Qing Nie
Distinguished Professor, Mathematics
School of Physical Sciences
School of Physical Sciences
Distinguished Professor, Developmental & Cell Biology
School of Biological Sciences
School of Biological Sciences
UC Presidential Chair
Ph.D., The Ohio State University, 1995
University of California, Irvine
Research Interests
Computational and Systems Biology; Machine Learning; Developmental Biology; Stochastic Dynamics; Scientific Computing and Numerical Analysis
Websites
Academic Distinctions
Chancellor's Professor, UC Irvine, 2017- 2023
Chancellor's Fellow, UC Irvine (2005-2008)
Chancellor's Fellow, UC Irvine (2005-2008)
Appointments
2017 - 2023: Chancellor's Professor, Dept of Mathematics and Dept of Developmental & Cell Biology, UC Irvine
2005-2016: Professor, Department of Mathematics, UC Irvine
2002-2005: Associate Professor, Department of Mathematics, UC Irvine
1999-2002: Assistant Professor, Department of Mathematics, UC Irvine
1997-1999: L.E. Dickson Instructor, Department of Mathematics, University of Chicago.
2005-2016: Professor, Department of Mathematics, UC Irvine
2002-2005: Associate Professor, Department of Mathematics, UC Irvine
1999-2002: Assistant Professor, Department of Mathematics, UC Irvine
1997-1999: L.E. Dickson Instructor, Department of Mathematics, University of Chicago.
Awards and Honors
Fellow, American Association for the Advancement of Science (AAAS)
Fellow, American Physical Society (APS)
Fellow, Society for Industrial and Applied Mathematics (SIAM)
Fellow, American Mathematical Society (AMS)
Fellow, American Physical Society (APS)
Fellow, Society for Industrial and Applied Mathematics (SIAM)
Fellow, American Mathematical Society (AMS)
Short Biography
Director, NSF-Simons Center for Multscale Cell Fate Research (2018 - )
Associate Director, UCI PhD Program on Mathematical, Computational, and Systems Biology (MCSB) (2009 - )
Associate Director, UCI PhD Program on Mathematical, Computational, and Systems Biology (MCSB) (2009 - )
Publications
Almet, A, Y Tsai, M Watanabe, Q. Nie. Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics. Nature Methods, 2024
Zhou P, F Bocci, T Li, and Q. Nie. Spatial transition tensor of single cells. Nature Methods, 21(6), 2024
Jin S, Plikus M, Q Nie. CellChat for systematic analysis of cell-cell communication from single-cell transcriptomics. Nature Protocols, 2024.
Sha Y, Y Qiu, P Zhou, Q Nie. Reconstructing growth and dynamic trajectories from single-cell transcriptomics data. Nature Machine Intelligence, 6(25), 2024.
Cang Z, Q. Nie. A mathematical method and software for spatially mapping intercellular communication. Nature Methods, 20(2):185-186. 2023
He C, P Zhou, Q Nie. exFINDER: identify external communication signals using single-cell transcriptomics data. Nucleic Acids Research, gkad262, in press, 2023.
Zhao W, K Johnston, H Ren, X Xu, Q. Nie. Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat. Nature Communications, 14(1128), 2023
Bocci F, P Zhou, Q. Nie. spliceJAC: Transition genes and state specific gene regulation from single-cell transcriptome data., Molecular Systems Biology, 18:e11176, 2022
Cang Z, Q. Nie, Y Zhao. Supervised Optimal Transport.
SIAM Journal on Applied Mathematics, 82(5), P1851-1877, 2022
SIAM Journal on Applied Mathematics, 82(5), P1851-1877, 2022
Ren H, B Walker, Z Cang, Q Nie. Identifying multicellular spatiotemporal
organization of cells with SpaceFlow. Nature Communications, 13(4076), 2022
organization of cells with SpaceFlow. Nature Communications, 13(4076), 2022
Zhang L, J. Zhang, Q. Nie. DIRECT-NET: An efficient method to discover cis-regulatory
elements and construct regulatory networks from single cell multi-omics data. Science Advances 8(22), 2022
elements and construct regulatory networks from single cell multi-omics data. Science Advances 8(22), 2022
Zhou P, S Wang, T Li, Q Nie. Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics, Nature Communications, 12:5609, 2021
Jin S, C. Guerrero-Juarez, L. Zhang, I. Chang, R. Ramos, C. Kuan, P. Myung, K. Plikus*, Q. Nie*. Inference and analysis of cell-cell communication using CellChat. Nature Communications, 12(1088), 2021. *:Co-corresponding authors
Zhang L, Q. Nie. scMC learns biological variation through the alignment of multiple single cell genomics datasets. Genome Biology, 22:10, 2021
Cang Z, Y. Wang, Q. Wang, K. Cho, W. Holmes, Q. Nie. A multiscale model via single-cell transcriptomics reveals robust patterning mechanism during early mammalian embryo development. PLoS Computational Biology, 17(3) e1008571, 2021.
Fu L., L Zhang, E. Dollinger, Q. Peng, Q. Nie*, X. Xie*. Predicting transcription factor binding in single cells through deep learning. Science Advances, 6:eaba9301, 2020. *:co-corresponding author.
Cang Z and Q. Nie. Inferring spatial and signaling relationships between cells from single cell transcriptomic data. Nature Communications, 11(2084), 2020.
Jin, S*., L. Zhang*, Q. Nie. scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles. Genome Biology, 21(1):25, 2020. * co-first authors
Professional Societies
Society for Applied and Industrial Mathematics (SIAM)
American Physical Society (APS)
American Association for the Advancement of Science (AAAS)
American Mathematical Society (AMS)
Research Centers
NSF-Simons Center for Multiscale Cell Fate Research
Center for Complex Biological Systems
Link to this profile
https://faculty.uci.edu/profile/?facultyId=4835
https://faculty.uci.edu/profile/?facultyId=4835
Last updated
10/20/2024
10/20/2024