Publications

Published Journal Articles

                                                                                2024

  1. Moreno J, O Dudchenko, …R Ramos, A Almet, …Q. Nie, ….M Plikus, E Kvon, E Aiden, and R Mallarino.   Emx2 underlies the development and evolution of marsupial gliding membranes.  Nature, accepted for publication, 2024.
  1. Sha Y, Y Qiu, P Zhou, Q Nie. Reconstructing growth and dynamic trajectories from single-cell  transcriptomics data. Nature Machine Intelligence, 6(25), 2024.

                                                                                  2023

  1. Walker B, Q. Nie. NeST: Nested hierarchical structure identification in spatial transcriptomics   data, Nature Communications, 14(6554), 2023
  1. Bocci F, D Jia, Q Nie, M Jolly, J Onuchic. Theoretical and computational tools to model    multistable gene regulatory networks.  Reports on Progress in Physics, 86-106601, 2023
  1. Johnson M, S Li, C Guerrero-Juarez, P Miller, B Brack, S Mereby, C Feigin, J Gaska, Q Nie, J Rivera-Perez, A Ploss, S Shvartsman, R Mallarino, A multifunctional Wnt regulator underlies the evolution of rodent stripe patterns. Nature Ecology and Evolution, Oct 9, online, 2023
  1. Kang TY, F Bocci, Q Nie, JN Onuchic, A Levchenko. Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification. eLife:12:RP89262, 2023.
  1. Yanai I, EJ Fertig, M Li, F Coscia, J Klughammer, Q Nie, J Chen, A Coskun. What do you most hope spatial molecular profiling will help us understand. Cell Systems, 14(7): 543-546. 2023
  1. Wang X, A Almet, Q Nie. The promising application of cell-cell interaction analysis in cancer from single-cell and spatial transcriptomics. Seminars in Cancer Biology, 95: 42-51, 2023
  1. Sha Y, Qiu Y, Q Nie. NeuralGene: Inferring gene regulation and cell fate dynamics from Neural ODEs. Journal of Machine Learning for Modeling and Computing. 4(1): 1-15, 2023          

211.   Coulis G, D Jaime, C Guerrero-Juraez, … A MacLean, Q Nie, L Wallace, …., S Armando  Villalta. Single-cell and spatial  transcriptomics identify            macrophage population associated with skeletal muscle fibrosis, Science Advances, in press,    2023

210.   Wang X …. Q Nie…. M Plikus.  Signaling by senescent melanocytes hyperactivate hair growth, Nature, 618(808-817),          2023

209.   Stabell A, S Wang G Lee, J Ling, S Nguyen, G Sen, Q Nie, S Atwood.  Single cell  transcriptomics of human skin  equivalent organoids, Cell Reports, 16:42(5):112511, 2023

208.   Almet, A. ….. Q Nie, ….  M Kasper, M Plikus. A roadmap for a consensus human skin cell atlas  and single-cell data standardization, Journal of Investigative Dermatology, in press, 2023.

207.   He C, P Zhou, Q Nie. exFINDER: identify external communication signals using single-cell  transcriptomics data. Nucleic Acids Research, gkad262, in press, 2023.

206.  Dover K, Z Cang, A Ma, Q Nie*, R Vershynin*. AVIDA: An Alternating method for visualizing and  integrating data, Journal of Computational Science, 68(101998), 2023. Co-corresponding authors

205.  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

  1. Cang Z, Q. Nie.  A mathematical method and software for spatially mapping intercellular communication. Nature Methods,  20(2):185-186. 2023

  1. 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

  1. Wiedemann J, A Billi, F Bocci, ……, Q Nie, J Gudjonsson, B Andersen. Body site changes in skin cell composition and differential use of dual epidermal differentiation trajectories in human palm, sole, and hip skin. Cell Reports, 42(1), 111994, 2023
  1. 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, in press. 2023
  1. Liau  E#, S Jin#, Y Chen W Liu, M Calon, S Nedelec, Q Nie*, J Chen*. Single-cell transcriptomic analysis unveils the diversity within mammalian spinal motor neurons. Nature Communications, 14(46).   2023. #: co-first, *: co-corresponding. Highlighted as feature article

                                                                                     2022

  1. Bocci F, P Zhou, Q. Nie. spliceJAC: Transition genes and state specific gene regulation from  single-cell transcriptome data. Accepted for publication, Molecular Systems Biology, 2022
  1. Cao Y, L Fu, J Wu, Q Peng, Q Nie, J Zhang, Xiaohui Xie. Integrated analysis of multimodal single-cell data with structural similarity. Nucleic Acids Research, gkac781, https://doi.org/10.1093/nar/gkac781, 2022

197.    Ren H, B Walker, Z Cang, Q Nie. Identifying multicellular spatiotemporal organization of cells with SpaceFlow. Nature Communications,  13(4076), 2022

  1. Wang X, A Almet, Q. Nie. Analyzing network diversity of cell-cell interactions in COVID-19 using single-cell transcriptomics. Frontiers in Genetics, fgene.2022.948508. August 29, 2022
  1. Cang Z, Q. Nie, Y Zhao. Supervised Optimal Transport. Accepted for publication, SIAM Journal on Applied Mathematics, 2022
  1. Vu R#, S Jin#, P Sun, D Haensel, Q Nguyen M Dragan, K Kressenbrock, Q Nie*, X. Dai*. Wound healing in aged skin exhibits systems-level alternations in cellular composition and cell-cell communication.  Accepted for publication, Cell Report, 2022, #:co-first authors. *: co-corresponding authors
  1. Karikomi M, P Zhou, Q. Nie. DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data. Briefings in Bioinformatics, bbac223, 2022
  1. Guerrero-Juarez C, G Lee, Y Liu, S Wang, M, Karikomi, Y Sha, R Chow T Nguyen V Iglesias, S Aasi, M Dromond, Q. Nie, K Sarin, S Atwood. Single-cell analysis of human basal cell carcinoma reveals novel regulators of tumor growth and the tumor microenvironment. 8(23), Science Advances, 2022.  (Guerrero-Juarez from Nie Lab)
  1. Liu Y*, C Guerrero-Juarez*, F Xiao, N Shettigar, R Ramos, C Kuan, Y Lin, L Lomeli, J Park J Oh, R Liu, S Lin, M Tartaglia, R Yang, Z Yu, Q. Nie, J Li, M Plikus. Hedgehog signaling reprograms hair follicle niche fibroblasts to a hyper-activated state. In press, Developmental Cell, 2022, * Co-first author (Guerrero-Juarez from Nie Lab)
  1. Shiu J.*, L Zhang*, G Lentsch J Flesher, S. Jin, C Poleys, S Jo, C Mizzoni, P Mobasher, J Kwan, F Diaz, B Tromberg, I Georgakoudi, Q Nie, M Balu A Ganesan. Multimodal analysis of vitiligo skin identifies tissue characteristics of stable disease.  Journal of Clinical Investigation (JCI) Insight, e154585, 2022, * co-first author (L Zhang from Nie lab).
  1. Hernandez J, E Dollinger, R Pone, J Feigner, S Strohmeier, S Jan, T Albin, A Jain, R Nakajima, A Jasinskas, F Krammer, A Esser, P Felgner, Q. Nie H Davies.   Magnitude and breadth of antibody cross-reactivity induced by recombinant influenza hemagglutinin trimer vaccine is enhanced by combination adjuvants. Scientific Reports,12-9198, 2022
  1. Zhang L, J. Zhang, Q. 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
  1. Johnston K, S Grieco, H Zhang, S Jin, X Xu*, Q. Nie*. Tracking longitudinal population  dynamics of single neuronal calcium signal using SCOUT. April, Cell Reports  Methods 2(5), 2022. *:co-corresponding author
  1. Ying X, S Leng, H Ma, Q. Nie Y. Lai, W. Lin. Continuity scaling: A rigorous framework for detecting and quantifying causality accurately. Research, a Science Partner Journal, 9870149, 2022
  1. Ming Deng, Christian 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 Plikus, Cong Lv, and Zhengquan Yu. Lepr+ mesenchymal cells sense diet to modulate intestinal stem/progenitor cells via Leptin-Igf1 axis. March 16, Cell Research (Impact Factor = 25), 2022
  1. Walker B, Z Cang, H Ren, E Chang, Q. Nie. Deciphering Tissue Structure and Function Using Spatial Transcriptomics. Communications Biology, 5(220) 2022
  1. Shakiba N, C Li, J Garcia-Ojalvo, K Cho, K Patil, A Walczak, Y Liu, S Kuehn, Q Nie, A Klein, G. Deco, M Kringelbach, S. Lyer-Biswas.  How can Waddington-like landscapes facilitate insights beyond developmental biology? Cell Systems, 13, 2022
  1. Liu R, E Dollinger, Q. Nie. Machine learning of single cell transcriptomic data from immunotherapy responders and non-responders reveals distinct resistance mechanisms in skin  and pancreatic cancers. Frontiers in Genetics, 12:806457, 2022.
  1. Hou J, H Ma, D He, J Sun, Q Nie*, W Lin*. Harvesting random embedding for high-frequencey change-point detection in temporal systems. Accepted for publication by National Science Review (Impact Factor = 17), 2021, *: co-corresponding authors

2021

  1. Takarakis D, Z Cang, X Wu, P Sharma, M. Karikomi, A MacLean, Q Nie, T Schilling. Single-cell transcriptomic analysis of zebrafish cranial neural crest reveals spatiotemporal regulation of lineage decisions during development, Cell Reports, 37,110140, 2021
  1. Fu L. Y Cao, J Wu, Q Peng, Q. Nie, X, Xie. UFold: Fast and accurate RNA secondary structure    prediction with deep learning, Nucleic Acids Research, https://doi.org/10.1093/nar/gkab1074,  2021
  1. F Bocci, P. Zhou, Q. Nie. Single cell RNA-seq analysis reveals acquisition of cancer stem cell traits and increase of cell-cell signaling during EMT progression. Cancers,13:5726, 2021
  1. 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
  1. Lang J, Q Nie, C. Li. Landscape and kinetic path quantify critical transitions in epithelial-mesenchymal transition. Biophysical Journal. 120(20), Page 4484, 2021
  1. Mehrsa M, T Morris, Z Cang, C Nguyen, Y Sha, M. Asad, N Khachikyan, T Greene, D. Becker, Nie, M. Zaragoza. A study of gene expression, structure, and contractility of iPSC-Derived cardiac myocytes from a family with heart disease due to LMNA mutation., Annals of Biomedical Engineering, PMID 34585335, in press, 2021.
  1. Chinn C*, H Ren*, J. Morival, Q. Nie, M. Wood, T. Downing. Examining age-dependent DNA methylation patterns and gene expression in the male and female hippocampus. Neurobiology of Aging, 10:54. 2021. Co-first authors
  1. MacLean A, Q. Nie. The diverse landscape of modeling in single-cell biology.  Physical Biology, 18(5), 2021
  1. Bergman D. M. Karikomi, M. Y, Q. Nie*, A. MacLean*. Modeling the effects of EMT-immune dynamics on carcinoma disease progression.  Communications Biology, 24:983, 2021. Co-corresponding author.
  1. Zhao W., L Qiao, S. Yan, Q. Nie*, L. Zhang*. Mathematical modeling of histone modification reveals the formation mechanism, composition, and function of bivalent chromatin. iScience 24:102732, 2021. Co-corresponding author.
  1. Qiu Y. L Fung. T. Schilling, Q. Nie.   Multiple morphogens and rapid elongation promote segmental patterning during Development.  PLoS Computational Biology, 17(6):e1009077, 2021
  1. Cao, Y, L Fu, J Wu, Q. Peng, Q. Nie, J. Zhang, and X. Xie.   SAILER: Scale and accurate invariant representation learning for single-cell ATAC-seq processing and integration, Bioinformatics, 37, i317-i326, 2021. ISMB/ECCB 2021
  1. Almet A, Z. Cang, S. Jin and Q. Nie.   The landscape of cell-cell communication through single-cell transcriptomics. Current Opinion in Systems Biology, 16:12-23, 2021

167.   Maseda, F, Z. Cang, Q. Nie.   DEEPsc: A deep learning-based map connecting single-cell transcriptomics and spatial imaging data.  Frontiers  in  Genetics, March, 2021.  

  1. Sun X. J. Zhang, Q. Nie    Inferring latent temporal progression and regulatory networks form cross-sectional transcriptomic data of cancer samples, 17 (3):e1008379. PLoS Computational Biology, 2021

165    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

164.  Zhang L, Q. Nie. scMC learns biological variation through the alignment of multiple single cell genomics datasets. Genome Biology, 22:10,  2021

163.   Zhao X, J Chen, P Xiao, J Feng, Q. Nie & X Zhao. Identifying age-specific gene signatures of the human cerebral cortex with joint analysis of  transcriptomes and functional connections. Briefings in Bioinformatics,  22(4),2021

162.   Sha Y, S. Wang, F. Bocci, P. Zhou, Q. Nie. Inference of intercellular communications and multilayer gene-regulations of Epithelia-Mesenchymal transition from single-cell  transcriptomic  data.  Frontiers in Genetics, Jan. 8,  2021 

161   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), 2020.

2020

160.  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.

159.  Villarreal-Ponce A., M. Tiruneh, J. Lee, C Guerrero-Juarez, J. Kun, J. David, K. Dammeyer, R. Kell, J Kwong, P. Rabbani, Q. Nie, D. Ceradini.  Keratinocyte-Macrophage crosstalk by the  Nrf2/Ccl2/EGF signaling axis orchestrates tissue regeneration. Cell Reports 33:108417. 2020

158. Lin Z, Suoqin Jin, Jefferson Chen1, Zhuorui Li, Zhongqi Lin, Li Tang, Qing Nie,*, Bogi Andersen* , Murine Interfollicular epidermal differentiation is gradualistic with GRHL3 controlling progression from stem to transition cell states. Nature Communications, 11:5434, 2020.  *: co-corresponding author.

  1. C. Rackauckas and Q. Nie, “Stability-Optimized High Order Methods and Stiffness Detection for Pathwise Stiff Stochastic Differential Equations,” 2020 IEEE High Performance Extreme Computing Conference (HPEC), Waltham, MA, USA, 2020, pp. 1-8, doi: 10.1109/HPEC43674.2020.9286178. Outstanding paper award of the conference (AI/Machine Learning Session).

156.  Dollinger E. D. Bergman, P. Zhou, S. Atwood, Q. Nie.  Divergent Resistance Mechanisms to Immunotherapy Explain Responses in Different Skin Cancers. Cancers, 12:2946, 2020.

155.  Xie J , Chang Zhao , Jiamin Sun , Jiaxin Li , Fuzhang Yang , Jiao Wang , Qing Nie, Prediction of Essential Genes in Comparison States Using Machine Learning. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Accepted for publication,2020

154. Sha Y. S. S. Wang, P. Zhou, Q. Nie.  Inference and multiscale model of Epithelial-to-Mesenchymal transition via single-cell transcriptomic data. Nucleic Acids Research, 48(17), Pages 9505-9530. 2020

153, Xiaole Sheng, Ziguang Lin, Cong Lv, Chunlei Shao, Xueyun Bi, Min Deng, Jiuzhi Xu, Christian F Guerrero-Juarez, Mengzhen Li, Xi Wu, Ran Zhao, Xu Yang, Guilin Li, Xiaowei Liu, Qingyu Wang, Qing Nie, Wei Cui, Shan Gao, Hongquan Zhang, Zhihua Liu, Yingzi Cong, Maksim V Plikus, Christopher J Lengner, Bogi Andersen, Fazheng Ren, Zhengquan Yu.  Cycling stem cells are radioresistant and regenerate the intestine.  Cell Reports,  32(4), Page 107952, 2020

152,  Wang S. M Drummond, C Guerrero-Juarez, E Tarapore, AL. MacLean, Adam R. Stabell, S Wu, G Gutierrez, B That, C Benavente, Qing Nie*, S Atwood*. Single cell   transcriptomics of human epidermis identifies basal stem cell transition states.  Nature Communications,11:4239, 2020 *: co-corresponding author.

151.  Zhu Y. Y Qiu, W Chen, Q Nie A Lander. Scaling a Dpp morphogen gradient through feedback control of receptors and co-receptors. Developmental Cell, 53,  724-739, 2020

150.  Cang Z and Q. Nie. Inferring spatial and signaling relationships between cells from single cell transcriptomic data. Nature Communications, 11(2084), 2020.

149.  Xie, J. F. Yang, J. Wang, M. Karikomi, Y. Yin, J. Sun, T. Wen, Q. Nie.  DNF: A differential network flow method to identify rewiring drivers for gene regulatory networks. Neurocomputing, to appear soon, 2020

148. Song Y, Guerrero-Juarez, Zhongjian Chen, Yichen Tang, Xianghui Ma, Cong Lv,    Xueyun Bi, Min Deng1, Lina Bu, Yuhua Tian, Ruiqi Liu, Ran Zhao, Jiuzhi Xu, Xiaole Sheng, Sujuan Du, Yeqiang Liu, Yunlu Zhu, Shi-jun Shan, Hong-duo Chen, Yiqiang Zhao, Guangbiao Zhou, Jianwei Shuai, Fazheng Ren, Lixiang Xue, Zhaoxia Ying, Xing Dai, Christopher J. Lengner, Bogi Andersen, Maksim V. Plikus, Q. Nie, Zhengquan Yu. The Msi1-mTOR pathway drives the pathogenesis of mammary and extramammary Paget’s Disease.  Cell Research, 2020, https://doi.org/10.1038/s41422-020-0334-5

147. Haensel, D#, S Jin#, P Sun, R Cinco, M Dragan, Q. Nguyen, Z, Xang, Y Gong, R Vu, A MacLean, K. Kessenbrock E. Gratton, Q. Nie*, X. Dai*.  Defining epidermal basal cell states during skin homeostasis and wound healing using single-cell transcriptomics. Cell Reports, 30, 3932-3947, 2020. *: co-corresponding author, #:equal-contributions

146. 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

145.  Greenberg E, M Marshall, S Jin, S Venkatesh, M Dragan, L Tsoi, J Gudjonsson, Q  Nie, Taskhashi, B Andersen. Circadian control of interferon-sensitive gene expression in murine skin. Proceedings of the National Academy of Sciences, 117(11) 5761-5771, 2020

144. Kashgari G, L. Meinecke, W. Gordon, B. Ruiz, J. Yang, Y Xie, A. Ma, H. Ho, Q. NieK.Jester, B. Andersen.  Epithelial migration and non-adhesive periderm are required for digit separation during mammalian development. Developmental Cell,  52 (764), 1-15,  2020.

  • Cover Story of Developmental Cell (April 2020)
  • “A sticky problem for digits” highlighted in Science, 368(6487), p151, 2020

143. Nie, Q, L. Qiao, Y. Qiu, L. Zhang, W. Zhao. Noise control and utility: from gene regulatory network to spatial patterning. Science China Mathematics, 63(3): 425-440. 2020

142   A. Lander, Q. Nie, C. Sanchez-Tapia, A. Simonyan, F. Wan.  Regulatory feedback on receptor and non-receptor synthesis for robust signaling.  Developmental Dynamics, 249:383-409, 2020

141. Xie, J, J. Sun, J. Feng, F. Yang, J. Wang, Tieqiao Wen & Q. Nie. Kernel differential subgraph analysis to reveal the key period affecting glioblastoma. Biomolecules, 10:318. 2020

2019

140. Zhang J, Q. Nie, T. Zhou. Revealing dynamic mechanisms of cell fate decisions from  single-cell transcriptomic data. Frontiers in Genetics, 10:1280.  2019

139. Qiao L. Zhao W, Tang C, Nie, Q*, Zhang L*.  Network topologies that can achieve dual function of adaptation and noise attenuation. Cell Systems, Vol 9 (3), P271-285. E7, 2019. * co-corresponding authors.

138.  Sun Y*, Jin S*, Lin X, Chen L, Qiao X, Jiang L, Zhou P. Johnston, Golshani P. Nie, Q. Holmes T, Nitz D, Xu X.  CA1-Projecting subiculum neurons facilitate object-place learning, Nature Neuroscience, 9/24, 2019. *: co-first authors

137. Nie Q and Plikus M. Equal Opportunities in Stemness. Nature Cell Biology,  21, pages921–923, 2019

136. Zheng X, Jin S, Nie Q*, Zou X*. scRCMF: Identification of cell subpopulations and transition states from single cell transcriptomes, IEEE Transactions on Biomedical Engineering, doi: 10.1109/TBME.2019.2937228, 2019.  * co-corresponding authors

135. S. Wang, M. Karikomi, A. MacLean, Q. Nie. Cell Lineage and Communication Inference via Optimization for Single-cell Transcriptomics.  Nucleic Acids Research, 47 (11), Page e66, 2019

134. C. Rackauckas and Q. Nie. Confederated Modular Differential Equation APIs for Accelerated Algorithm Development and Benchmark. Advances in Engineering Software, 132, 1-6, 2019

133. Y. Wang, C. Guerrero-Juarez, Y. Qiu, H. Du, W. Chen, S. Figueroa, M. Plikus, Q. Nie. A Multi-scale Mathematical Model of Epidermal-dermal Interactions during Skin Wound Healing. Accepted for publication, Experimental Dermatology, 28 (4) 493-502. 2019.

132.  Y. Qiu, W. Chen, and Q. Nie. A Hybrid Method for Stiff Reaction-diffusion Equations.  Accepted for publication, Discrete and Continuous Dynamical Systems-B, 2019.

131. C. Guerrero-Juarez, P. Dedhia, S. Jin, R. Ruiz-Vega, D. Ma, Y. Liu, K. Yamaga, O. Shestova, D. Gay, Z. Yang, K. Kessenbrock, Q. Nie, W. Pear, G. Cotsarelis, M. V. Plikus. Single-cell Analysis Reveals Fibroblast Heterogeneity and Myeloid-derived Adipocyte Progenitors in Skin Wounds, Nature Communications. 10(1):650, 2019.

130. Y. Sha, D. Haensel, G. Guitierrez, H. Du, X. Dai, Q. Nie. Intermediate Cell States in Epithelial-to-Mesenchymal Transition. Physical Biology, 18:16(2):021001, 2019.

2018

129. P. Sharma, A. MacLean, L. Meinecke, D. Clouthier, Q. Nie, T. Schilling. Transcriptomics Reveals Complex Kinetics of Dorsal-Ventral Patterning Gene Expression in the Mandibular Arch. The Journal of Genetics and Development, 2018:e23275, 2018.

128. C. Rackauckas, T. Schilling, Q. Nie. Interdisciplinary Case Study:How Mathematicians and Biologists Found Order in Cellular Noise. iScience 8, 267-270, 2018. Featured as a cover article for the iScience.

127. L. Meinecke, P. Sharma, H. Du, L. Zhang, Q. Nie*, T. Schilling*. Modeling Craniofacial Development Reveals Spatiotemporal Constrains on Robust Patterning of the Mandibular Arch. PLoS Computational Biology 14(11):e1006569. 2018. *co-corresponding authors.

126. D. Haensel, P. Sun, A. MacLean, X. Ma, Y. Zhou, M. Stemmler, S. Brabletz, G. Berx, M Plolis, Q. Nie, T. Brabletz, X. Dai. An Ovol2-Zeb1 Transcriptional Circuit Regulates   Epithelial Directional Migration and Proliferation. EMBO Reports, e46273. 2018.

125. Y. Qiu, W. Chen, Q. Nie. Stochastic Dynamics of Cell Lineages in Tissue
Homeostasis. Discrete and Continuous Dynamic Systems–B,
doi: 10.3934/dcdsb.2018339, 2018.

124. Q. Nie. Stem Cells: a Window of Opportunity of Low-Dimensional EMT Space. Oncotarget, Vol. 9 (61), pp31790, 2018

123. C. Li, L. Zhang, Q. Nie. Landscape reveals critical network structures for sharpening gene expression boundaries. BMC Systems Biology.12:67, 2018.

122. C. Rackaukas, T. Schilling, Q. Nie. Mean-Independent Noise Control of Cell Fates via Intermediate State. iScience, DOI: https://doi.org/10.1016/j.isci.2018.04.002, Vol. 3, Pages 11-20. 2018.

121. 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.

120. A. MacLean, H. Tian, Q. Nie. Exploring intermediate cell states through the lens of single cells. Current Opinion in Systems Biology. Vol 9. Pages 32-41, 2018.

119. 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.

118. 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.

117. 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. https://doi.org/10.1371/journal.pcbi.1006006, 2018.

116. P. Yu, Q. Nie*, C. Tang*, L. Zhang*. Nanog induced intermediate state in regulating stem cell differentiation and reprogramming. *: co-corresponding author BMC Systems Biology, 12:22 doi.org/10.1186/s12918-018-0552-3, 2018.

2017
115. J. Xie, D. Lu, J. Li, J. Wang, Y. Li, Q. Nie. Kernel differential subgraph reveals dynamic changes in biomolecular network. J. Bioinformatics and Computational Biology, 4:1750027. doi:10.1142/S0219720017500275. 2017.
114. 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. doi:10.1158/0008-5472.CAN-17-1662, 2017.
113. 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.
112. C. Rackauckas, Q. Nie. DifferentialEquations.jl-A Performant and Feature-Rich Ecosystem for Solving Differential equations in Julia, Journal of Open Research Software, 5(1), 2017.
111. T. Peng, L. Liu, A. MacLean, C. Wong, W. Zhao, and Q. Nie. A Mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions. BMC Systems Biology, 11:55, 2017. PMCID: PMC5434622.
110. 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.
109. 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
108. 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,
http://dx.doi.org/10.1371/journal.pcbi.1005320, PLoS Computational Biology, 2017. PMID 28114387
107. 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
106. C. Rackauacks, Q. Nie, Adaptive Methods for Stochastic Differential Equations via Natural Embeddings and Rejection Sampling with Memory, Vol 22(7), p2731-2761, Discrete and Continuous Dynamic systems – B, 2016
105. J. Xie, J. Xu, C. Nie, Q. Nie. Machine Learning of Swimming Data via Wisdom of Crowd and Regression Analysis. Mathematical Biosciences and Engineering. 14(2), 511-527, doi:10.3934/mbe.2017031, 2017.

2016
104. J. Lo, L. Zheng, Q. Nie.   A Hybrid Continuous-Discrete Method for Stochastic Reaction-Diffusion Processes. Royal Society Open Science, 3:160485, 2016.
103. C. Li, T. Hong, C. Webb, H. Karner, S. Sun, Q. Nie. A Self-Enhanced Transport Mechanism through Long Non-Coding RNAs for X Chromosome Inactivation. 6-31517,
doi:10.1038/srep31517 Scientific Report, 2016.
102.W. Chen. Q. Nie, T. Yi, and C. Chou, Modeling of Yeast Mating Reveals Robustness Strategies for Cell-Cell Interactions. Accepted for publication, PLoS Computational Biology, 2016
101.Chunhe Li, Hong TIan, and Qing Nie. Quantifying the landscape and kinetic paths for epithelial-mesenchymal transition from a core circuit. DOI: 10.1039/c6cp03174a, Physical Chemistry Chemical Physics, 2016
100. Jiajun Zhang, Qing Nie, and Tianshou Zhou, A moment-convergence method for stochastic analysis of biochemical reaction networks. The Journal of Chemical Physics, 144, 194109 (2016); http://dx.doi.org/10.1063/1.4950767, 2016
99. Catherine Ta, Qing Nie*, Hong Tian*. Controlling stochasticity in epithelial-mesenchymal transition through multiple intermediate cellular states, Accepted for publication, Discrete and Continuous Dynamical Systems-B, 2016. Co-corresponding author
98. Jinzhi. Lei, Wing-Cheong Lo, and Qing Nie Mathematical models of morphogen dynamics and growth control. Accepted for publication, Annals of Mathematical Sciences and Applications. 2016
97. J. Julian, L. Zheng, C. Rackaukas, M. Digman, E. Gratton. Q. Nie, T. Schilling. Noise modulation in retinoic acid signaling sharpens segmental boundaries of gene expression in the zebrafish hindbrain, eLife, e14034, 2016
96. Xu, N. Olivas, T. Ikrar, T. Peng, T. C Holmes, Q. Nie, and Y. Shi, Primary Visual Cortex Shows Laminar Specific and Balanced Circuit Organization of Excitatory and Inhibitory Synaptic Connectivity. J. of Physiology, Vol 594 (7), pp 1891, DOI: 10.1113/JP271891, 2016

2015
95. A. Cinquin, L. Zheng, P. Taytor, L. Zhang, M. Chiang, J. Snow, Q. Nie, and O. Cinquin. Semi-permeable diffusion barriers enhance patterning robustness in C. elegans germ line. Developmental Cell, 35, pp405-417, 2015.
94. T. Hong, K. Watanabe, C. Ta, A. Villarreal-Ponce, Q. Nie* and X. Dai*. An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States. *co-corresponding author, PLoS Computational Biology, 11(11): e1004569. doi:10.1371/journal.pcbi.1004569, 2015.
93. H. Du, Q. Nie*, W. Holmes*. The Interplay between Wnt Mediated Expansion and Negative Regulation of Growth Promotes Robust Intestinal Crypt Structure and Homeostasis. *co-corresponding author, PLoS Computational Biology, 11(8): e1004285. doi:10.1371/journal.pcbi.1004285 , 2015.
92. J. Xie, C. Xiang, J. Ma, J. Tan, T. Wen, J. Lei, and Q. Nie. An Adaptive Hybrid Algorithm for Global Network Alignmen. IEEE/ACM Transactions on Computational Biology and Bioinformatics. doi:10.1109/TCBB.2015.2465957, 2015.
91. A. Li, Y. Lai, S. Figueroa. T. Yan. R. Widelitz, K. Kobielak, Q. Nie, and C. Chuong. Deciphering Principles of Morphogenesis from Temporal and Spatial Patterns on the Integument. Developmental Dynamics, doi: 10.1002/dvdy.24281, 2015.
90. C. Ta, D. Wang, and Q. Nie. An Integration Factor Method for Stochastic and Stiff Reaction-diffusion Systems. J. of Computational Physics, 295:505-522, 2015.
89. T. Hong, E. Fung, L. Zhang, G. Huynh, E. Monuki, and Q. Nie. Semi-adaptive Response and Noise Attenuation in BMP Signaling. Journal of the Royal Society Interface, 12(107) 2015.
88. J. Xie, Z. Zhou, J. Ma, C. Xiang. Q. Nie, and W. Zhang. Graphics Processing Unit-based Alignment of Protein Interaction Networks. IET Systems Biology, IET Systems Biology, 10.1049/iet-syb.2014.0052 2015.
87. D. Wang, W. Chen, Q. Nie. Semi-implicit Integration Factor Methods on Sparse Grids for High-dimensional Systems. Journal of Computational Physics, 292, 43-55,2015
86. W. Lo, S. Zhou, F. Wan, A. Lander, Q. Nie. Robust and Precise Morphogen-Mediated Patterning: Tradeoffs, Constraints, and Mechanisms. Journal of the Royal Society Interface, 12, 2015.
85. C. Chou, T. Moore, Q. Nie, and T. Yi. Alternative Cell Polarity Behaviors Arise from Changes in G-Protein Spatial Dynamics. IET Systems Biology, 9(2), pp52-63, 2015.

2014
84. A. Gord, W. Holmes, X. Dai, Q. Nie. Computational Modeling of Epidermal Stratification Highlights the Importance of Asymmetric Cell Division for Predictable and Robust Layer Formation. Journal of the Royal Society Interface, 11:99, 2014.
83. B. Lee, A. Villarreal-Ponce, M. Fallahi, J. Ovadia, P. Sun. Q. Yu, S. Ito, S. Sinha, Q. Nie, and X. Dai. Transcriptional Mechanism Link Epithelial Plasticity to Adhesion and Differentiation of Epidermal Progenitor Cells. Developmental Cell, 29(1), p47-58, 2014. –
Highlighted in preview article, 29(1), pp1-2, Developmental Cell.
82. J. Lei, S. Levin and Q. Nie. A Mathematical Model of Adult Stem Cells Regeneration with Crosstalk between Genetic and Epigenetic Regulation. Proceeding of National Academy of Sciences, USA, E880-E887, doi: 10.1073/pnas.1324267111, 2014. – Highlighted in PNAS Early Edition; commentary article: PNAS 111 (10) pp. 3653-3654.
81. W. Holmes and Q. Nie. Interactions and Tradeoffs between Cell Recruitment, Proliferation, and Differentiation Affect CNS Regeneration. 106:1528-1536, 2014.
80. Z. Zheng, S. Christley, W. Chiu, I. Blitz, X. Xie, K. Cho, Q. Nie. Inference of the Xenopus tropicalis Embryonic Regulatory Network and Spatial Gene Expression Patterns. BMC Systems Biology, 8:3, doi:101186/1752-0509-8-3, 2014.
79. D. Wang, L. Zhang, and Q. Nie. Array-representation Integration Factor Method for High-dimensional Systems. Journal of Computational Physics, 258, pp585-600, 2014.
78. G. Ye, M. Tang, J. Cai, Q. Nie, X. Xie. Low-Rank Regularization for Learning Gene Expression Programs. PLoS One, 9(1), doi:10.1371, 2014.

2013
77. X. Liu, S. Johnson, S. Liu, D. KanoJia, W. Yue, U. Singn,Qian Wang, Qi, Wang, Q. Nie and H. Chen. Non-linear Growth Kinetics of Breast Cancer Stem Cells: Implications for Cancer Stem Cell Targeted Therapy. 3:2473, DOI: 10.1038/srep02473, Scientific Reports, 2013.
76. M. Chen, L. Wang, C. Liu, and Q. Nie. Noise Attenuation in the ON and OFF States of Biological Switches. Featured and cover article, ACS Synthetic Biology, 2, pp587-593, 2013, DOI: 10.1021/sb400044g.
75. J. Ovadia and Q. Nie. Numerical Methods for Two-Dimensional Stem Cell Tissue Growth. Journal of Scientific Computing.2013, DOI 10.1007/s10915-013-9728-6.
74. A. Li, M. Chen, T. Jiang, P. Wu, Q. Nie, R. Widelitz, C. Choung. Shaping Organs by a Wnt/Notch/non-muscle Myosin Module Which Orients Feather Bud Elongation. Proceeding of the National Academy of Sciences, USA, E1452-E1461, 2013.
73. J. Zhang, Q. Nie, M. He, and T. Zhou. An Effective Method for Computing the Noise in Biochemical Networks. Journal of Chemical Physics, 138, 084106, p. 1-16, 2013.
72. J. Ovadia and Q. Nie. Stem Cell Niche As an Inherent Cause of Undulating Epithelial Morphologies. Biophysical Journal, 104 (1): 237-46, 2013.
71. J. Lei, D. Wang, Y. Song, Q. Nie and Y. Wan. Robustness of Morphogen Gradients with “Bucket Brigade” Transport through membrane-associated Non-receptor. Discrete and Continuous Dynamical Systems-B, 18(3), 2013

2012
70. T. Schilling, Q. Nie, A. Lander. Dynamics and Precision in Retinoic Acid Morphogen Gradients. Current Opinion in Genetics & Development, 22 (6), 2012.
69. C. Chou, T. Moore, S. Chang, Q. Nie and T. Yi. Signaling Regulated Endocytosis and Exocytosis Lead to Mating Pheromone Concentration Dependent Morphologies in Yeast. FEBS Letters, 586 (23), Page 4208-4214, 2012.
68. L. Zheng, M. Chen, Q. Nie. External Noise Control in Inherently Stochastic Biological Systems. Journal of Mathematical Physics, 53, 115616, 201.
67. L. Zhang, K. Radtke, L. Zheng, T. Schilling, Q. Nie. Noise Drives Sharpening of Gene Experssion Boundaries in Zebrafish Hindbrain. Nature Molecular Systems Biology. Nature Molecular Systems Biology, 8:613, 2012.
66. L. Zhang, A. Lander, Q. Nie. A Reaction-Diffusion Mechanism Influences Cell Lineage Progression as a Basis for Formation, Regeneration, and Stability of Intestinal Crypts. BMC Systems Biology, 6:93, 2012.
65. Q. Nie, Challenges for Training at the Interface. Bioengineering & Biomedical Science, 2:3, 1000e105, 2012.
64. C. Chan, X. Liu, L.Wang, L. Bardwell, Q. Nie*, and G. Enciso*. Protein Scaffolds Can Enhance the Bistability of Multisite Phosphorylation Systems. *Co-corresponding authors, PLoS Computational Biology, 8(6) e1002551, 2012.
63. A. Cai, K. Radtke, A. Linville, A. Lander, Q. Nie*, T. Schilling. *Cellular Retinoic Acid-Binding Proteins Are Essential For Hindbrainpatterning and Signal Robustness in Zebrafish. *Co-corresponding authors, Development, 139, 2150-2155. 2012.
62. W. Lo, L. Chen, M. Wang, and Q. Nie. A Robust and Efficient Method for Steady State Patterns in Reaction-Diffusion Systems. J. of Computational Physics, 231, 5062-5077, 2012.
61. S. Zhou, W. Lo, J. Suhalim, M. Digman, E. Gratton, Q. Nie, and A. Lander. Free Extracellular Diffusion Creates the Dpp Morphogen Gradient of the Drosophila Wing Disc. Current Biology, 22, 668-675, 2012.

2011
60. C. Chou, L. Bardwell, Q. Nie*, T. Yi*. Noise Filtering Tradeoffs in Spatial Gradient Sensing and Cell Polarization Response. *Co-corresponding authors, BMC Systems Biology, 5:196 2011.
59. S. Zhao, J. Ovadia, X. Liu, Y.T. Zhang. Q. Nie. Operator Splitting Implicit Integration Factor Methods for Stiff Reaction-diffusion-Advection Systems. J. of Computational Physics, 230(15), pp 5996-6009, 2011.
58. Z. Zheng, C. Chou, T. M. Yi, Q. Nie. Mathematical Analysis of Steady-State Solutions in Compartment and Continuum models of Cell Polarization. Mathematical Biosciences and Engineering. 8(4), 2011.
57. J. Lei, F.Y.M. Wan, A. Lander, Q. Nie. Robustness of Signaling Gradient in Drosophila Wing Imaginal Disc. Discrete and Continuous Dynamical Systems-B, 16(3), 2011.

2010
56. C. Chou, Lo, W, Gokoffski, K., Zhang, Y., Wan, F., Calof, A., and Q. Nie. Spatial Dynamics of Multi-stage Cell Lineages in Tissue Stratification. Biophysical Journal, 99(10), 2010.
55. L. Wang, Q. Nie, G. Enciso. Non-essential Sites Improve Phosphorylation Switch. Biophysical Journal, 99(6), 2010.
54. S. Haney, L. Bardwell, Q. Nie. Ultrasensitive Responses and Specificity in Cell Signaling. BMC Systems Biology, 4 (119), 2010
53. S. Christley, B. Lee, X. Dai and Q. Nie. Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms. BMC Systems Biology, 4(107), 2010
52. L. Wang, J. Xin, and Q. Nie. A Critical Quantity for Noise Attenuation in Feedback Systems. PLoS Computational Biology, 6(4): e1000764, 2010.
51. X. Liu and Q. Nie. A Compact Integration Factor Methods for Complex Domains and Adaptive Mesh Refinement. J. of Computational Physics. 229, pp 5692-5706, 2010.
50. A.D. Lander, Q. Nie, B. Vargas, and F.Y.M. Wan. Size-normalized Robustness of Dpp Gradient in Drosophila Wing Imaginal Disc. J. Mat. Mech. Struc. (JoMMS). Accepted 2010.
49. X. Liu, L. Bardwell, and Q. Nie. A Combination of Multisite Phosphorylation and Substrate Sequestration Produces Switch-Like Responses. Biophysicsl Journal. 98(8), pp1396-1407, 2010

2009
48. J. Lei, G. He, H. Liu, and Q. Nie. A Delay Model for Noise-Induced Bi-Directional Switching. Nonlinearity, 22, pp 2845-2859, 2009.
47. S. Christley, Q. Nie and X. Xie. Incorporating Existing Network Information into Gene Network Inference.  PLoS ONE, 4(8): e6799, 2009.
46. J. Wells, B. Lee, A. Cai, A. Karapetyan, W. Lee, E. Rugg, S. Sinha, Q. Nie, X. Dai. Ovol2 Suppresses Cell Cycling and Terminal Differentiation of Keratinocytes by Directly Repressing C-Myc And Notch1.  J. of Biological Chemistry, 284, pp 29125-29135, 2009.
45. A. Cai, Y. Peng, J.. Wells, X. Dai, Q. Nie. Multi-scale Modeling for Threshold Dependent Differentiation. Math. Model of Nat. Phenom. 4(4), pp 103-117. 2009
44. X. Li and Q. Nie. A High-Order Boundary Integral Method for Surface Diffusions on Elastically Stressed Axi-Symmetric Rods. J. of Computational Physics, 228(12), pp 4625-4637, 2009.
43. A. Lander, W. Lo, Q. Nie, and F. Wan. The Measure of Success: Contraints, Objectives, and Tradeoffs in Morphogen-Mediated Patterning. Cold Spring Harb Perspectives in Biology, 1:a002022, 2009.
42. A. Lander, K. Gokoffski, F. Wan, Q. Nie, and A. Calof. Cell Lineages and the Logic of Proliferative Control. PLoS Biology, 7(1):e1000015, 2009.
41. W. Lo, C. Chou, K. Gokoffski, F. Wan, A. Lander, A. Calof and Q. Nie. Feedback Regulation in Multistage Cell Lineages. Mathematical Biosciences and Engineering, 6(1), pp 59-82, 2009.
40. Y. Zhou, J. He and Q. Nie. A Comparative Runtime Analysis of Heuristic Algorithms for Satisfiability Problems. Artificial Intelligence, 173(2):240-257, 2009.
39. A. Lander, Q. Nie, F. Wan, Y. Zhang. Localized Ectopic Expression of Dpp Receptors in a Drosophila Embryo. Studies in Applied Mathematics, 123, pp 175-214, 2009.

2008
38 T. Moore, C.S. Chou, Q. Nie, Jeon, N.L. and T. M. Yi. Robust Spatial Sensing of Mating Pheromone Gradients by Yeast Cells. PLoS ONE, 3(12):e3865, 2008.
37. S. Chou, S. Zhao, Y. Song, H. LIu, and Q. Nie. Fus3-Triggered Tec1 Degradation Modulates Mating Transcriptional Output during the Pheromone Response. Nature Molecular Systems Biology, 4:212, 2008. [supplementary Info]
36. C. Chou, Q. Nie, and T. Yi. Modeling Robustness Tradeoffs in Yeast Cell Polarization Induced by Spatial Gradients. PLoS ONE, 3(9):e3103, 2008.
35. Q. Nie, F.Y.M. Wan, Y-T Zhang, and X-F Liu. Compact Integration Factor Methods in High Spatial Dimensions. Journal of Computational Physics, 227(10), pp 5238-5255, 2008.
34. D. Iron, A. Syed, H. Theisen, T. Lukacsovich, M. Naghibi, L.J. Marsh, F.Y.M. Wan, and Q. Nie. The Role of Feedback in the Formation of Morphogen Territories. Mathematical Biosciences of Engineering, 5(2), pp 277-298, 2008.

2007
33. R. White, Q. Nie, L. Lander, and T. Schilling. Complex Regulation of cyp26a1 Creates a Robust Retinoic Acid Gradient in the Zebrafish Embryo. PLoS Biology, 5(11), e304, 2007. (Press Release)
32. Y. Zhang, A. Lander and Q. Nie. Computational Analysis of BMP Gradients in Dorsal-ventral Patterning of the Zebrafish Embryo. Journal of Theoretical Biology, 248, pp 579-589, 2007.
31. L. Bardwell, X. Zou, Q. Nie, and N. Kamorova. Mathematical Models of Specificity in Cell Signaling. Biophysical Journal. 92, pp 3425-3441, 2007.
30. T. Yi, S. Chen, C. Chou, and Q. Nie. Modeling Yeast Cell Polarization Induced by Pheromone Gradients. J. of Statistical Physics. 128(1), pp 193-207, 2007.
29. C. Chou, Y. Zhang, R. Zhao, and Q. Nie. Numerical Methods for Stiff Reaction-Diffusion Systems. Discrete and Continuous Dynamical Systems-B, 7(3), pp 515-525, 2007.
28. X. Li, V. Cristini, Q. Nie, and J. Lowengrub.  Nonlinear Three-Dimensional Simulation of Solid Tumor Growth. Discrete and Continuous Dynamical System-B, 7(3), pp 581-604, 2007.
27. A. Lander, Q. Nie and F. Wan. Membrane Associated Non-receptors and Morphogen Gradients. Bulletin of Mathematical Biology, 69, pp 33-54, 2007.
26. H. Theisen, A. Syed, B. Nguyen, T. Lukasovich, J. Purcell, G. Srivastava, D. Irons, K. Gaudenz, Q. Nie, F. Wan, M. Waterman, and J. Marsh. Wingless Directly Represses DPP Morphogen Expression via an Armadillo/TCF/Brinker Complex. PLoS ONE, 2(1): e142, 2007.
25. X. Li and Q. Nie. Surface Diffusion on Stressed Solid Surface. Communications in Computational Physics, 2(1), pp 73-86, 2007.

2006-2000
24. Q. Nie, Y. Zhang and R. Zhao. Efficient Semi-implicit Schemes for Stiff Systems. Journal of Computational Physics, 214, pp 521-537, 2006.
23. A. Lander, Q. Nie and F. Wan. Internalization and End Flux in Morphogen Gradient Formation. Journal of Computational and Applied Mathematics, 190(1-2), pp 232-251, 2006.
22. N. Komarova, X. Zou, Q. Nie and L. Bardwell. A Theoretical Framework for Specificity in Cell Signaling. Nature Molecular Systems Biology, 1:2005.0023, 2005. Supplement
21. C. Mizutant, Q. Nie, F. Wan, Y. Zhang, P. Vilmos, E. Bier, L. Marsh and A. Lander. Formation of the BMP Activity Gradient in the Drosophia Embryo. Developmental Cell, 8(6), pp 915-924, 2005. Supplement
20. Y. Lou, Q. Nie and F. Wan. Effects of Sog on Dpp-Receptor Binding. SIAM J. on Applied Math., 66 (5), pp 1748-1771, 2005.
19. A. Lander, Q. Nie and F. Wan. Spatially Distributed Morphogen Production and Morphogen Gradient Formation.  Mathematical Biosciences and Engineering, 2(2), pp 239-262, 2005.
18. A. Lander, Q. Nie, B. Vargas and F. Wan. Aggregation of a Distributed Source in Morphogee Gradient Formation. Studies in Applied Mathematics, 114(4), pp 343-374, 2005.
17. X. Li, K. Thornton, Q. Nie, P. Voorhees and J. Lowengrub. Two- and Three-dimensional Equilibrium Morphology of a Misfitting Particle and the Gibbs-Thomson Effect. Acta Materialia, Vol 52/20, pp 5829-5843, 2004.
16. Y. Lou, Q. Nie, and F. Wan. Nonlinear Eigenvalue Problems in the Stability Analysis of Morphogen Gradients.  Studies in Applied Mathematics, Vol 113, pp 183-215, 2004.
15. X. Li, J. Lowengrub, Q. Nie, V. Cristini and P. Leo. Microstructural Evolution in Three-Dimensional Inhomogeneous Elastic Media. Metall. Mater. Tran. A, 34A(7), pp 1421-1431, 2003.
14. V. Cristini, J. Lowengrub and Q. Nie. Nonlinear Simulation of Tumor Growth. J. of Mathematical Biology, 46(3), pp 191-224, 2003.
13. A. Lander, Q. Nie and F. Wan. Do Morphogen Gradients Arise by Diffusion? Developmental Cell, Vol. 2, no. 6, pp 785-796, 2002. Previews
12. Q. Nie. The Nonlinear Evolution of Vortex Sheets with Surface Tension in Axi-symmetric Flows. J. of Computational Physics, 174, pp 438-459, 2001.
11. Q. Nie and F. Tian. Singularities in Hele-Shaw Flows Driven by a Multipole. SIAM J. on Applied Mathematics, 62(2), pp 385-406, 2001.
10. P. Leo, J. Lowengrub and Q. Nie. On an Elastically Induced Splitting Instability. Acta Mater. 49, pp. 2761-2772, 2001.
9. P. Leo, J. Lowengrub and Q. Nie. Microstructural Evolution in Inhomogeneous and Anisotropic Elastic Media. J. of Computational Physics, 157, pp 44-88, 2000.

1999-1995
8. P. Constantin, Q. Nie and N. Schorghofer. Front Formation in an Active Scalar. Physical Review E, 60(3), pp. 2858-2863, 1999.
7. P. Constantin, Q. Nie and S. Tanveer. Bounds for Second Order Structure Functions and Energy Spectrum in Turbulence. Physics of Fluids, 11(8), pp. 2251-2256, 1999.
6. Q. Nie and S. Tanveer. A Note on Third Order Structure Functions in Turbulence. Proc. Royal Soc. London A, 455, pp 1615-1636, 1999.
5. P. Constantin, Q. Nie and N. Schorghofer. Nonsingular Surface Quasi-Geostrophic flows. Physics Letters A 241, pp 168-172, 1998.
4. Q. Nie and G. Baker. Application of Adaptive Quadrature to Axi-symmetric Vortex Sheet Motion. J. of Computational Physics 143, pp. 49-69, 1998.
3. G. Baker and Q. Nie. The Asymptotic Motion of an Accelerating, Thick Layer of Inviscid Liquid. Physics of Fluids 10(1), pp. 101-112, 1998.
2. Q. Nie and F. Tian. Singularities in Hele-Shaw Flows. SIAM J. on Applied Mathematics 58(1), pp. 34-54, 1998.
1. Q. Nie and S. Tanveer. The Stability of a Two-dimensional Rising Bubble. Physics of Fluids 7 (6), pp. 1292-1306, 1995.

Published Refereed Proceeding Articles and Book Chapters, Editor for Special Issues
10. Jiang Xie, Junfu Xu, Celine Nie, and Qing Nie. “Prediction on Performance of Age Group Swimming Using Machine Learning”, The Third International Conference of High Performance Computing and Applications, Lecture Notes in Computer Science (LNCS), Springer, Switzerland, 2016.
9 . Xiaoying Han and Qing Nie, Editor, Special Issue on “Analysis and quantification of noise effects in biological systems”. Discrete and Continuous Dynamical Systems -B, 2016.
8. Schilling TF, Sosnik J and Nie Q). Visualizing retinoic acid morphogen gradients. Methods in Cell Biology 133, 139-163. In The Zebrafish: Cellular and Molecular Biology, Part A, Cellular Biology (eds. HW Detrich III, M Westerfield, LI Zon). Elsevier, Academic Press. 2016
7. Qing Nie. Systems Biology. The Princeton Companion to Applied Mathematics, editors: N. Higham, M. Dennis, P. Glendinning, P. Martin, F. Santosa. Princeton University Press, Princeton, NJ. 2014.6.
6. Youfang Cao, Claire Liang, Hammad Naveed, Yingzi Li, Meng Chen and Qing Nie, Modeling spatial population dynamics of stem cell lineage in tissue growth, Proc. 34th Annual International Conference of the IEEE EMBS San Diego, California USA, 5502-5505, 2012
5. Y. Cao, C. Liang, H. Naveed, Y. Li, M. Chen, and Q. Nie. Modeling Spatial Population Dynamics of Stem Cell Lineage in Tissue Growth. Proceeding 34th Annual International Conference of the IEEE EMBS, San Diego, California, 5502-5505, 2012.
4. Q. Nie and Y.-T. Zhang. Cell Biology Modeling Development, Encyclopedia of Applied and Computational Mathematics, Springer, accepted, 2011.
3. X. F. Liu and Q. Nie. Spatially-localized scaffold proteins may facilitate to transmit long-range signals. Acta Mathematicia, Scientia, 29B (6), pp 1657-1669, 2009
2. J. Kao, Q. Nie, A. Teng, F. Wan, A. Lander, and J. Marsh. Can Morphogen Activity be Enhanced by its Inhibitors? Proceedings of the 2nd MIT Conference on Computational Fluid and Solid Mechanics, pp1729-1733, 2003.
1. Q. Nie, S. Tanveer, T. Dupont and X. Li. Singularity Formation in Free-Surface Stokes Flows. Contemporary Mathematics, Vol 306, pp 147-165, 2002.