 12 (2024)
Yutong Sha, Yuchi Qiu, Peijie Zhou, Qing Nie
Reconstructing growth and dynamic trajectories from single-cell transcriptomics data. Nature machine intelligence 6 (1) (2023)
Zixuan Cang, Yanxiang Zhao, Axel A Almet, Adam Stabell, Raul Ramos, Maksim V Plikus, Scott X Atwood, Qing Nie
Screening cell-cell communication in spatial transcriptomics via collective optimal transport. Nature methods 20 (2) (2023)
Wei Zhao, Kevin G Johnston, Honglei Ren, Xiangmin Xu, Qing Nie
Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat. Nature communications 14 (1) (2023)
Benjamin L Walker, Qing Nie
NeST: nested hierarchical structure identification in spatial transcriptomic data. Nature communications 14 (1) (2023)
Zixuan Cang, Yanxiang Zhao, Axel A Almet, Adam Stabell, Raul Ramos, Maksim V Plikus, Scott X Atwood, Qing Nie
Screening cell-cell communication in spatial transcriptomics via collective optimal transport. Nature methods (2023)
Wei Zhao, Kevin G Johnston, Honglei Ren, Xiangmin Xu, Qing Nie
Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat. Nature communications 14 (1) (2023)
Zixuan Cang, Yanxiang Zhao, Axel A Almet, Adam Stabell, Raul Ramos, Maksim V Plikus, Scott X Atwood, Qing Nie
Screening cell-cell communication in spatial transcriptomics via collective optimal transport. Nature methods 20 (2) (2023)
Ee Shan Liau, Suoqin Jin, Yen-Chung Chen, Wei-Szu Liu, Maëliss Calon, Stéphane Nedelec, Qing Nie, Jun-An Chen
Single-cell transcriptomic analysis reveals diversity within mammalian spinal motor neurons. Nature communications 14 (1) (2023)
Zixuan Cang, Yanxiang Zhao, Axel A Almet, Adam Stabell, Raul Ramos, Maksim V Plikus, Scott X Atwood, Qing Nie
Screening cell-cell communication in spatial transcriptomics via collective optimal transport. Nature methods 20 (2) (2023)
Zixuan Cang, Yanxiang Zhao, Axel A Almet, Adam Stabell, Raul Ramos, Maksim V Plikus, Scott X Atwood, Qing Nie
Screening cell-cell communication in spatial transcriptomics via collective optimal transport. Nature methods (2023)
Kevin Nee, Dennis Ma, Quy H Nguyen, Maren Pein, Nicholas Pervolarakis, Jacob Insua-Rodríguez, Yanwen Gong, Grace Hernandez, Hamad Alshetaiwi, Justice Williams, Maha Rauf, Kushal Rajiv Dave, Keerti Boyapati, Aliza Hasnain, Christian Calderon, Anush Markaryan, Robert Edwards, Erin Lin, Ritesh Parajuli, Peijie Zhou, Qing Nie, Sundus F Shalabi, Mark A LaBarge, Kai Kessenbrock
Preneoplastic stromal cells promote BRCA1-mediated breast tumorigenesis. Nature genetics (2023)
Ee Shan Liau, Suoqin Jin, Yen-Chung Chen, Wei-Szu Liu, Maëliss Calon, Stéphane Nedelec, Qing Nie, Jun-An Chen
Single-cell transcriptomic analysis reveals diversity within mammalian spinal motor neurons. Nature communications 14 (1) (2023)
Zixuan Cang, Yanxiang Zhao, Axel A Almet, Adam Stabell, Raul Ramos, Maksim V Plikus, Scott X Atwood, Qing Nie
Screening cell-cell communication in spatial transcriptomics via collective optimal transport. Nature methods (2023)
Gérald Coulis, Diego Jaime, Christian F Guerrero-Juarez, Jenna M Kastenschmidt, Philip K Farahat, Quy Nguyen, Nicholas Pervolarakis, Katherine McLinden, Lauren Thurlow, Saba Movahedi, Brandon S Hughes, Jorge Duarte, Andrew M Sorn, Elizabeth Montoya, Izza Mozaffar, Morgan A Dragan, Shivashankar Othy, Trupti Joshi, Chetan P Hans, Virginia E Kimonis, Adam L MacLean, Qing Nie, Lindsay M Wallace, Scott Q Harper, Tahseen Mozaffar, Marshall W Hogarth, Surajit Bhattacharya, Jyoti K Jaiswal, David R Golann, Qi Su, Kai Kessenbrock, Michael J Stec, Melissa J Spencer, Jesse R Zamudio, S Armando Villalta
Single-cell and spatial transcriptomics identify a macrophage population associated with skeletal muscle fibrosis. Science advances 9 (27) (2023)
Federico Bocci, Dongya Jia, Qing Nie, Mohit Kumar Jolly, Jose Onuchic
Theoretical and computational tools to model multistable gene regulatory networks. Reports on progress in physics. Physical Society (Great Britain) (2023)
Changhan He, Peijie Zhou, Qing Nie
exFINDER: identify external communication signals using single-cell transcriptomics data. Nucleic acids research (2023)
Yutong Sha, Yuchi Qiu, Peijie Zhou, Qing Nie
Reconstructing growth and dynamic trajectories from single-cell transcriptomics data. Nature machine intelligence 6 (1) (2023)
Yutong Sha, Yuchi Qiu, Peijie Zhou, Qing Nie
Reconstructing growth and dynamic trajectories from single-cell transcriptomics data. Nature machine intelligence 6 (1) (2023)
Zixuan Cang, Yanxiang Zhao, Axel A Almet, Adam Stabell, Raul Ramos, Maksim V Plikus, Scott X Atwood, Qing Nie
Screening cell-cell communication in spatial transcriptomics via collective optimal transport. Nature methods 20 (2) (2023)
Ee Shan Liau, Suoqin Jin, Yen-Chung Chen, Wei-Szu Liu, Maëliss Calon, Stéphane Nedelec, Qing Nie, Jun-An Chen
Single-cell transcriptomic analysis reveals diversity within mammalian spinal motor neurons. Nature communications 14 (1) (2023)
Xiaojie Wang, Raul Ramos, Anne Q Phan, Kosuke Yamaga, Jessica L Flesher, Shan Jiang, Ji Won Oh, Suoqin Jin, Sohail Jahid, Chen-Hsiang Kuan, Truman Kt Nguyen, Heidi Y Liang, Nitish Udupi Shettigar, Renzhi Hou, Kevin H Tran, Andrew Nguyen, Kimberly N Vu, Jennie L Phung, Jonard P Ingal, Katelyn M Levitt, Xiaoling Cao, Yingzi Liu, Zhili Deng, Nobuhiko Taguchi, Vanessa M Scarfone, Guangfang Wang, Kara Nicole Paolilli, Xiaoyang Wang, Christian F Guerrero-Juarez, Ryan T Davis, Elyse Noelani Greenberg, Rolando Ruiz-Vega, Priya Vasudeva, Rabi Murad, Lily Halida Putri Widyastuti, Hye-Lim Lee, Kevin J McElwee, Alain-Pierre Gadeau, Devon A Lawson, Bogi Andersen, Ali Mortazavi, Zhengquan Yu, Qing Nie, Takahiro Kunisada, Michael Karin, Jan P Tuckermann, Jeffrey D Esko, Anand K Ganesan, Ji Li, Maksim V Plikus
Signalling by senescent melanocytes hyperactivates hair growth. Nature 618 (7966) (2023)
Wei Zhao, Kevin G Johnston, Honglei Ren, Xiangmin Xu, Qing Nie
Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat. Nature communications 14 (1) (2023)
Zixuan Cang, Yanxiang Zhao, Axel A Almet, Adam Stabell, Raul Ramos, Maksim V Plikus, Scott X Atwood, Qing Nie
Screening cell-cell communication in spatial transcriptomics via collective optimal transport. Nature methods 20 (2) (2023)
Ee Shan Liau, Suoqin Jin, Yen-Chung Chen, Wei-Szu Liu, Maëliss Calon, Stéphane Nedelec, Qing Nie, Jun-An Chen
Single-cell transcriptomic analysis reveals diversity within mammalian spinal motor neurons. Nature communications 14 (1) (2023)
Zixuan Cang, Yanxiang Zhao, Axel A Almet, Adam Stabell, Raul Ramos, Maksim V Plikus, Scott X Atwood, Qing Nie
Screening cell-cell communication in spatial transcriptomics via collective optimal transport. Nature methods 20 (2) (2023)
Zixuan Cang, Yanxiang Zhao, Axel A Almet, Adam Stabell, Raul Ramos, Maksim V Plikus, Scott X Atwood, Qing Nie
Screening cell-cell communication in spatial transcriptomics via collective optimal transport. Nature methods 20 (2) (2023)
Wei Zhao, Kevin G Johnston, Honglei Ren, Xiangmin Xu, Qing Nie
Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat. Nature communications 14 (1) (2023)
Wei Zhao, Kevin G Johnston, Honglei Ren, Xiangmin Xu, Qing Nie
Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat. Nature communications 14 (1) (2023)
Wei Zhao, Kevin G Johnston, Honglei Ren, Xiangmin Xu, Qing Nie
Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat. Nature communications 14 (1) (2023)
Xiong Ying, Si-Yang Leng, Huan-Fei Ma, Qing Nie, Ying-Cheng Lai, Wei Lin
Continuity Scaling: A Rigorous Framework for Detecting and Quantifying Causality Accurately. Research (Washington, D.C.) 2022 (2022)
Min Deng, Christian F Guerrero-Juarez, Xiaole Sheng, Jiuzhi Xu, Xi Wu, Kai Yao, Mengzhen Li, Xu Yang, Guilin Li, Jintao Xiao, Xiaowei Liu, Kaichun Wu, Fazheng Ren, Qing Nie, Maksim V Plikus, Zhengquan Yu, Cong Lv
Lepr + mesenchymal cells sense diet to modulate intestinal stem/progenitor cells via Leptin-Igf1 axis. Cell research 32 (7) (2022)
Honglei Ren, Benjamin L Walker, Zixuan Cang, Qing Nie
Identifying multicellular spatiotemporal organization of cells with SpaceFlow. Nature communications 13 (1) (2022)
Christian F Guerrero-Juarez, Gun Ho Lee, Yingzi Liu, Shuxiong Wang, Matthew Karikomi, Yutong Sha, Rachel Y Chow, Tuyen T L Nguyen, Venus Sosa Iglesias, Sumaira Z Aasi, Michael L Drummond, Qing Nie, Kavita Y Sarin, Scott X Atwood
Single-cell analysis of human basal cell carcinoma reveals novel regulators of tumor growth and the tumor microenvironment. Science advances 8 (23) (2022)
Lihua Zhang, Jing Zhang, Qing Nie
DIRECT-NET: An efficient method to discover cis-regulatory elements and construct regulatory networks from single-cell multiomics data. Science advances 8 (22) (2022)
Yingxin Cao, Laiyi Fu, Jie Wu, Qinke Peng, Qing Nie, Jing Zhang, Xiaohui Xie
Integrated analysis of multimodal single-cell data with structural similarity. Nucleic acids research (2022)
Benjamin L Walker, Zixuan Cang, Honglei Ren, Eric Bourgain-Chang, Qing Nie
Deciphering tissue structure and function using spatial transcriptomics. Communications biology 5 (1) (2022)
Federico Bocci, Peijie Zhou, Qing Nie
spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data. Molecular systems biology 18 (11) (2022)
Yuchi Qiu, Lianna Fung, Thomas F Schilling, Qing Nie
Multiple morphogens and rapid elongation promote segmental patterning during development. PLoS computational biology 17 (6) (2021)
Zixuan Cang, Yangyang Wang, Qixuan Wang, Ken W Y Cho, William C Holmes, Qing Nie
A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development. PLoS computational biology 17 (3) (2021)
Adam L MacLean, Qing Nie
The diverse landscape of modeling in single-cell biology. Physical biology 18 (5) (2021)
Lihua Zhang, Qing Nie
scMC learns biological variation through the alignment of multiple single-cell genomics datasets. Genome biology 22 (1) (2021)
Jia-Wen Hou, Huan-Fei Ma, Dake He, Jie Sun, Qing Nie, Wei Lin
Harvesting random embedding for high-frequency change-point detection in temporal complex systems. National science review 9 (4) (2021)
Suoqin Jin, Christian F Guerrero-Juarez, Lihua Zhang, Ivan Chang, Raul Ramos, Chen-Hsiang Kuan, Peggy Myung, Maksim V Plikus, Qing Nie
Inference and analysis of cell-cell communication using CellChat. Nature communications 12 (1) (2021)
Xiaoqiang Sun, Ji Zhang, Qing Nie
Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples. PLoS computational biology 17 (3) (2021)
Laiyi Fu, Lihua Zhang, Emmanuel Dollinger, Qinke Peng, Qing Nie, Xiaohui Xie
Predicting transcription factor binding in single cells through deep learning. Science advances 6 (51) (2020)
Suoqin Jin, Lihua Zhang, Qing Nie
scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles. Genome biology 21 (1) (2020)
Zixuan Cang, Qing Nie
Inferring spatial and signaling relationships between cells from single cell transcriptomic data. Nature communications 11 (1) (2020)
Yangyang Wang, Christian F Guerrero-Juarez, Yuchi Qiu, Huijing Du, Weitao Chen, Seth Figueroa, Maksim V Plikus, Qing Nie
A multiscale hybrid mathematical model of epidermal-dermal interactions during skin wound healing. Experimental dermatology 28 (4) (2020)
Praveer P Sharma, Adam L MacLean, Lina Meinecke, David E Clouthier, Qing Nie, Thomas Friedrich Schilling
Transcriptomics reveals complex kinetics of dorsal-ventral patterning gene expression in the mandibular arch. Genesis (New York, N.Y. : 2000) 57 (1) (2018)
Huijing Du, Yangyang Wang, Daniel Haensel, Briana Lee, Xing Dai, Qing Nie
Multiscale modeling of layer formation in epidermis. PLoS computational biology 14 (2) (2018)
William R Holmes, Nabora Soledad Reyes de Mochel, Qixuan Wang, Huijing Du, Tao Peng, Michael Chiang, Olivier Cinquin, Ken Cho, Qing Nie
Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst. PLoS computational biology 13 (1) (2017)
Tao Peng, Linan Liu, Adam L MacLean, Chi Wut Wong, Weian Zhao, Qing Nie
A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions. BMC systems biology 11 (1) (2017)
Qixuan Wang, Julian Sosnik, Thomas Friedrich Schilling, Qing Nie
Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains. PLoS computational biology 13 (1) (2017)