Distinguished Professor of Mathematics and Developmental & Cell Biology.  Director, The NSF-Simons Center for Multiscale Cell Fate Research

We are interested in using novel computational tools and  mathematical modeling to study complex biology systems. Our current research include methods for single-cell genomics, stem cell, development,  multiscale biology, and spatial modeling.  We closely collaborate with experimental laboratories on various animal models and diseases systems. We interrogate and integrate datasets from multiple different sources to dissect specific mechanisms and discover general principles.

Selected recent publications

  • Cang Z, Y Zhao, A Almet, A Stabell, R Ramos, M Plikus, S Atwood, Q. Nie.  Screening cell-cell communication in spatial transcriptomics via collective optimal transport. Nature Methods, 20, 218-228. 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
  • Wang X …. Q. Nie…. M Plikus.  Signaling by senescent melanocytes hyper-activate hair growth, Nature, in press, 2023
  • Nee K, D Ma, Q Nguyen, ….. , P Zhou, Q. Nie, S Shalabi, M LaBarge, K Kessenbrock, Pre-neoplastic stromal cells promote BRCA1-mediated breast tumorigenesis. Nature Genetics, 55(595-606), 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
  • Ren H, B Walker, Z Cang, Q. Nie. Identifying multicellular spatiotemporal 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
  • 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. Selected as Top 25 Life and Biological Sciences Article by the journal for 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
  • 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

Faculty Log In