Qing Nie

72 papers B 1Journal 62Unranked 9
YearRankTypeTitle / Venue / Authors
2026 J jnl
WFR-FM: Simulation-Free Dynamic Unbalanced Optimal Transport.
CoRR
Qiangwei Peng, Zihan Wang, Junda Ying, Yuhao Sun, Qing Nie, Lei Zhang, Tiejun Li, Peijie Zhou
2025 — conf
Caption: Generating Informative Content Labels for Image Buttons Using Next-Screen Context.
UIST Adjunct
Mingyuan Zhong, Ajit Mallavarapu, Qing Nie
2025 J jnl
Caption: Generating Informative Content Labels for Image Buttons Using Next-Screen Context.
CoRR
Mingyuan Zhong, Ajit Mallavarapu, Qing Nie
2025 J jnl
Cell-cell communication inference and analysis: biological mechanisms, computational approaches, and future opportunities.
CoRR
Xiangzheng Cheng, Haili Huang, Ye Su, Qing Nie, Xiufen Zou, Suoqin Jin
2025 J jnl
Multiscale Modeling of Tumor-Macrophage Interactions Underlying Immunotherapy Resistance in Glioblastoma.
Multiscale Model. Simul.
Haofeng Lin, Ji Zhang, Qing Nie, Xiaoqiang Sun
2025 J jnl
Quasi-Optimization Problems: Existence, Iterative Algorithms and Well-Posedness.
J. Optim. Theory Appl.
Shengda Zeng, Qing Nie, Calogero Vetro
2025 J jnl
Statistically principled feature selection for single cell transcriptomics.
BMC Bioinform.
Emmanuel P. Dollinger, Kai Silkwood, Scott Atwood, Qing Nie, Arthur D. Lander
2024 J jnl
Leveraging gene correlations in single cell transcriptomic data.
BMC Bioinform.
Kai Silkwood, Emmanuel P. Dollinger, Joshua Gervin, Scott Atwood, Qing Nie, Arthur D. Lander
2024 J jnl
Optimal Transport for Latent Integration with An Application to Heterogeneous Neuronal Activity Data.
CoRR
Yubai Yuan, Babak Shahbaba, Norbert Fortin, Keiland W. Cooper, Qing Nie, Annie Qu
2024 J jnl
Publisher Correction: Reconstructing growth and dynamic trajectories from single-cell transcriptomics data.
Nat. Mac. Intell.
Yutong Sha, Yuchi Qiu, Peijie Zhou, Qing Nie
2024 J jnl
Reconstructing growth and dynamic trajectories from single-cell transcriptomics data.
Nat. Mac. Intell.
Yutong Sha, Yuchi Qiu, Peijie Zhou, Qing Nie
2023 J jnl
AVIDA: An alternating method for visualizing and integrating data.
J. Comput. Sci.
Kathryn Dover, Zixuan Cang, Anna Ma, Qing Nie, Roman Vershynin
2022 J jnl
AVIDA: Alternating method for Visualizing and Integrating Data.
CoRR
Kathryn Dover, Zixuan Cang, Anna Ma, Qing Nie, Roman Vershynin
2022 J jnl
Continuity scaling: A rigorous framework for detecting and quantifying causality accurately.
CoRR
Xiong Ying, Si-Yang Leng, Huanfei Ma, Qing Nie, Ying-Cheng Lai, Wei Lin
2022 J jnl
DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data.
Briefings Bioinform.
Mathew Karikomi, Peijie Zhou, Qing Nie
2022 J jnl
Supervised Optimal Transport.
SIAM J. Appl. Math.
Zixuan Cang, Qing Nie, Yanxiang Zhao
2021 J jnl
A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development.
PLoS Comput. Biol.
Zixuan Cang, Yangyang Wang, Qixuan Wang, Ken W. Y. Cho, William R. Holmes, Qing Nie
2021 J jnl
Identifying age-specific gene signatures of the human cerebral cortex with joint analysis of transcriptomes and functional connectomes.
Briefings Bioinform.
Xingzhong Zhao, Jingqi Chen, Peipei Xiao, Jianfeng Feng, Qing Nie, Xing-Ming Zhao
2021 J jnl
Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples.
PLoS Comput. Biol.
Xiaoqiang Sun, Ji Zhang, Qing Nie
2021 J jnl
Multiple morphogens and rapid elongation promote segmental patterning during development.
PLoS Comput. Biol.
Yuchi Qiu, Lianna Fung, Thomas F. Schilling, Qing Nie
2021 J jnl
Optimization of the Sino-Europe Transport Networks Under Uncertain Demand.
Asia Pac. J. Oper. Res.
Qing Nie, Songyun Liu, Qiyuan Qian, Zheyi Tan, Huiwen Wang
2021 J jnl
Prediction of Essential Genes in Comparison States Using Machine Learning.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jiang Xie, Chang Zhao, Jiamin Sun, Jiaxin Li, Fuzhang Yang, Jiao Wang, Qing Nie
2021 J jnl
SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration.
Bioinform.
Yingxin Cao, Laiyi Fu, Jie Wu, Qinke Peng, Qing Nie, Jing Zhang, Xiaohui Xie
2020 J jnl
DNF: A differential network flow method to identify rewiring drivers for gene regulatory networks.
Neurocomputing
Jiang Xie, Fuzhang Yang, Jiao Wang, Mathew Karikomi, Yiting Yin, Jiamin Sun, Tieqiao Wen, Qing Nie
2020 — conf
Stability-Optimized High Order Methods and Stiffness Detection for Pathwise Stiff Stochastic Differential Equations.
HPEC
Christopher Rackauckas, Qing Nie
2020 J jnl
scRCMF: Identification of Cell Subpopulations and Transition States From Single-Cell Transcriptomes.
IEEE Trans. Biomed. Eng.
Xiaoying Zheng, Suoqin Jin, Qing Nie, Xiufen Zou
2019 J jnl
Confederated modular differential equation APIs for accelerated algorithm development and benchmarking.
Adv. Eng. Softw.
Christopher Rackauckas, Qing Nie
2018 J jnl
Confederated Modular Differential Equation APIs for Accelerated Algorithm Development and Benchmarking.
CoRR
Christopher Rackauckas, Qing Nie
2018 J jnl
Kernel differential subgraph reveals dynamic changes in biomolecular networks.
J. Bioinform. Comput. Biol.
Jiang Xie, Dongfang Lu, Jiaxin Li, Jiao Wang, Yong Zhang, Yanhui Li, Qing Nie
2018 J jnl
Landscape reveals critical network structures for sharpening gene expression boundaries.
BMC Syst. Biol.
Chunhe Li, Lei Zhang, Qing Nie
2018 J jnl
Modeling craniofacial development reveals spatiotemporal constraints on robust patterning of the mandibular arch.
PLoS Comput. Biol.
Lina Meinecke, Praveer P. Sharma, Huijing Du, Lei Zhang, Qing Nie, Thomas F. Schilling
2018 J jnl
Multiscale modeling of layer formation in epidermis.
PLoS Comput. Biol.
Huijing Du, Yangyang Wang, Daniel Haensel, Briana Lee, Xing Dai, Qing Nie
2018 J jnl
Nanog induced intermediate state in regulating stem cell differentiation and reprogramming.
BMC Syst. Biol.
Peijia Yu, Qing Nie, Chao Tang, Lei Zhang
2018 J jnl
scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data.
Bioinform.
Suoqin Jin, Adam L. Maclean, Tao Peng, Qing Nie
2017 — conf
A global biomolecular network alignment method based on network flow model.
BIBM
Jiang Xie, Jiaxin Li, Jiao Wang, Qing Nie, Wu Zhang
2017 J jnl
A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions.
BMC Syst. Biol.
Tao Peng, Linan Liu, Adam L. Maclean, Chi Wut Wong, Weian Zhao, Qing Nie
2017 J jnl
Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains.
PLoS Comput. Biol.
Qixuan Wang, William R. Holmes, Julian Sosnik, Thomas F. Schilling, Qing Nie
2017 J jnl
Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst.
PLoS Comput. Biol.
William R. Holmes, Nabora de Mochel, Qixuan Wang, Huijing Du, Tao Peng, Michael Chiang, Olivier Cinquin, Ken Cho, Qing Nie
2016 B conf
A dictionary based survival error compensation for robust adaptive filtering.
IJCNN
Lei Sun, Badong Chen, Jie Yang, Ronghua Zhou, Qing Nie, Aihua Wang
2016 J jnl
An Adaptive Hybrid Algorithm for Global Network Alignment.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jiang (Linda) Xie, Chaojuan Xiang, Jin Ma, Jun Tan, Tieqiao Wen, Jinzhi Lei, Qing Nie
2016 J jnl
Modelling of Yeast Mating Reveals Robustness Strategies for Cell-Cell Interactions.
PLoS Comput. Biol.
Weitao Chen, Qing Nie, Tau-Mu Yi, Ching-Shan Chou
2015 J jnl
An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States.
PLoS Comput. Biol.
Tian Hong, Kazuhide Watanabe, Catherine Ha Ta, Alvaro Villarreal-Ponce, Qing Nie, Xing Dai
2015 J jnl
An integration factor method for stochastic and stiff reaction-diffusion systems.
J. Comput. Phys.
Catherine Ha Ta, Dongyong Wang, Qing Nie
2015 — conf
Prediction on Performance of Age Group Swimming Using Machine Learning.
HPCA (China)
Jiang Xie, Junfu Xu, Celine Nie, Qing Nie
2015 J jnl
Semi-implicit integration factor methods on sparse grids for high-dimensional systems.
J. Comput. Phys.
Dongyong Wang, Weitao Chen, Qing Nie
2015 J jnl
The Interplay between Wnt Mediated Expansion and Negative Regulation of Growth Promotes Robust Intestinal Crypt Structure and Homeostasis.
PLoS Comput. Biol.
Huijing Du, Qing Nie, William R. Holmes
2014 J jnl
A retinal vessel boundary tracking method based on Bayesian theory and multi-scale line detection.
Comput. Medical Imaging Graph.
Jia Zhang, Huiqi Li, Qing Nie, Li Cheng
2014 J jnl
Array-representation integration factor method for high-dimensional systems.
J. Comput. Phys.
Dongyong Wang, Lei Zhang, Qing Nie
2014 J jnl
Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns.
BMC Syst. Biol.
Zhenzhen Zheng, Scott Christley, William T. Chiu, Ira L. Blitz, Xiaohui Xie, Ken W. Y. Cho, Qing Nie
2014 J jnl
Numerical Methods for Two-Dimensional Stem Cell Tissue Growth.
J. Sci. Comput.
Jeremy Ovadia, Qing Nie
2013 J jnl
Fast Acquisition and Reconstruction of Optical Coherence Tomography Images via Sparse Representation.
IEEE Trans. Medical Imaging
Leyuan Fang, Shutao Li, Ryan P. McNabb, Qing Nie, Anthony N. Kuo, Cynthia A. Toth, Joseph A. Izatt, Sina Farsiu
2012 J jnl
A reaction-diffusion mechanism influences cell lineage progression as a basis for formation, regeneration, and stability of intestinal crypts.
BMC Syst. Biol.
Lei Zhang, Arthur D. Lander, Qing Nie
2012 J jnl
A robust and efficient method for steady state patterns in reaction-diffusion systems.
J. Comput. Phys.
Wing-Cheong Lo, Long Chen, Ming Wang, Qing Nie
2012 — conf
Modeling spatial population dynamics of stem cell lineage in tissue growth.
EMBC
Youfang Cao, Claire Liang, Hammad Naveed, Yingzi Li, Meng Chen, Qing Nie
2012 J jnl
Protein Scaffolds Can Enhance the Bistability of Multisite Phosphorylation Systems.
PLoS Comput. Biol.
Carlo Chan, Xinfeng Liu, Liming Wang, Lee Bardwell, Qing Nie, Germán A. Enciso
2011 J jnl
Noise filtering tradeoffs in spatial gradient sensing and cell polarization response.
BMC Syst. Biol.
Ching-Shan Chou, Lee Bardwell, Qing Nie, Tau-Mu Yi
2011 J jnl
Operator splitting implicit integration factor methods for stiff reaction-diffusion-advection systems.
J. Comput. Phys.
Su Zhao, Jeremy Ovadia, Xinfeng Liu, Yong-Tao Zhang, Qing Nie
2010 J jnl
A Critical Quantity for Noise Attenuation in Feedback Systems.
PLoS Comput. Biol.
Liming Wang, Jack Xin, Qing Nie
2010 J jnl
Compact integration factor methods for complex domains and adaptive mesh refinement.
J. Comput. Phys.
Xinfeng Liu, Qing Nie
2010 J jnl
Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms.
BMC Syst. Biol.
Scott Christley, Briana Lee, Xing Dai, Qing Nie
2010 — conf
The Construction of Diversified Learning Platform Based on Bilingual Education - The Teaching Practice of E-commerce Course in SIFT.
ICEE
Yiqun Li, Qing Nie
2010 J jnl
Ultrasensitive Responses and Specificity in Cell Signaling.
BMC Syst. Biol.
Seth Haney, Lee Bardwell, Qing Nie
2009 J jnl
A comparative runtime analysis of heuristic algorithms for satisfiability problems.
Artif. Intell.
Yuren Zhou, Jun He, Qing Nie
2009 J jnl
A high-order boundary integral method for surface diffusions on elastically stressed axisymmetric rods.
J. Comput. Phys.
Xiaofan Li, Qing Nie
2009 — conf
Object Recognition Based on Efficient Sub-window Search.
AICI
Qing Nie, Shou-yi Zhan, Weiming Li
2009 — conf
Study on The construction and development of Shanghai E-port system.
SOLI
Yiqun Li, Qing Nie
2008 J jnl
Compact integration factor methods in high spatial dimensions.
J. Comput. Phys.
Qing Nie, Frederic Y. M. Wan, Yong-Tao Zhang, Xinfeng Liu
2008 — conf
Contour Based Multi-object Classification Technology.
ICIRA (1)
Qing Nie, Shou-yi Zhan
2006 J jnl
Efficient semi-implicit schemes for stiff systems.
J. Comput. Phys.
Qing Nie, Yong-Tao Zhang, Rui Zhao
2005 J jnl
Effects of Sog on Dpp-Receptor Binding.
SIAM J. Appl. Math.
Yuan Lou, Qing Nie, Frederic Y. M. Wan
2001 J jnl
Singularities in Hele--Shaw Flows Driven by a Multipole.
SIAM J. Appl. Math.
Qing Nie, Fei-Ran Tian
1998 J jnl
Singularities in Hele-Shaw Flows.
SIAM J. Appl. Math.
Fei-Ran Tian, Qing Nie