Qing Nie

Publication Activity (10 Years)

Years Active: 1998-2024
Publications (10 Years): 37

Top Topics

Gene Expression

Regulatory Networks

Invariant Representation

Top Venues

PLoS Comput. Biol.

BMC Syst. Biol.

J. Comput. Phys.

Publications

Yutong Sha, Yuchi Qiu, Peijie Zhou, Qing Nie
Reconstructing growth and dynamic trajectories from single-cell transcriptomics data. Nat. Mac. Intell. 6 (1) (2024)
Yutong Sha, Yuchi Qiu, Peijie Zhou, Qing Nie
Publisher Correction: Reconstructing growth and dynamic trajectories from single-cell transcriptomics data. Nat. Mac. Intell. 6 (1) (2024)
Yubai Yuan, Babak Shahbaba, Norbert Fortin, Keiland W. Cooper, Qing Nie, Annie Qu
Optimal Transport for Latent Integration with An Application to Heterogeneous Neuronal Activity Data. CoRR (2024)
Kathryn Dover, Zixuan Cang, Anna Ma, Qing Nie, Roman Vershynin
AVIDA: An alternating method for visualizing and integrating data. J. Comput. Sci. 68 (2023)
Kathryn Dover, Zixuan Cang, Anna Ma, Qing Nie, Roman Vershynin
AVIDA: Alternating method for Visualizing and Integrating Data. CoRR (2022)
Zixuan Cang, Qing Nie, Yanxiang Zhao
Supervised Optimal Transport. SIAM J. Appl. Math. 82 (5) (2022)
Xiong Ying, Si-Yang Leng, Huan-Fei Ma, Qing Nie, Ying-Cheng Lai, Wei Lin
Continuity scaling: A rigorous framework for detecting and quantifying causality accurately. CoRR (2022)
Mathew Karikomi, Peijie Zhou, Qing Nie
DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data. Briefings Bioinform. 23 (4) (2022)
Xiaoqiang Sun, Ji Zhang, Qing Nie
Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples. PLoS Comput. Biol. 17 (3) (2021)
Qing Nie, Songyun Liu, Qiyuan Qian, Zheyi Tan, Huiwen Wang
Optimization of the Sino-Europe Transport Networks Under Uncertain Demand. Asia Pac. J. Oper. Res. 38 (3) (2021)
Jiang Xie, Chang Zhao, Jiamin Sun, Jiaxin Li, Fuzhang Yang, Jiao Wang, Qing Nie
Prediction of Essential Genes in Comparison States Using Machine Learning. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (5) (2021)
Yuchi Qiu, Lianna Fung, Thomas F. Schilling, Qing Nie
Multiple morphogens and rapid elongation promote segmental patterning during development. PLoS Comput. Biol. 17 (6) (2021)
Yingxin Cao, Laiyi Fu, Jie Wu, Qinke Peng, Qing Nie, Jing Zhang, Xiaohui Xie
SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration. Bioinform. 37 (Supplement) (2021)
Zixuan Cang, Yangyang Wang, Qixuan Wang, Ken W. Y. Cho, William R. Holmes, Qing Nie
A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development. PLoS Comput. Biol. 17 (3) (2021)
Xiaoying Zheng, Suoqin Jin, Qing Nie, Xiufen Zou
scRCMF: Identification of Cell Subpopulations and Transition States From Single-Cell Transcriptomes. IEEE Trans. Biomed. Eng. 67 (5) (2020)
Jiang Xie, Fuzhang Yang, Jiao Wang, Mathew Karikomi, Yiting Yin, Jiamin Sun, Tieqiao Wen, Qing Nie
DNF: A differential network flow method to identify rewiring drivers for gene regulatory networks. Neurocomputing 410 (2020)
Christopher Rackauckas, Qing Nie
Stability-Optimized High Order Methods and Stiffness Detection for Pathwise Stiff Stochastic Differential Equations. HPEC (2020)
Christopher Rackauckas, Qing Nie
Confederated modular differential equation APIs for accelerated algorithm development and benchmarking. Adv. Eng. Softw. 132 (2019)
Chunhe Li, Lei Zhang, Qing Nie
Landscape reveals critical network structures for sharpening gene expression boundaries. BMC Syst. Biol. 12 (1) (2018)
Suoqin Jin, Adam L. Maclean, Tao Peng, Qing Nie
scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data. Bioinform. 34 (12) (2018)
Huijing Du, Yangyang Wang, Daniel Haensel, Briana Lee, Xing Dai, Qing Nie
Multiscale modeling of layer formation in epidermis. PLoS Comput. Biol. 14 (2) (2018)
Christopher Rackauckas, Qing Nie
Confederated Modular Differential Equation APIs for Accelerated Algorithm Development and Benchmarking. CoRR (2018)
Lina Meinecke, Praveer P. Sharma, Huijing Du, Lei Zhang, Qing Nie, Thomas Schilling
Modeling craniofacial development reveals spatiotemporal constraints on robust patterning of the mandibular arch. PLoS Comput. Biol. 14 (11) (2018)
Peijia Yu, Qing Nie, Chao Tang, Lei Zhang
Nanog induced intermediate state in regulating stem cell differentiation and reprogramming. BMC Syst. Biol. 12 (1) (2018)
Jiang Xie, Dongfang Lu, Jiaxin Li, Jiao Wang, Yong Zhang, Yanhui Li, Qing Nie
Kernel differential subgraph reveals dynamic changes in biomolecular networks. J. Bioinform. Comput. Biol. 16 (1) (2018)
William R. Holmes, Nabora de Mochel, Qixuan Wang, Huijing Du, Tao Peng, Michael Chiang, Olivier Cinquin, Ken Cho, Qing Nie
Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst. PLoS Comput. Biol. 13 (1) (2017)
Jiang Xie, Jiaxin Li, Jiao Wang, Qing Nie, Wu Zhang
A global biomolecular network alignment method based on network flow model. BIBM (2017)
Qixuan Wang, William R. Holmes, Julian Sosnik, Thomas Schilling, Qing Nie
Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains. PLoS Comput. Biol. 13 (1) (2017)
Tao Peng, Linan Liu, Adam L. Maclean, Chi Wut Wong, Weian Zhao, Qing Nie
A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions. BMC Syst. Biol. 11 (1) (2017)
Weitao Chen, Qing Nie, Tau-Mu Yi, Ching-Shan Chou
Modelling of Yeast Mating Reveals Robustness Strategies for Cell-Cell Interactions. PLoS Comput. Biol. 12 (7) (2016)
Lei Sun, Badong Chen, Jie Yang, Ronghua Zhou, Qing Nie, Aihua Wang
A dictionary based survival error compensation for robust adaptive filtering. IJCNN (2016)
Jiang (Linda) Xie, Chaojuan Xiang, Jin Ma, Jun Tan, Tieqiao Wen, Jinzhi Lei, Qing Nie
An Adaptive Hybrid Algorithm for Global Network Alignment. IEEE ACM Trans. Comput. Biol. Bioinform. 13 (3) (2016)
Catherine Ha Ta, Dongyong Wang, Qing Nie
An integration factor method for stochastic and stiff reaction-diffusion systems. J. Comput. Phys. 295 (2015)
Huijing Du, Qing Nie, William R. Holmes
The Interplay between Wnt Mediated Expansion and Negative Regulation of Growth Promotes Robust Intestinal Crypt Structure and Homeostasis. PLoS Comput. Biol. 11 (8) (2015)
Dongyong Wang, Weitao Chen, Qing Nie
Semi-implicit integration factor methods on sparse grids for high-dimensional systems. J. Comput. Phys. 292 (2015)
Jiang Xie, Junfu Xu, Celine Nie, Qing Nie
Prediction on Performance of Age Group Swimming Using Machine Learning. HPCA (China) (2015)
Tian Hong, Kazuhide Watanabe, Catherine Ha Ta, Alvaro Villarreal-Ponce, Qing Nie, Xing Dai
An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States. PLoS Comput. Biol. 11 (11) (2015)
Jia Zhang, Huiqi Li, Qing Nie, Li Cheng
A retinal vessel boundary tracking method based on Bayesian theory and multi-scale line detection. Comput. Medical Imaging Graph. 38 (6) (2014)
Dongyong Wang, Lei Zhang, Qing Nie
Array-representation integration factor method for high-dimensional systems. J. Comput. Phys. 258 (2014)
Jeremy Ovadia, Qing Nie
Numerical Methods for Two-Dimensional Stem Cell Tissue Growth. J. Sci. Comput. 58 (1) (2014)
Zhenzhen Zheng, Scott Christley, William T. Chiu, Ira L. Blitz, Xiaohui Xie, Ken W. Y. Cho, Qing Nie
Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns. BMC Syst. Biol. 8 (2014)
Leyuan Fang, Shutao Li, Ryan P. McNabb, Qing Nie, Anthony N. Kuo, Cynthia A. Toth, Joseph A. Izatt, Sina Farsiu
Fast Acquisition and Reconstruction of Optical Coherence Tomography Images via Sparse Representation. IEEE Trans. Medical Imaging 32 (11) (2013)
Carlo Chan, Xinfeng Liu, Liming Wang, Lee Bardwell, Qing Nie, Germán A. Enciso
Protein Scaffolds Can Enhance the Bistability of Multisite Phosphorylation Systems. PLoS Comput. Biol. 8 (6) (2012)
Lei Zhang, Arthur D. Lander, Qing Nie
A reaction-diffusion mechanism influences cell lineage progression as a basis for formation, regeneration, and stability of intestinal crypts. BMC Syst. Biol. 6 (2012)
Youfang Cao, Claire Liang, Hammad Naveed, Yingzi Li, Meng Chen, Qing Nie
Modeling spatial population dynamics of stem cell lineage in tissue growth. EMBC (2012)
Wing-Cheong Lo, Long Chen, Ming Wang, Qing Nie
A robust and efficient method for steady state patterns in reaction-diffusion systems. J. Comput. Phys. 231 (15) (2012)
Su Zhao, Jeremy Ovadia, Xinfeng Liu, Yong-Tao Zhang, Qing Nie
Operator splitting implicit integration factor methods for stiff reaction-diffusion-advection systems. J. Comput. Phys. 230 (15) (2011)
Ching-Shan Chou, Lee Bardwell, Qing Nie, Tau-Mu Yi
Noise filtering tradeoffs in spatial gradient sensing and cell polarization response. BMC Syst. Biol. 5 (2011)
Yiqun Li, Qing Nie
The Construction of Diversified Learning Platform Based on Bilingual Education - The Teaching Practice of E-commerce Course in SIFT. ICEE (2010)
Seth Haney, Lee Bardwell, Qing Nie
Ultrasensitive Responses and Specificity in Cell Signaling. BMC Syst. Biol. 4 (2010)
Scott Christley, Briana Lee, Xing Dai, Qing Nie
Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms. BMC Syst. Biol. 4 (2010)
Liming Wang, Jack Xin, Qing Nie
A Critical Quantity for Noise Attenuation in Feedback Systems. PLoS Comput. Biol. 6 (4) (2010)
Xinfeng Liu, Qing Nie
Compact integration factor methods for complex domains and adaptive mesh refinement. J. Comput. Phys. 229 (16) (2010)
Qing Nie, Shou-yi Zhan, Weiming Li
Object Recognition Based on Efficient Sub-window Search. AICI (2009)
Yuren Zhou, Jun He, Qing Nie
A comparative runtime analysis of heuristic algorithms for satisfiability problems. Artif. Intell. 173 (2) (2009)
Xiaofan Li, Qing Nie
A high-order boundary integral method for surface diffusions on elastically stressed axisymmetric rods. J. Comput. Phys. 228 (12) (2009)
Yiqun Li, Qing Nie
Study on The construction and development of Shanghai E-port system. SOLI (2009)
Qing Nie, Shou-yi Zhan
Contour Based Multi-object Classification Technology. ICIRA (1) (2008)
Qing Nie, Frederic Y. M. Wan, Yong-Tao Zhang, Xinfeng Liu
Compact integration factor methods in high spatial dimensions. J. Comput. Phys. 227 (10) (2008)
Qing Nie, Yong-Tao Zhang, Rui Zhao
Efficient semi-implicit schemes for stiff systems. J. Comput. Phys. 214 (2) (2006)
Yuan Lou, Qing Nie, Frederic Y. M. Wan
Effects of Sog on Dpp-Receptor Binding. SIAM J. Appl. Math. 65 (5) (2005)
Qing Nie, Fei-Ran Tian
Singularities in Hele--Shaw Flows Driven by a Multipole. SIAM J. Appl. Math. 62 (2) (2001)
Fei-Ran Tian, Qing Nie
Singularities in Hele-Shaw Flows. SIAM J. Appl. Math. 58 (1) (1998)