Qing Nie

According to our database, Qing Nie authored at least 63 papers between 1998 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Leveraging gene correlations in single cell transcriptomic data.

Kai Silkwood, Emmanuel Dollinger, Joshua Gervin, Scott Atwood, Qing Nie, Arthur D. Lander

BMC Bioinform., December, 2024

Publisher Correction: Reconstructing growth and dynamic trajectories from single-cell transcriptomics data.

Yutong Sha, Yuchi Qiu, Peijie Zhou, Qing Nie

Nat. Mac. Intell., 2024

Reconstructing growth and dynamic trajectories from single-cell transcriptomics data.

Yutong Sha, Yuchi Qiu, Peijie Zhou, Qing Nie

Nat. Mac. Intell., 2024

Optimal Transport for Latent Integration with An Application to Heterogeneous Neuronal Activity Data.

Yubai Yuan, Babak Shahbaba, Norbert Fortin, Keiland W. Cooper, Qing Nie, Annie Qu

CoRR, 2024

2023

AVIDA: An alternating method for visualizing and integrating data.

Kathryn Dover, Zixuan Cang, Anna Ma, Qing Nie, Roman Vershynin

J. Comput. Sci., April, 2023

2022

Supervised Optimal Transport.

Zixuan Cang, Qing Nie, Yanxiang Zhao

SIAM J. Appl. Math., December, 2022

AVIDA: Alternating method for Visualizing and Integrating Data.

Kathryn Dover, Zixuan Cang, Anna Ma, Qing Nie, Roman Vershynin

CoRR, 2022

Continuity scaling: A rigorous framework for detecting and quantifying causality accurately.

Xiong Ying, Si-Yang Leng, Huanfei Ma, Qing Nie, Ying-Cheng Lai, Wei Lin

CoRR, 2022

DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data.

Mathew Karikomi, Peijie Zhou, Qing Nie

Briefings Bioinform., 2022

2021

Prediction of Essential Genes in Comparison States Using Machine Learning.

Jiang Xie, Chang Zhao, Jiamin Sun, Jiaxin Li, Fuzhang Yang, Jiao Wang, Qing Nie

IEEE ACM Trans. Comput. Biol. Bioinform., 2021

Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples.

Xiaoqiang Sun, Ji Zhang, Qing Nie

PLoS Comput. Biol., 2021

Multiple morphogens and rapid elongation promote segmental patterning during development.

Yuchi Qiu, Lianna Fung, Thomas F. Schilling, Qing Nie

PLoS Comput. Biol., 2021

A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development.

Zixuan Cang, Yangyang Wang, Qixuan Wang, Ken W. Y. Cho, William R. Holmes, Qing Nie

PLoS Comput. Biol., 2021

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

Yingxin Cao, Laiyi Fu, Jie Wu, Qinke Peng, Qing Nie, Jing Zhang, Xiaohui Xie

Bioinform., 2021

Optimization of the Sino-Europe Transport Networks Under Uncertain Demand.

Qing Nie, Songyun Liu, Qiyuan Qian, Zheyi Tan, Huiwen Wang

Asia Pac. J. Oper. Res., 2021

2020

scRCMF: Identification of Cell Subpopulations and Transition States From Single-Cell Transcriptomes.

Xiaoying Zheng, Suoqin Jin, Qing Nie, Xiufen Zou

IEEE Trans. Biomed. Eng., 2020

DNF: A differential network flow method to identify rewiring drivers for gene regulatory networks.

Jiang Xie, Fuzhang Yang, Jiao Wang, Mathew Karikomi, Yiting Yin, Jiamin Sun, Tieqiao Wen, Qing Nie

Neurocomputing, 2020

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

Christopher Rackauckas, Qing Nie

Proceedings of the 2020 IEEE High Performance Extreme Computing Conference, 2020

2019

Confederated modular differential equation APIs for accelerated algorithm development and benchmarking.

Christopher Rackauckas, Qing Nie

Adv. Eng. Softw., 2019

2018

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

Lina Meinecke, Praveer P. Sharma, Huijing Du, Lei Zhang, Qing Nie, Thomas F. Schilling

PLoS Comput. Biol., 2018

Multiscale modeling of layer formation in epidermis.

Huijing Du, Yangyang Wang, Daniel Haensel, Briana Lee, Xing Dai, Qing Nie

PLoS Comput. Biol., 2018

Kernel differential subgraph reveals dynamic changes in biomolecular networks.

Jiang Xie, Dongfang Lu, Jiaxin Li, Jiao Wang, Yong Zhang, Yanhui Li, Qing Nie

J. Bioinform. Comput. Biol., 2018

Nanog induced intermediate state in regulating stem cell differentiation and reprogramming.

Peijia Yu, Qing Nie, Chao Tang, Lei Zhang

BMC Syst. Biol., 2018

Landscape reveals critical network structures for sharpening gene expression boundaries.

Chunhe Li, Lei Zhang, Qing Nie

BMC Syst. Biol., 2018

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

Suoqin Jin, Adam L. Maclean, Tao Peng, Qing Nie

Bioinform., 2018

2017

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

Qixuan Wang, William R. Holmes, Julian Sosnik, Thomas F. Schilling, Qing Nie

PLoS Comput. Biol., 2017

Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst.

William R. Holmes, Nabora de Mochel, Qixuan Wang, Huijing Du, Tao Peng, Michael Chiang, Olivier Cinquin, Ken Cho, Qing Nie

PLoS Comput. Biol., 2017

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

Tao Peng, Linan Liu, Adam L. Maclean, Chi Wut Wong, Weian Zhao, Qing Nie

BMC Syst. Biol., 2017

A global biomolecular network alignment method based on network flow model.

Jiang Xie, Jiaxin Li, Jiao Wang, Qing Nie, Wu Zhang

Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

2016

An Adaptive Hybrid Algorithm for Global Network Alignment.

Jiang (Linda) Xie, Chaojuan Xiang, Jin Ma, Jun Tan, Tieqiao Wen, Jinzhi Lei, Qing Nie

IEEE ACM Trans. Comput. Biol. Bioinform., 2016

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

Weitao Chen, Qing Nie, Tau-Mu Yi, Ching-Shan Chou

PLoS Comput. Biol., 2016

A dictionary based survival error compensation for robust adaptive filtering.

Lei Sun, Badong Chen, Jie Yang, Ronghua Zhou, Qing Nie, Aihua Wang

Proceedings of the 2016 International Joint Conference on Neural Networks, 2016

2015

An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States.

Tian Hong, Kazuhide Watanabe, Catherine Ha Ta, Alvaro Villarreal-Ponce, Qing Nie, Xing Dai

PLoS Comput. Biol., 2015

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

Huijing Du, Qing Nie, William R. Holmes

PLoS Comput. Biol., 2015

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

Dongyong Wang, Weitao Chen, Qing Nie

J. Comput. Phys., 2015

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

Catherine Ha Ta, Dongyong Wang, Qing Nie

J. Comput. Phys., 2015

Prediction on Performance of Age Group Swimming Using Machine Learning.

Jiang Xie, Junfu Xu, Celine Nie, Qing Nie

Proceedings of the High Performance Computing and Applications, 2015

2014

Numerical Methods for Two-Dimensional Stem Cell Tissue Growth.

Jeremy Ovadia, Qing Nie

J. Sci. Comput., 2014

Array-representation integration factor method for high-dimensional systems.

Dongyong Wang, Lei Zhang, Qing Nie

J. Comput. Phys., 2014

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

Jia Zhang, Huiqi Li, Qing Nie, Li Cheng

Comput. Medical Imaging Graph., 2014

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

Zhenzhen Zheng, Scott Christley, William T. Chiu, Ira L. Blitz, Xiaohui Xie, Ken W. Y. Cho, Qing Nie

BMC Syst. Biol., 2014

2013

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

Leyuan Fang, Shutao Li, Ryan P. McNabb, Qing Nie, Anthony N. Kuo, Cynthia A. Toth, Joseph A. Izatt, Sina Farsiu

IEEE Trans. Medical Imaging, 2013

2012

Protein Scaffolds Can Enhance the Bistability of Multisite Phosphorylation Systems.

Carlo Chan, Xinfeng Liu, Liming Wang, Lee Bardwell, Qing Nie, Germán A. Enciso

PLoS Comput. Biol., 2012

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

Wing-Cheong Lo, Long Chen, Ming Wang, Qing Nie

J. Comput. Phys., 2012

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

BMC Syst. Biol., 2012

Modeling spatial population dynamics of stem cell lineage in tissue growth.

Youfang Cao, Claire Liang, Hammad Naveed, Yingzi Li, Meng Chen, Qing Nie

Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2012

2011

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

Su Zhao, Jeremy Ovadia, Xinfeng Liu, Yong-Tao Zhang, Qing Nie

J. Comput. Phys., 2011

Noise filtering tradeoffs in spatial gradient sensing and cell polarization response.

Ching-Shan Chou, Lee Bardwell, Qing Nie, Tau-Mu Yi

BMC Syst. Biol., 2011

2010

A Critical Quantity for Noise Attenuation in Feedback Systems.

Liming Wang, Jack Xin, Qing Nie

PLoS Comput. Biol., 2010

Compact integration factor methods for complex domains and adaptive mesh refinement.

Xinfeng Liu, Qing Nie

J. Comput. Phys., 2010

Ultrasensitive Responses and Specificity in Cell Signaling.

Seth Haney, Lee Bardwell, Qing Nie

BMC Syst. Biol., 2010

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

Scott Christley, Briana Lee, Xing Dai, Qing Nie

BMC Syst. Biol., 2010

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

Yiqun Li, Qing Nie

Proceedings of the International Conference on E-Business and E-Government, 2010

2009

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

Xiaofan Li, Qing Nie

J. Comput. Phys., 2009

A comparative runtime analysis of heuristic algorithms for satisfiability problems.

Yuren Zhou, Jun He, Qing Nie

Artif. Intell., 2009

Study on The construction and development of Shanghai E-port system.

Yiqun Li, Qing Nie

Proceedings of the 2009 IEEE/INFORMS International Conference on Service Operations, 2009

Object Recognition Based on Efficient Sub-window Search.

Qing Nie, Shou-yi Zhan, Weiming Li

Proceedings of the Artificial Intelligence and Computational Intelligence, 2009

2008

Compact integration factor methods in high spatial dimensions.

Qing Nie, Frederic Y. M. Wan, Yong-Tao Zhang, Xinfeng Liu

J. Comput. Phys., 2008

Contour Based Multi-object Classification Technology.

Qing Nie, Shou-yi Zhan

Proceedings of the Intelligent Robotics and Applications, First International Conference, 2008

2006

Efficient semi-implicit schemes for stiff systems.

Qing Nie, Yong-Tao Zhang, Rui Zhao

J. Comput. Phys., 2006

2005

Effects of Sog on Dpp-Receptor Binding.

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

SIAM J. Appl. Math., 2005

2001

Singularities in Hele--Shaw Flows Driven by a Multipole.

Qing Nie, Fei-Ran Tian

SIAM J. Appl. Math., 2001

1998

Singularities in Hele-Shaw Flows.

Fei-Ran Tian, Qing Nie

SIAM J. Appl. Math., 1998