Qing Nie

Pubilications

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. Op erator 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. Siz-normalized Robustness of Dpp Gradient in Drosophila WingImaginal 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. [Review: Biological Systems from an Engineer's Point of View.]
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 System-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. Siscrete abd Continuous 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

5. Y. Cao, C. Liang, H. Naveed, Y. Li, M. Chen, and Q. Nie. ModelingSpatial 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.