Qing Nie - Publications

University of California, Irvine, Irvine, CA 

105 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Sun Y, Jin S, Lin X, Chen L, Qiao X, Jiang L, Zhou P, Johnston KG, Golshani P, Nie Q, Holmes TC, Nitz DA, Xu X. CA1-projecting subiculum neurons facilitate object-place learning. Nature Neuroscience. PMID 31548723 DOI: 10.1038/s41593-019-0496-y  0.56
2019 Qiao L, Zhao W, Tang C, Nie Q, Zhang L. Network Topologies That Can Achieve Dual Function of Adaptation and Noise Attenuation. Cell Systems. PMID 31542414 DOI: 10.1016/j.cels.2019.08.006  0.96
2019 Zheng X, Jin S, Nie Q, Zou X. scRCMF: Identification of cell subpopulations and transition states from single cell transcriptomes. Ieee Transactions On Bio-Medical Engineering. PMID 31449003 DOI: 10.1109/TBME.2019.2937228  0.56
2019 Nie Q, Plikus MV. Equal opportunities in stemness. Nature Cell Biology. PMID 31358967 DOI: 10.1038/s41556-019-0366-6  0.4
2019 Wang S, Karikomi M, MacLean AL, Nie Q. Cell lineage and communication network inference via optimization for single-cell transcriptomics. Nucleic Acids Research. PMID 30923815 DOI: 10.1093/nar/gkz204  0.32
2019 Wang Y, Guerrero-Juarez CF, Qiu Y, Du H, Chen W, Figueroa S, Plikus MV, Nie Q. A multiscale hybrid mathematical model of epidermal-dermal interactions during skin wound healing. Experimental Dermatology. PMID 30801791 DOI: 10.1111/exd.13909  0.52
2019 Guerrero-Juarez CF, Dedhia PH, Jin S, Ruiz-Vega R, Ma D, Liu Y, Yamaga K, Shestova O, Gay DL, Yang Z, Kessenbrock K, Nie Q, Pear WS, Cotsarelis G, Plikus MV. Single-cell analysis reveals fibroblast heterogeneity and myeloid-derived adipocyte progenitors in murine skin wounds. Nature Communications. 10: 650. PMID 30737373 DOI: 10.1038/s41467-018-08247-x  0.56
2018 Sharma PP, MacLean AL, Meinecke L, Clouthier DE, Nie Q, Schilling TF. Transcriptomics reveals complex kinetics of dorsal-ventral patterning gene expression in the mandibular arch. Genesis (New York, N.Y. : 2000). e23275. PMID 30561090 DOI: 10.1002/dvg.23275  0.32
2018 Sha Y, Haensel D, Gutierrez G, Du H, Dai X, Nie Q. Intermediate cell states in epithelial-to-mesenchymal transition. Physical Biology. PMID 30560804 DOI: 10.1088/1478-3975/aaf928  0.4
2018 Meinecke L, Sharma PP, Du H, Zhang L, Nie Q, Schilling TF. Modeling craniofacial development reveals spatiotemporal constraints on robust patterning of the mandibular arch. Plos Computational Biology. 14: e1006569. PMID 30481168 DOI: 10.1371/journal.pcbi.1006569  0.96
2018 MacLean AL, Hong T, Nie Q. Exploring intermediate cell states through the lens of single cells. Current Opinion in Systems Biology. 9: 32-41. PMID 30450444 DOI: 10.1016/j.coisb.2018.02.009  0.36
2018 Haensel D, Sun P, MacLean AL, Ma X, Zhou Y, Stemmler MP, Brabletz S, Berx G, Plikus MV, Nie Q, Brabletz T, Dai X. An Ovol2-Zeb1 transcriptional circuit regulates epithelial directional migration and proliferation. Embo Reports. PMID 30413481 DOI: 10.15252/embr.201846273  0.4
2018 Li C, Zhang L, Nie Q. Landscape reveals critical network structures for sharpening gene expression boundaries. Bmc Systems Biology. 12: 67. PMID 29898720 DOI: 10.1186/s12918-018-0595-5  0.96
2018 He Y, Zuo Q, Edwards J, Zhao K, Lei J, Cai W, Nie Q, Li B, Song J. DNA Methylation and Regulatory Elements during Chicken Germline Stem Cell Differentiation. Stem Cell Reports. PMID 29681542 DOI: 10.1016/j.stemcr.2018.03.018  0.32
2018 Lei J, Nie Q, Chen DB. A single-cell epigenetic model for parental psychological stress-induced transgenerational reprogramming in offspring. Biology of Reproduction. PMID 29506130 DOI: 10.1093/biolre/ioy050  0.32
2018 Yu P, Nie Q, Tang C, Zhang L. Nanog induced intermediate state in regulating stem cell differentiation and reprogramming. Bmc Systems Biology. 12: 22. PMID 29486740 DOI: 10.1186/s12918-018-0552-3  0.96
2018 Du H, Wang Y, Haensel D, Lee B, Dai X, Nie Q. Multiscale modeling of layer formation in epidermis. Plos Computational Biology. 14: e1006006. PMID 29481568 DOI: 10.1371/journal.pcbi.1006006  0.4
2018 Jin S, MacLean AL, Peng T, Nie Q. scEpath: Energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data. Bioinformatics (Oxford, England). PMID 29415263 DOI: 10.1093/bioinformatics/bty058  0.56
2017 Xie J, Lu D, Li J, Wang J, Zhang Y, Li Y, Nie Q. Kernel differential subgraph reveals dynamic changes in biomolecular networks. Journal of Bioinformatics and Computational Biology. 1750027. PMID 29281952 DOI: 10.1142/S0219720017500275  0.56
2017 Ba L, Chen XH, Chen YL, Nie Q, Li ZJ, Ding FF, Zhang M. Distinct Rab7-related Endosomal-Autophagic-Lysosomal Dysregulation Observed in Cortex and Hippocampus in APPswe/PSEN1dE9 Mouse Model of Alzheimer's Disease. Chinese Medical Journal. 130: 2941-2950. PMID 29237927 DOI: 10.4103/0366-6999.220311  0.4
2017 Guo Y, Nie Q, MacLean AL, Li Y, Lei J, Li S. Multiscale modeling of inflammation-induced tumorigenesis reveals competing oncogenic and onco-protective roles for inflammation. Cancer Research. PMID 28951462 DOI: 10.1158/0008-5472.CAN-17-1662  0.56
2017 Dower K, Zhao S, Schlerman FJ, Savary L, Campanholle G, Johnson BG, Xi L, Nguyen V, Zhan Y, Lech MP, Wang J, Nie Q, Karsdal MA, Genovese F, Boucher G, et al. High resolution molecular and histological analysis of renal disease progression in ZSF1 fa/faCP rats, a model of type 2 diabetic nephropathy. Plos One. 12: e0181861. PMID 28746409 DOI: 10.1371/journal.pone.0181861  0.84
2017 Wang Q, Oh JW, Lee HL, Dhar A, Peng T, Ramos R, Guerrero-Juarez CF, Wang X, Zhao R, Cao X, Le J, Fuentes MA, Jocoy SC, Rossi AR, Vu B, ... ... Nie Q, et al. A multi-scale model for hair follicles reveals heterogeneous domains driving rapid spatiotemporal hair growth patterning. Elife. 6. PMID 28695824 DOI: 10.7554/eLife.22772  0.4
2017 Peng T, Liu L, MacLean AL, Wong CW, Zhao W, Nie Q. A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions. Bmc Systems Biology. 11: 55. PMID 28511648 DOI: 10.1186/s12918-017-0429-x  0.6
2017 Li CJ, Hong T, Tung YT, Yen YP, Hsu HC, Lu YL, Chang M, Nie Q, Chen JA. MicroRNA filters Hox temporal transcription noise to confer boundary formation in the spinal cord. Nature Communications. 8: 14685. PMID 28337978 DOI: 10.1038/ncomms14685  0.36
2017 Holmes WR, Reyes de Mochel NS, Wang Q, Du H, Peng T, Chiang M, Cinquin O, Cho K, Nie Q. Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst. Plos Computational Biology. 13: e1005320. PMID 28114387 DOI: 10.1371/journal.pcbi.1005320  0.4
2017 Li A, Figueroa S, Jiang TX, Wu P, Widelitz R, Nie Q, Chuong CM. Diverse feather shape evolution enabled by coupling anisotropic signalling modules with self-organizing branching programme. Nature Communications. 8: ncomms14139. PMID 28106042 DOI: 10.1038/ncomms14139  0.4
2017 Xie J, Xu J, Nie C, Nie Q. Machine learning of swimming data via wisdom of crowd and regression analysis. Mathematical Biosciences and Engineering : Mbe. 14: 511-527. PMID 27879112  0.56
2016 Ta CH, Nie Q, Hong T. Controlling Stochasticity in Epithelial-Mesenchymal Transition Through Multiple Intermediate Cellular States. Discrete and Continuous Dynamical Systems. Series B. 21: 2275-2291. PMID 29497351 DOI: 10.3934/dcdsb.2016047  0.36
2016 Nie Q, Liu Y, Chen J. [Reduction of ADRs of essential traditional Chinese medicines]. Zhongguo Zhong Yao Za Zhi = Zhongguo Zhongyao Zazhi = China Journal of Chinese Materia Medica. 41: 340-344. PMID 28861983  0.4
2016 Lo WC, Zheng L, Nie Q. A hybrid continuous-discrete method for stochastic reaction-diffusion processes. Royal Society Open Science. 3: 160485. PMID 27703710 DOI: 10.1098/rsos.160485  0.56
2016 Li C, Hong T, Webb CH, Karner H, Sun S, Nie Q. A self-enhanced transport mechanism through long noncoding RNAs for X chromosome inactivation. Scientific Reports. 6: 31517. PMID 27527711 DOI: 10.1038/srep31517  0.6
2016 Chen W, Nie Q, Yi TM, Chou CS. Modelling of Yeast Mating Reveals Robustness Strategies for Cell-Cell Interactions. Plos Computational Biology. 12: e1004988. PMID 27404800 DOI: 10.1371/journal.pcbi.1004988  1
2016 Li C, Hong T, Nie Q. Quantifying the landscape and kinetic paths for epithelial-mesenchymal transition from a core circuit. Physical Chemistry Chemical Physics : Pccp. PMID 27328302 DOI: 10.1039/c6cp03174a  0.6
2016 Xie J, Xiang C, Ma J, Tan J, Wen T, Lei J, Nie Q. An Adaptive Hybrid Algorithm for Global Network Alignment. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 13: 483-493. PMID 27295633 DOI: 10.1109/TCBB.2015.2465957  1
2016 Sosnik J, Zheng L, Rackauckas CV, Digman M, Gratton E, Nie Q, Schilling TF. Noise modulation in retinoic acid signaling sharpens segmental boundaries of gene expression in the embryonic zebrafish hindbrain. Elife. 5. PMID 27067377 DOI: 10.7554/eLife.14034  0.56
2015 Liu Y, Nie Q, Chen J. [Suggestions to strengthen quality management of herbal decoction pieces--based on production chain of herbal decoction pieces]. Zhongguo Zhong Yao Za Zhi = Zhongguo Zhongyao Zazhi = China Journal of Chinese Materia Medica. 40: 3319-22. PMID 26790314  0.4
2015 Cinquin A, Zheng L, Taylor PH, Paz A, Zhang L, Chiang M, Snow JJ, Nie Q, Cinquin O. Semi-permeable Diffusion Barriers Enhance Patterning Robustness in the C. elegans Germline. Developmental Cell. 35: 405-417. PMID 26609956 DOI: 10.1016/j.devcel.2015.10.027  1
2015 Hong T, Watanabe K, Ta CH, Villarreal-Ponce A, Nie Q, Dai X. An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States. Plos Computational Biology. 11: e1004569. PMID 26554584 DOI: 10.1371/journal.pcbi.1004569  1
2015 Du H, Nie Q, Holmes WR. The Interplay between Wnt Mediated Expansion and Negative Regulation of Growth Promotes Robust Intestinal Crypt Structure and Homeostasis. Plos Computational Biology. 11: e1004285. PMID 26288152 DOI: 10.1371/journal.pcbi.1004285  1
2015 Xie J, Zhou Z, Ma J, Xiang C, Nie Q, Zhang W. Graphics processing unit-based alignment of protein interaction networks. Iet Systems Biology. 9: 120-7. PMID 26243827 DOI: 10.1049/iet-syb.2014.0052  0.56
2015 Chou CS, Moore TI, Nie Q, Yi TM. Alternative cell polarity behaviours arise from changes in G-protein spatial dynamics. Iet Systems Biology. 9: 52-63. PMID 26029251 DOI: 10.1049/iet-syb.2013.0018  0.52
2015 Ta C, Wang D, Nie Q. An Integration Factor Method for Stochastic and Stiff Reaction-Diffusion Systems. Journal of Computational Physics. 295: 505-522. PMID 25983341 DOI: 10.1016/j.jcp.2015.04.028  0.96
2015 Hong T, Fung ES, Zhang L, Huynh G, Monuki ES, Nie Q. Semi-adaptive response and noise attenuation in bone morphogenetic protein signalling. Journal of the Royal Society, Interface / the Royal Society. 12. PMID 25972436 DOI: 10.1098/rsif.2015.0258  0.96
2015 Wang D, Chen W, Nie Q. Semi-implicit Integration Factor Methods on Sparse Grids for High-Dimensional Systems. Journal of Computational Physics. 292: 43-55. PMID 25897178 DOI: 10.1016/j.jcp.2015.03.033  0.96
2015 Li A, Lai YC, Figueroa S, Yang T, Widelitz RB, Kobielak K, Nie Q, Chuong CM. Deciphering principles of morphogenesis from temporal and spatial patterns on the integument. Developmental Dynamics : An Official Publication of the American Association of Anatomists. PMID 25858668 DOI: 10.1002/dvdy.24281  0.4
2015 Lo WC, Zhou S, Wan FY, Lander AD, Nie Q. Robust and precise morphogen-mediated patterning: trade-offs, constraints and mechanisms. Journal of the Royal Society, Interface / the Royal Society. 12: 20141041. PMID 25551154 DOI: 10.1098/rsif.2014.1041  0.56
2014 Gord A, Holmes WR, Dai X, Nie Q. Computational modelling of epidermal stratification highlights the importance of asymmetric cell division for predictable and robust layer formation. Journal of the Royal Society, Interface / the Royal Society. 11. PMID 25100322 DOI: 10.1098/rsif.2014.0631  1
2014 Lee B, Villarreal-Ponce A, Fallahi M, Ovadia J, Sun P, Yu QC, Ito S, Sinha S, Nie Q, Dai X. Transcriptional mechanisms link epithelial plasticity to adhesion and differentiation of epidermal progenitor cells. Developmental Cell. 29: 47-58. PMID 24735878 DOI: 10.1016/j.devcel.2014.03.005  1
2014 Holmes WR, Nie Q. Interactions and tradeoffs between cell recruitment, proliferation, and differentiation affect CNS regeneration. Biophysical Journal. 106: 1528-36. PMID 24703314 DOI: 10.1016/j.bpj.2014.02.010  1
2014 Kang J, Nie Q, DU R, Zhang L, Zhang J, Li Q, Li J, Qi W. Stereotactic body radiotherapy combined with transarterial chemoembolization for hepatocellular carcinoma with portal vein tumor thrombosis. Molecular and Clinical Oncology. 2: 43-50. PMID 24649306 DOI: 10.3892/mco.2013.196  0.96
2014 Lei J, Levin SA, Nie Q. Mathematical model of adult stem cell regeneration with cross-talk between genetic and epigenetic regulation. Proceedings of the National Academy of Sciences of the United States of America. 111: E880-7. PMID 24501127 DOI: 10.1073/pnas.1324267111  1
2014 Ovadia J, Nie Q. Numerical Methods for Two-Dimensional Stem Cell Tissue Growth. Journal of Scientific Computing. 58: 149-175. PMID 24415847 DOI: 10.1007/s10915-013-9728-6  1
2014 Wang D, Zhang L, Nie Q. Array-representation Integration Factor Method for High-dimensional Systems. Journal of Computational Physics. 258. PMID 24415797 DOI: 10.1016/j.jcp.2013.11.002  0.96
2014 Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q. Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns. Bmc Systems Biology. 8: 3. PMID 24397936 DOI: 10.1186/1752-0509-8-3  1
2013 Lei J, Wang D, Song Y, Nie Q, Wan FY. ROBUSTNESS OF MORPHOGEN GRADIENTS WITH "BUCKET BRIGADE" TRANSPORT THROUGH MEMBRANE-ASSOCIATED NON-RECEPTORS. Discrete and Continuous Dynamical Systems. Series B. 18. PMID 24244111 DOI: 10.3934/dcdsb.2013.18.721  0.96
2013 Liu X, Johnson S, Liu S, Kanojia D, Yue W, Singh UP, Singn U, Wang Q, Wang Q, Nie Q, Chen H. Nonlinear growth kinetics of breast cancer stem cells: implications for cancer stem cell targeted therapy. Scientific Reports. 3: 2473. PMID 23959163 DOI: 10.1038/srep02473  1
2013 Fang L, Li S, McNabb RP, Nie Q, Kuo AN, Toth CA, Izatt JA, Farsiu S. Fast acquisition and reconstruction of optical coherence tomography images via sparse representation. Ieee Transactions On Medical Imaging. 32: 2034-49. PMID 23846467 DOI: 10.1109/TMI.2013.2271904  0.32
2013 Chen M, Wang L, Liu CC, Nie Q. Noise attenuation in the ON and OFF states of biological switches. Acs Synthetic Biology. 2: 587-93. PMID 23768065 DOI: 10.1021/sb400044g  0.36
2013 Li A, Chen M, Jiang TX, Wu P, Nie Q, Widelitz R, Chuong CM. Shaping organs by a wingless-int/Notch/nonmuscle myosin module which orients feather bud elongation. Proceedings of the National Academy of Sciences of the United States of America. 110: E1452-61. PMID 23576731 DOI: 10.1073/pnas.1219813110  1
2013 Ovadia J, Nie Q. Stem cell niche structure as an inherent cause of undulating epithelial morphologies. Biophysical Journal. 104: 237-46. PMID 23332076 DOI: 10.1016/j.bpj.2012.11.3807  1
2012 Cao Y, Liang C, Naveed H, Li Y, Chen M, Nie Q. Modeling spatial population dynamics of stem cell lineage in tissue growth. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2012: 5502-5. PMID 23367175 DOI: 10.1109/EMBC.2012.6347240  1
2012 Schilling TF, Nie Q, Lander AD. Dynamics and precision in retinoic acid morphogen gradients. Current Opinion in Genetics & Development. 22: 562-9. PMID 23266215 DOI: 10.1016/j.gde.2012.11.012  1
2012 Zheng L, Chen M, Nie Q. External noise control in inherently stochastic biological systems. Journal of Mathematical Physics. 53: 115616. PMID 23213267 DOI: 10.1063/1.4762825  1
2012 Chou CS, Moore TI, Chang SD, Nie Q, Yi TM. Signaling regulated endocytosis and exocytosis lead to mating pheromone concentration dependent morphologies in yeast. Febs Letters. 586: 4208-14. PMID 23108052 DOI: 10.1016/j.febslet.2012.10.024  1
2012 Zhang L, Radtke K, Zheng L, Cai AQ, Schilling TF, Nie Q. Noise drives sharpening of gene expression boundaries in the zebrafish hindbrain. Molecular Systems Biology. 8: 613. PMID 23010996 DOI: 10.1038/msb.2012.45  1
2012 Zhang L, Lander AD, Nie Q. A reaction-diffusion mechanism influences cell lineage progression as a basis for formation, regeneration, and stability of intestinal crypts. Bmc Systems Biology. 6: 93. PMID 22849824 DOI: 10.1186/1752-0509-6-93  1
2012 Lo WC, Chen L, Wang M, Nie Q. A Robust and Efficient Method for Steady State Patterns in Reaction-Diffusion Systems. Journal of Computational Physics. 231: 5062-5077. PMID 22773849 DOI: 10.1016/j.jcp.2012.04.006  0.56
2012 Chan C, Liu X, Wang L, Bardwell L, Nie Q, Enciso G. Protein scaffolds can enhance the bistability of multisite phosphorylation systems. Plos Computational Biology. 8: e1002551. PMID 22737061 DOI: 10.1371/journal.pcbi.1002551  1
2012 Cai AQ, Radtke K, Linville A, Lander AD, Nie Q, Schilling TF. Cellular retinoic acid-binding proteins are essential for hindbrain patterning and signal robustness in zebrafish. Development (Cambridge, England). 139: 2150-5. PMID 22619388 DOI: 10.1242/dev.077065  1
2012 Fang L, Li S, Nie Q, Izatt JA, Toth CA, Farsiu S. Sparsity based denoising of spectral domain optical coherence tomography images. Biomedical Optics Express. 3: 927-42. PMID 22567586 DOI: 10.1364/BOE.3.000927  0.32
2012 Zhou S, Lo WC, Suhalim JL, Digman MA, Gratton E, Nie Q, Lander AD. Free extracellular diffusion creates the Dpp morphogen gradient of the Drosophila wing disc. Current Biology : Cb. 22: 668-75. PMID 22445299 DOI: 10.1016/j.cub.2012.02.065  1
2011 Lei J, Wan FY, Lander AD, Nie Q. ROBUSTNESS OF SIGNALING GRADIENT IN DROSOPHILA WING IMAGINAL DISC. Discrete and Continuous Dynamical Systems. Series B. 16: 835-866. PMID 24098092 DOI: 10.3934/dcdsb.2011.16.835  1
2011 Chou CS, Bardwell L, Nie Q, Yi TM. Noise filtering tradeoffs in spatial gradient sensing and cell polarization response. Bmc Systems Biology. 5: 196. PMID 22166067 DOI: 10.1186/1752-0509-5-196  1
2011 Zheng Z, Chou CS, Yi TM, Nie Q. Mathematical analysis of steady-state solutions in compartment and continuum models of cell polarization. Mathematical Biosciences and Engineering : Mbe. 8: 1135-68. PMID 21936604  0.52
2011 Zhao S, Ovadia J, Liu X, Zhang YT, Nie Q. Operator Splitting Implicit Integration Factor Methods for Stiff Reaction-Diffusion-Advection Systems. Journal of Computational Physics. 230: 5996-6009. PMID 21666863 DOI: 10.1016/j.jcp.2011.04.009  1
2011 Liu Y, Cui Z, Luan W, Song C, Nie Q, Wang S, Li Q. Three isoforms of anti-lipopolysaccharide factor identified from eyestalk cDNA library of swimming crab Portunus trituberculatus. Fish & Shellfish Immunology. 30: 583-91. PMID 21168510 DOI: 10.1016/j.fsi.2010.12.005  0.4
2010 Chou CS, Lo WC, Gokoffski KK, Zhang YT, Wan FY, Lander AD, Calof AL, Nie Q. Spatial dynamics of multistage cell lineages in tissue stratification. Biophysical Journal. 99: 3145-54. PMID 21081061 DOI: 10.1016/j.bpj.2010.09.034  1
2010 Wang L, Nie Q, Enciso G. Nonessential sites improve phosphorylation switch. Biophysical Journal. 99: L41-3. PMID 20858409 DOI: 10.1016/j.bpj.2010.07.030  0.36
2010 Wang G, Nie Q, Wang X, Chen F, Dai S, Xu T, Shen X, Wang D, Lv X. Effect of KI/AgI on the thermal and optical properties of the GeS₂-In₂S₃ chalcogenide glasses. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 77: 821-4. PMID 20800537 DOI: 10.1016/j.saa.2010.08.011  0.96
2010 Haney S, Bardwell L, Nie Q. Ultrasensitive responses and specificity in cell signaling. Bmc Systems Biology. 4: 119. PMID 20735856 DOI: 10.1186/1752-0509-4-119  1
2010 Christley S, Lee B, Dai X, Nie Q. Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms. Bmc Systems Biology. 4: 107. PMID 20696053 DOI: 10.1186/1752-0509-4-107  1
2010 Liu X, Nie Q. Compact integration factor methods for complex domains and adaptive mesh refinement. Journal of Computational Physics. 229: 5692-5706. PMID 20543883 DOI: 10.1016/j.jcp.2010.04.003  1
2010 Wang L, Xin J, Nie Q. A critical quantity for noise attenuation in feedback systems. Plos Computational Biology. 6: e1000764. PMID 20442870 DOI: 10.1371/journal.pcbi.1000764  0.36
2010 Liu X, Bardwell L, Nie Q. A combination of multisite phosphorylation and substrate sequestration produces switchlike responses. Biophysical Journal. 98: 1396-407. PMID 20409458 DOI: 10.1016/j.bpj.2009.12.4307  1
2009 Lei J, He G, Liu H, Nie Q. A delay model for noise-induced bi-directional switching. Nonlinearity. 22: 2845-2859. PMID 20592956 DOI: 10.1088/0951-7715/22/12/003  0.32
2009 Lander AD, Lo WC, Nie Q, Wan FY. The measure of success: constraints, objectives, and tradeoffs in morphogen-mediated patterning. Cold Spring Harbor Perspectives in Biology. 1: a002022. PMID 20066078 DOI: 10.1101/cshperspect.a002022  1
2009 Christley S, Nie Q, Xie X. Incorporating existing network information into gene network inference. Plos One. 4: e6799. PMID 19710931 DOI: 10.1371/journal.pone.0006799  1
2009 Wells J, Lee B, Cai AQ, Karapetyan A, Lee WJ, Rugg E, Sinha S, Nie Q, Dai X. Ovol2 suppresses cell cycling and terminal differentiation of keratinocytes by directly repressing c-Myc and Notch1. The Journal of Biological Chemistry. 284: 29125-35. PMID 19700410 DOI: 10.1074/jbc.M109.008847  0.4
2009 Lo WC, Chou CS, Gokoffski KK, Wan FY, Lander AD, Calof AL, Nie Q. Feedback regulation in multistage cell lineages. Mathematical Biosciences and Engineering : Mbe. 6: 59-82. PMID 19292508 DOI: 10.3934/mbe.2009.6.59  1
2009 Lander AD, Gokoffski KK, Wan FY, Nie Q, Calof AL. Cell lineages and the logic of proliferative control. Plos Biology. 7: e15. PMID 19166268 DOI: 10.1371/journal.pbio.1000015  1
2008 Chou CS, Nie Q, Yi TM. Modeling robustness tradeoffs in yeast cell polarization induced by spatial gradients. Plos One. 3: e3103. PMID 21267054 DOI: 10.1371/journal.pone.0003103  0.52
2008 Nie Q, Wan FY, Zhang YT, Liu XF. Compact integration factor methods in high spatial dimensions. Journal of Computational Physics. 227: 5238-5255. PMID 19809596 DOI: 10.1016/j.jcp.2008.01.050  1
2008 Moore TI, Chou CS, Nie Q, Jeon NL, Yi TM. Robust spatial sensing of mating pheromone gradients by yeast cells. Plos One. 3: e3865. PMID 19052645 DOI: 10.1371/journal.pone.0003865  1
2008 Chou S, Zhao S, Song Y, Liu H, Nie Q. Fus3-triggered Tec1 degradation modulates mating transcriptional output during the pheromone response. Molecular Systems Biology. 4: 212. PMID 18682702 DOI: 10.1038/msb.2008.47  0.84
2008 Iron D, Syed A, Theisen H, Lukacsovich T, Naghibi M, Marsh LJ, Wan FY, Nie Q. The role of feedback in the formation of morphogen territories. Mathematical Biosciences and Engineering : Mbe. 5: 277-98. PMID 18613734  1
2007 White RJ, Nie Q, Lander AD, Schilling TF. Complex regulation of cyp26a1 creates a robust retinoic acid gradient in the zebrafish embryo. Plos Biology. 5: e304. PMID 18031199 DOI: 10.1371/journal.pbio.0050304  1
2007 Zhang YT, Lander AD, Nie Q. Computational analysis of BMP gradients in dorsal-ventral patterning of the zebrafish embryo. Journal of Theoretical Biology. 248: 579-89. PMID 17673236 DOI: 10.1016/j.jtbi.2007.05.026  1
2007 Bardwell L, Zou X, Nie Q, Komarova NL. Mathematical models of specificity in cell signaling. Biophysical Journal. 92: 3425-41. PMID 17325015 DOI: 10.1529/biophysj.106.090084  1
2007 Theisen H, Syed A, Nguyen BT, Lukacsovich T, Purcell J, Srivastava GP, Iron D, Gaudenz K, Nie Q, Wan FYM, Waterman ML, Marsh JL. Wingless directly represses DPP morphogen expression via and Aarmadillo/TCF/brinker complex Plos One. 2. PMID 17206277 DOI: 10.1371/journal.pone.0000142  1
2005 Lander AD, Nie Q, Wan FY. Spatially distributed morphogen production and morphogen gradient formation. Mathematical Biosciences and Engineering : Mbe. 2: 239-62. PMID 20369921  0.48
2005 Komarova NL, Zou X, Nie Q, Bardwell L. A theoretical framework for specificity in cell signaling. Molecular Systems Biology. 1: 2005.0023. PMID 16729058 DOI: 10.1038/msb4100031  1
2005 Mizutani CM, Nie Q, Wan FY, Zhang YT, Vilmos P, Sousa-Neves R, Bier E, Marsh JL, Lander AD. Formation of the BMP activity gradient in the Drosophila embryo. Developmental Cell. 8: 915-24. PMID 15935780 DOI: 10.1016/j.devcel.2005.04.009  1
2003 Cristini V, Lowengrub J, Nie Q. Nonlinear simulation of tumor growth. Journal of Mathematical Biology. 46: 191-224. PMID 12728333 DOI: 10.1007/s00285-002-0174-6  1
2002 Lander AD, Nie Q, Wan FY. Do morphogen gradients arise by diffusion? Developmental Cell. 2: 785-96. PMID 12062090 DOI: 10.1016/S1534-5807(02)00179-X  1
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