Director, The NSF-Simons Center for Multiscale Cell Fate Research

Systems Biology – We are interested in using sophisticated computational tools and novel mathematical modeling to study complex biology systems. Our current research focuses include cell fate dynamics, stem cell, developmental patterning, cancer, multiscale biology, development of tools on analyzing single-cell sequencing data, and spatial modeling.  We closely collaborate with many experimental laboratories on various animal models and systems. We also interrogate and integrate datasets from multiple different sources to discover biological principles with broader applications.

Recent publications

  • C. Rackaukas, T. Schilling, Q. Nie. Mean-Independent Noise Control of Cell Fates via Intermediate State. iScience, DOI:, Vol. 3, Pages 11-20. 2018
  • Y. He, Q. Zuo, J. Edwards, K. Zhao, J. Leo, W. Cai. Q. Nie, B. L. J. Song. DNA
    Methylationand Regulatory Element during Chicken Germline Stem Cell Differentiation. Stem Cell Report, 10:6, pp1793-1806, 2018.
  • A. MacLean, H. Tian, Q. Nie. Exploring intermediate cell states through the lens of
    single cells. Current Opinion in Systems Biology. Vol 9. Pages32-41, 2018
  • S. Jin, A. MacLean, T. Peng, and Q. Nie. scEpath: Energy landscape-based
    inference of transition probabilities and cellular trajectories from single-cell transcriptomic data, Bioinformatics, 34:12, Pages 2077-2086, 2018
  • J. Lei, Q. Nie*, D. Chen*. A single-cell epigenetic model for parental psychological
    stress-induced transgenerational reprogramming in offspring. Biology of Reproduction. 98(6):846-855.. *: co-corresponding author, 2018
  • H. Du, Y, Wang, D. Haensel, B. Lee, X. Dai, Q. Nie. Multiscale modeling of layer
    formation of epidermis. PLoS Computational. Biology, 4(2):e1006006., 2018.
  • Y. Guo, Q. Nie, A. MacLean, Y. Li, J. Lei, S. Li. Multiscale modeling of inflammation-
    induced tumorigenesis reveals competing oncogenic and onco-protective roles for inflammation, Cancer Research. 77(22):6429-6441, 2017
  • Qixuan, Wang, Ji Won Oh, Anukriti Dhar, Jonathan Le, Shelby C. Jocoy, Antoni R. Rossi, Hoang T. Ha, Melisa A. Fuentes, Manda P. Nguyen, Julien Legrand, Eve Kandyba, Jung Chul Kim, Moonkyu Kim, Krzysztof Kobielak, Kiarash Khosrotehrani, Qing Nie*, Maksim V. Plikus*. A multi-scale model for the hair follicle reveals a pacemaker mechanism driving rapid hair growth patterning, *co-corresponding author, eLife 2017;6:e22772, 2017
  • C. Li**, T. Hong**, Y. Tung, Y. Yen, H. Hsu2, Y. Lu, M. Chang, Q. Nie3,*, J. Chen*. MicroRNA
    Filters Hox Temporal Transcription Noise to Confer Boundary Formation in the Spinal Cord **: equal-contribution, *:co-corresponding authors. Nature Communication, 8:14685, 2017
  • A. Li, S. Figueroa, T. Jiang, P. Wu, R. Widelitz, Q. Nie, C. Chuong. Diverse feather shape evolution enabled by coupling anisotropic signaling modules with self-organizing branching programme. Nature Communication, 8:14139, 2017, PMID: 28106042
  • W. R. Holmes, Nabora Soledad Reyes de Mochel, Qixian Wang, Huijing Du, Michael Chiang, Olivier Cinquin, Ken W.Y. Cho, Qing Nie, Gene expression noise enhances robust organization of the early mammalian balstocyst., 13(1): e1005320, PLoS Computational Biology, 2017. PMID 28114387
  • Q. Wang, W. R. Holmes, J. Julian, T. Schilling, Q. Nie. Cell sorting and noise-induced cell plasticity coordinate to sharpen boundaries between gene expression domains, 13(1): e1005307, PLoS Computational Biology, 2017, PMID: 28135279

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