Qing Nie

发表

A reaction–diffusion mechanism influences cell lineage progression as a basis for formation, regeneration, and stability of intestinal crypts

Lei Zhang, Arthur D. Lander, Qing Nie, 2012, BMC Systems Biology.

A retinal vessel boundary tracking method based on Bayesian theory and multi-scale line detection

Jia Zhang, Huiqi Li, Qing Nie, 2014, Comput. Medical Imaging Graph..

Numerical Methods for Two-Dimensional Stem Cell Tissue Growth

Qing Nie, Jeremy Ovadia, Q. Nie, 2013, Journal of Scientific Computing.

Machine learning of swimming data via wisdom of crowd and regression analysis.

Jiang Xie, Qing Nie, Junfu Xu, 2016, Mathematical biosciences and engineering : MBE.

Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms

Qing Nie, Xing Dai, Scott Christley, 2010, BMC Systems Biology.

Compact integration factor methods for complex domains and adaptive mesh refinement

Qing Nie, Xinfeng Liu, Q. Nie, 2010, J. Comput. Phys..

DifferentialEquations.jl – A Performant and Feature-Rich Ecosystem for Solving Differential Equations in Julia

Qing Nie, Christopher Rackauckas, Christopher Rackauckas, 2017, Journal of Open Research Software.

Confederated Modular Differential Equation APIs for Accelerated Algorithm Development and Benchmarking

Qing Nie, Christopher Rackauckas, Christopher Rackauckas, 2018, Adv. Eng. Softw..

Semi-implicit integration factor methods on sparse grids for high-dimensional systems

Weitao Chen, Qing Nie, Dongyong Wang, 2015, J. Comput. Phys..

Array-representation integration factor method for high-dimensional systems

Lei Zhang, Qing Nie, Dongyong Wang, 2014, J. Comput. Phys..

Singularities in Hele-Shaw Flows

Qing Nie, Fei-Ran Tian, F. Tian, 1998, SIAM J. Appl. Math..

Nanog induced intermediate state in regulating stem cell differentiation and reprogramming

Lei Zhang, Qing Nie, Chao Tang, 2018, BMC Systems Biology.

Modelling of Yeast Mating Reveals Robustness Strategies for Cell-Cell Interactions

Weitao Chen, Qing Nie, Tau-Mu Yi, 2016, PLoS Comput. Biol..

Network Topologies That Can Achieve Dual Function of Adaptation and Noise Attenuation.

Lei Zhang, Qing Nie, Chao Tang, 2019, Cell systems.

Prediction on Performance of Age Group Swimming Using Machine Learning

Jiang Xie, Qing Nie, Junfu Xu, 2015, HPCA.

Efficient semi-implicit schemes for stiff systems

Qing Nie, Rui Zhao, Yong-Tao Zhang, 2006, J. Comput. Phys..

Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns

Xiaohui Xie, Qing Nie, Zhenzhen Zheng, 2014, BMC Systems Biology.

A high-order boundary integral method for surface diffusions on elastically stressed axisymmetric rods

Xiaofan Li, Qing Nie, Q. Nie, 2009, J. Comput. Phys..

Fast Acquisition and Reconstruction of Optical Coherence Tomography Images via Sparse Representation

Shutao Li, Joseph A. Izatt, Cynthia A. Toth, 2013, IEEE Transactions on Medical Imaging.

Noise filtering tradeoffs in spatial gradient sensing and cell polarization response

Qing Nie, Tau-Mu Yi, Ching-Shan Chou, 2011, BMC Systems Biology.

Qing Nie, Shuxiong Wang, Adam L. MacLean, 2018 .

A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions

Tao Peng, Qing Nie, Weian Zhao, 2017, BMC Systems Biology.

Landscape reveals critical network structures for sharpening gene expression boundaries

Lei Zhang, Qing Nie, Chunhe Li, 2018, BMC Syst. Biol..

Contour Based Multi-object Classification Technology

Qing Nie, Shou-yi Zhan, 2008, ICIRA.

A comparative runtime analysis of heuristic algorithms for satisfiability problems

Yuren Zhou, Qing Nie, Jun He, 2009, Artif. Intell..

Effects of Sog on Dpp-Receptor Binding

Yuan Lou, Qing Nie, Frederic Y. M. Wan, 2005, SIAM J. Appl. Math..

The Construction of Diversified Learning Platform Based on Bilingual Education - The Teaching Practice of E-commerce Course in SIFT

Qing Nie, Yiqun Li, 2010, 2010 International Conference on E-Business and E-Government.

Cell Lineage and Communication Network Inference via Optimization for Single-Cell Transcriptomics

Qing Nie, Shuxiong Wang, Adam L. MacLean, 2019 .

SPATIALLY-LOCALIZED SCAFFOLD PROTEINS MAY FACILITATE TO TRANSMIT LONG-RANGE SIGNALS ! Dedicated to Professor James Glimm on the occasion of his 75th birthday

Qing Nie, Xinfeng Liu, Q. Nie, 2009 .

A dictionary based survival error compensation for robust adaptive filtering

Badong Chen, Ronghua Zhou, Jie Yang, 2016, 2016 International Joint Conference on Neural Networks (IJCNN).

Active Shape Model for Contour Detection of Anatomical Structure

Qing Nie, Huiqi Li, 2015 .

Kernel differential subgraph reveals dynamic changes in biomolecular networks

Yong Zhang, Jiaxin Li, Jiang Xie, 2017, J. Bioinform. Comput. Biol..

An Adaptive Hybrid Algorithm for Global Network Alignment

Jun Tan, Jinzhi Lei, Jin Ma, 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

External noise control in inherently stochastic biological systems.

Meng Chen, Qing Nie, Likun Zheng, 2012, Journal of mathematical physics.

Modeling craniofacial development reveals spatiotemporal constraints on robust patterning of the mandibular arch

Qing Nie, Lei Zhang, Huijing Du, 2018, PLoS Comput. Biol..

Ultrasensitive Responses and Specificity in Cell Signaling

Qing Nie, Seth Haney, Lee Bardwell, 2010, BMC Systems Biology.

Modeling spatial population dynamics of stem cell lineage in tissue growth

Meng Chen, Qing Nie, Yingzi Li, 2012, 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

Singularities in Hele--Shaw Flows Driven by a Multipole

Qing Nie, Fei-Ran Tian, 2001, SIAM J. Appl. Math..

Noise Attenuation in the ON and OFF States of Biological Switches

Meng Chen, Qing Nie, Liming Wang, 2013, ACS synthetic biology.

Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst

Tao Peng, Qing Nie, Huijing Du, 2017, PLoS Comput. Biol..

A compact finite difference method for reaction–diffusion problems using compact integration factor methods in high spatial dimensions

Qing Nie, Yong-Tao Zhang, Frederic Y. M. Wan, 2008, Advances in Difference Equations.

Virtual technology on CPSE-Bio

Wu Zhang, Jiang Xie, Qing Nie, 2012, 2012 7th International Conference on Computing and Convergence Technology (ICCCT).

Operator splitting implicit integration factor methods for stiff reaction-diffusion-advection systems

Su Zhao, Qing Nie, Yong-Tao Zhang, 2011, J. Comput. Phys..

Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains

Qing Nie, Thomas Schilling, William R. Holmes, 2017, PLoS Comput. Biol..

A global biomolecular network alignment method based on network flow model

Wu Zhang, Jiaxin Li, Jiang Xie, 2017, 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Computational study of signaling specificity and epigenetic regulation

Su Zhao, Qing Nie, 2011 .

A HYBRID METHOD FOR STIFF REACTION-DIFFUSION EQUATIONS.

Qing Nie, Weitao Chen, Yuchi Qiu, 2019, Discrete and continuous dynamical systems. Series B.

Object Recognition Based on Efficient Sub-window Search

Qing Nie, Weiming Li, Shou-yi Zhan, 2009, AICI.

The Interplay between Wnt Mediated Expansion and Negative Regulation of Growth Promotes Robust Intestinal Crypt Structure and Homeostasis

Qing Nie, Huijing Du, William R. Holmes, 2015, PLoS Comput. Biol..

An integration factor method for stochastic and stiff reaction-diffusion systems

Qing Nie, Dongyong Wang, Catherine Ha Ta, 2015, J. Comput. Phys..

A hybrid continuous-discrete method for stochastic reaction–diffusion processes

Qing Nie, Likun Zheng, Wing-Cheong Lo, 2016, Royal Society Open Science.

Interdisciplinary Case Study: How Mathematicians and Biologists Found Order in Cellular Noise

Qing Nie, Thomas Schilling, Christopher Rackauckas, 2018, iScience.

scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data

Tao Peng, Qing Nie, Adam L MacLean, 2018, Bioinform..

Protein Scaffolds Can Enhance the Bistability of Multisite Phosphorylation Systems

Liming Wang, Qing Nie, Germán A. Enciso, 2012, PLoS Comput. Biol..

A moment-convergence method for stochastic analysis of biochemical reaction networks.

Qing Nie, Tianshou Zhou, Jiajun Zhang, 2016, The Journal of chemical physics.

Stability-Optimized High Order Methods and Stiffness Detection for Pathwise Stiff Stochastic Differential Equations

Qing Nie, Christopher Rackauckas, Christopher Rackauckas, 2018, 2020 IEEE High Performance Extreme Computing Conference (HPEC).

A robust and efficient method for steady state patterns in reaction-diffusion systems

Ming Wang, Long Chen, Qing Nie, 2012, J. Comput. Phys..

Multiscale modeling of layer formation in epidermis

Qing Nie, Yangyang Wang, Huijing Du, 2018, PLoS Comput. Biol..

A Critical Quantity for Noise Attenuation in Feedback Systems

Jack Xin, Liming Wang, Qing Nie, 2010, PLoS Comput. Biol..

Tracking longitudinal population dynamics of single neuronal calcium signal using SCOUT

Qing Nie, Suoqin Jin, Kevin G. Johnston, 2021, Cell reports methods.

SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration

Qinke Peng, Qing Nie, Xiaohui Xie, 2021, Bioinform..

The nonlinear evolution of vortex sheets with surface tension in axisymmetric flows

Qing Nie, Q. Nie, 2001 .

Primary visual cortex shows laminar‐specific and balanced circuit organization of excitatory and inhibitory synaptic connectivity

Qing Nie, Yulin Shi, Xiangmin Xu, 2016, The Journal of physiology.

Spatially distributed morphogen production and morphogen gradient formation.

Qing Nie, Frederic Y M Wan, Arthur D Lander, 2005, Mathematical biosciences and engineering : MBE.

Internalization and end flux in morphogen gradient formation

Arthur D. Lander, Qing Nie, Frederic Y. M. Wan, 2006 .

Noise modulation in retinoic acid signaling sharpens segmental boundaries of gene expression in the embryonic zebrafish hindbrain

Enrico Gratton, Qing Nie, Likun Zheng, 2016, eLife.

CORRIGENDUM: Nonlinear Growth Kinetics of Breast Cancer Stem Cells: Implications for Cancer Stem Cell Targeted Therapy

Qing Nie, Qian Wang, Q. Nie, 2013, Scientific Reports.

Signaling regulated endocytosis and exocytosis lead to mating pheromone concentration dependent morphologies in yeast

Qing Nie, Tau-Mu Yi, Ching-Shan Chou, 2012, FEBS letters.

Ovol2 Suppresses Cell Cycling and Terminal Differentiation of Keratinocytes by Directly Repressing c-Myc and Notch1*

Qing Nie, Briana Lee, Elizabeth Rugg, 2009, The Journal of Biological Chemistry.

Computational modelling of epidermal stratification highlights the importance of asymmetric cell division for predictable and robust layer formation

Qing Nie, William R Holmes, Xing Dai, 2014, Journal of The Royal Society Interface.

Can morphogen activity be enhanced by its inhibitors

Arthur D. Lander, Qing Nie, Frederic Y. M. Wan, 2003 .

Multiscale Modeling of Inflammation-Induced Tumorigenesis Reveals Competing Oncogenic and Oncoprotective Roles for Inflammation.

Jinzhi Lei, Qing Nie, Yanda Li, 2017, Cancer research.

A multi-scale model for hair follicles reveals heterogeneous domains driving rapid spatiotemporal hair growth patterning

Qing Nie, Zhengquan Yu, Qixuan Wang, 2017, eLife.

SOMSC: Self-Organization-Map for High-Dimensional Single-Cell Data of Cellular States and Their Transitions

Qing Nie, Q. Nie, Tao Peng, 2017, bioRxiv.

Feedback regulation in multistage cell lineages.

Qing Nie, Ching-Shan Chou, Wing-Cheong Lo, 2008, Mathematical biosciences and engineering : MBE.

Transcriptional mechanisms link epithelial plasticity to adhesion and differentiation of epidermal progenitor cells.

Qing Nie, Jeremy Ovadia, Briana Lee, 2014, Developmental cell.

A theoretical framework for specificity in cell signaling

Xiufen Zou, Qing Nie, Natalia L Komarova, 2005, Molecular systems biology.

Cell lineage and communication network inference via optimization for single-cell transcriptomics

Qing Nie, Shuxiong Wang, Adam L MacLean, 2019, Nucleic acids research.

Topographer Reveals Dynamic Mechanisms of Cell Fate Decisions from Single-Cell Transcriptomic Data

Qing Nie, Tianshou Zhou, Jiajun Zhang, 2018, bioRxiv.

The measure of success: constraints, objectives, and tradeoffs in morphogen-mediated patterning.

Qing Nie, Wing-Cheong Lo, Frederic Y M Wan, 2009, Cold Spring Harbor perspectives in biology.

Efficient and Robust Methods for Steady-State Patterns in Reaction-Diffusion Systems

Qing Nie, Wing-Cheong Lo, Q. Nie, 2011 .

Interactions and tradeoffs between cell recruitment, proliferation, and differentiation affect CNS regeneration.

Qing Nie, William R Holmes, W. Holmes, 2014, Biophysical journal.

Exploring intermediate cell states through the lens of single cells

Qing Nie, Tian Hong, Adam L. MacLean, 2018, Current opinion in systems biology.

Spatial dynamics of multistage cell lineages in tissue stratification.

Qing Nie, Yong-Tao Zhang, Ching-Shan Chou, 2010, Biophysical journal.

Do morphogen gradients arise by diffusion?

Qing Nie, Frederic Y M Wan, Arthur D Lander, 2002, Developmental cell.

A combination of multisite phosphorylation and substrate sequestration produces switchlike responses.

Qing Nie, Lee Bardwell, L. Bardwell, 2010, Biophysical journal.

Nonlinear three-dimensional simulation of solid tumor growth

Qing Nie, Vittorio Cristini, John Lowengrub, 2007 .

Correction: Low-Rank Regularization for Learning Gene Expression Programs

Qing Nie, Jian-Feng Cai, Xiaohui Xie, 2014, PLoS ONE.

Computational analysis of BMP gradients in dorsal-ventral patterning of the zebrafish embryo.

Qing Nie, Yong-Tao Zhang, Arthur D Lander, 2007, Journal of theoretical biology.

Stem cell niche structure as an inherent cause of undulating epithelial morphologies.

Qing Nie, Jeremy Ovadia, Q. Nie, 2013, Biophysical journal.

Intermediate cell states in epithelial-to-mesenchymal transition

Qing Nie, Huijing Du, Xing Dai, 2019, Physical biology.

Formation of the BMP activity gradient in the Drosophila embryo.

Qing Nie, Yong-Tao Zhang, Ethan Bier, 2005, Developmental cell.

Nonlinear Eigenvalue Problems in the Stability Analysis of Morphogen Gradients

Qing Nie, Frederic Y. M. Wan, Y. Lou, 2004 .

Incorporating Existing Network Information into Gene Network Inference

Qing Nie, Xiaohui Xie, Scott Christley, 2009, PloS one.

Complex Regulation of cyp26a1 Creates a Robust Retinoic Acid Gradient in the Zebrafish Embryo

Qing Nie, Thomas F Schilling, Arthur D Lander, 2007, PLoS biology.

Modeling Robustness Tradeoffs in Yeast Cell Polarization Induced by Spatial Gradients

Qing Nie, Tau-Mu Yi, Ching-Shan Chou, 2008, PloS one.

Single-cell analysis reveals fibroblast heterogeneity and myeloid-derived adipocyte progenitors in murine skin wounds

Qing Nie, Warren S. Pear, Suoqin Jin, 2019, Nature Communications.

Modeling Yeast Cell Polarization Induced by Pheromone Gradients

Qing Nie, Tau-Mu Yi, Ching-Shan Chou, 2007 .

Robust Spatial Sensing of Mating Pheromone Gradients by Yeast Cells

Qing Nie, Tau-Mu Yi, Noo Li Jeon, 2008, PloS one.

Quantifying the landscape and kinetic paths for epithelial-mesenchymal transition from a core circuit.

Qing Nie, Tian Hong, Chunhe Li, 2016, Physical chemistry chemical physics : PCCP.

Free Extracellular Diffusion Creates the Dpp Morphogen Gradient of the Drosophila Wing Disc

Enrico Gratton, Arthur D. Lander, Qing Nie, 2012, Current Biology.

Noise drives sharpening of gene expression boundaries in the zebrafish hindbrain

Qing Nie, Likun Zheng, Lei Zhang, 2012, Molecular systems biology.

Mouse cardiac surgery: comprehensive techniques for the generation of mouse models of human diseases and their application for genomic studies.

Qing Nie, Martina Schinke, Q. Nie, 2004, Physiological genomics.

Nonessential sites improve phosphorylation switch.

Qing Nie, German Enciso, Q. Nie, 2010, Biophysical journal.

Qing Nie, Shuxiong Wang, Adam L. MacLean, 2017, bioRxiv.

Numerical methods for stiff reaction-diffusion systems

Qing Nie, Yong-Tao Zhang, Ching-Shan Chou, 2007 .

Mathematical models of specificity in cell signaling.

Xiufen Zou, Qing Nie, Natalia L Komarova, 2007, Biophysical journal.

Two- and three-dimensional equilibrium morphology of a misfitting particle and the Gibbs-Thomson effect

Qing Nie, John Lowengrub, Katsuyo Thornton, 2004 .