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2020 – today
- 2024
[j51]Kai Silkwood, Emmanuel Dollinger
, Joshua Gervin, Scott Atwood, Qing Nie, Arthur D. Lander:
Leveraging gene correlations in single cell transcriptomic data. BMC Bioinform. 25(1): 305 (2024)- [j50]Yutong Sha, Yuchi Qiu, Peijie Zhou, Qing Nie:
Reconstructing growth and dynamic trajectories from single-cell transcriptomics data. Nat. Mac. Intell. 6(1): 25-39 (2024) - [j49]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): 119 (2024) - [i4]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 abs/2407.00099 (2024) - 2023
- [j48]Kathryn Dover, Zixuan Cang, Anna Ma, Qing Nie, Roman Vershynin:
AVIDA: An alternating method for visualizing and integrating data. J. Comput. Sci. 68: 101998 (2023) - 2022
- [j47]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) - [j46]Zixuan Cang, Qing Nie, Yanxiang Zhao:
Supervised Optimal Transport. SIAM J. Appl. Math. 82(5): 1851-1877 (2022) - [i3]Xiong Ying, Si-Yang Leng, Huanfei Ma, Qing Nie, Ying-Cheng Lai, Wei Lin:
Continuity scaling: A rigorous framework for detecting and quantifying causality accurately. CoRR abs/2203.14006 (2022) - [i2]Kathryn Dover, Zixuan Cang, Anna Ma, Qing Nie, Roman Vershynin:
AVIDA: Alternating method for Visualizing and Integrating Data. CoRR abs/2206.00135 (2022) - 2021
- [j45]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): 2140019:1-2140019:29 (2021) - [j44]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): 317-326 (2021) - [j43]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) - [j42]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) - [j41]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) - [j40]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): 1784-1792 (2021) - 2020
- [j39]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: 202-210 (2020) - [j38]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): 1418-1428 (2020) - [c9]Christopher Rackauckas, Qing Nie:
Stability-Optimized High Order Methods and Stiffness Detection for Pathwise Stiff Stochastic Differential Equations. HPEC 2020: 1-8
2010 – 2019
- 2019
- [j37]Christopher Rackauckas, Qing Nie:
Confederated modular differential equation APIs for accelerated algorithm development and benchmarking. Adv. Eng. Softw. 132: 1-6 (2019) - 2018
- [j36]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): 2077-2086 (2018) - [j35]Peijia Yu, Qing Nie, Chao Tang, Lei Zhang:
Nanog induced intermediate state in regulating stem cell differentiation and reprogramming. BMC Syst. Biol. 12(1): 22:1-22:13 (2018) - [j34]Chunhe Li, Lei Zhang, Qing Nie:
Landscape reveals critical network structures for sharpening gene expression boundaries. BMC Syst. Biol. 12(1): 67:1-67:13 (2018) - [j33]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): 1750027:1-1750027:29 (2018) - [j32]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) - [j31]Lina Meinecke, Praveer P. Sharma, Huijing Du, Lei Zhang, Qing Nie, Thomas F. Schilling:
Modeling craniofacial development reveals spatiotemporal constraints on robust patterning of the mandibular arch. PLoS Comput. Biol. 14(11) (2018) - [i1]Christopher Rackauckas, Qing Nie:
Confederated Modular Differential Equation APIs for Accelerated Algorithm Development and Benchmarking. CoRR abs/1807.06430 (2018) - 2017
- [j30]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): 55:1-55:15 (2017) - [j29]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) - [j28]Qixuan Wang, William R. Holmes, Julian Sosnik, Thomas F. Schilling, Qing Nie:
Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains. PLoS Comput. Biol. 13(1) (2017) - [c8]Jiang Xie, Jiaxin Li, Jiao Wang, Qing Nie, Wu Zhang:
A global biomolecular network alignment method based on network flow model. BIBM 2017: 1746-1751 - 2016
- [j27]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) - [j26]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): 483-493 (2016) - [c7]Lei Sun, Badong Chen, Jie Yang, Ronghua Zhou, Qing Nie, Aihua Wang:
A dictionary based survival error compensation for robust adaptive filtering. IJCNN 2016: 1408-1414 - 2015
- [j25]Dongyong Wang, Weitao Chen, Qing Nie:
Semi-implicit integration factor methods on sparse grids for high-dimensional systems. J. Comput. Phys. 292: 43-55 (2015) - [j24]Catherine Ha Ta, Dongyong Wang, Qing Nie:
An integration factor method for stochastic and stiff reaction-diffusion systems. J. Comput. Phys. 295: 505-522 (2015) - [j23]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) - [j22]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) - [c6]Jiang Xie, Junfu Xu, Celine Nie, Qing Nie:
Prediction on Performance of Age Group Swimming Using Machine Learning. HPCA (China) 2015: 178-184 - 2014
- [j21]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: 3 (2014) - [j20]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): 517-525 (2014) - [j19]Dongyong Wang, Lei Zhang, Qing Nie:
Array-representation integration factor method for high-dimensional systems. J. Comput. Phys. 258: 585-600 (2014) - [j18]Jeremy Ovadia, Qing Nie:
Numerical Methods for Two-Dimensional Stem Cell Tissue Growth. J. Sci. Comput. 58(1): 149-175 (2014) - 2013
- [j17]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): 2034-2049 (2013) - 2012
- [j16]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: 93 (2012) - [j15]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): 5062-5077 (2012) - [j14]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) - [c5]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: 5502-5505 - 2011
- [j13]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: 196 (2011) - [j12]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): 5996-6009 (2011) - 2010
- [j11]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: 107 (2010) - [j10]Seth Haney, Lee Bardwell, Qing Nie:
Ultrasensitive Responses and Specificity in Cell Signaling. BMC Syst. Biol. 4: 119 (2010) - [j9]Xinfeng Liu, Qing Nie:
Compact integration factor methods for complex domains and adaptive mesh refinement. J. Comput. Phys. 229(16): 5692-5706 (2010) - [j8]Liming Wang, Jack Xin, Qing Nie:
A Critical Quantity for Noise Attenuation in Feedback Systems. PLoS Comput. Biol. 6(4) (2010) - [c4]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: 5560-5563
2000 – 2009
- 2009
- [j7]Yuren Zhou, Jun He, Qing Nie:
A comparative runtime analysis of heuristic algorithms for satisfiability problems. Artif. Intell. 173(2): 240-257 (2009) - [j6]Xiaofan Li, Qing Nie:
A high-order boundary integral method for surface diffusions on elastically stressed axisymmetric rods. J. Comput. Phys. 228(12): 4625-4637 (2009) - [c3]Qing Nie, Shou-yi Zhan, Weiming Li:
Object Recognition Based on Efficient Sub-window Search. AICI 2009: 435-443 - [c2]Yiqun Li, Qing Nie:
Study on The construction and development of Shanghai E-port system. SOLI 2009: 295-299 - 2008
- [j5]Qing Nie, Frederic Y. M. Wan, Yong-Tao Zhang, Xinfeng Liu:
Compact integration factor methods in high spatial dimensions. J. Comput. Phys. 227(10): 5238-5255 (2008) - [c1]Qing Nie, Shou-yi Zhan:
Contour Based Multi-object Classification Technology. ICIRA (1) 2008: 795-803 - 2006
- [j4]Qing Nie, Yong-Tao Zhang, Rui Zhao:
Efficient semi-implicit schemes for stiff systems. J. Comput. Phys. 214(2): 521-537 (2006) - 2005
- [j3]Yuan Lou, Qing Nie, Frederic Y. M. Wan:
Effects of Sog on Dpp-Receptor Binding. SIAM J. Appl. Math. 65(5): 1748-1771 (2005) - 2001
- [j2]Qing Nie, Fei-Ran Tian:
Singularities in Hele--Shaw Flows Driven by a Multipole. SIAM J. Appl. Math. 62(2): 385-406 (2001)
1990 – 1999
- 1998
- [j1]Fei-Ran Tian, Qing Nie:
Singularities in Hele-Shaw Flows. SIAM J. Appl. Math. 58(1): 34-54 (1998)
Coauthor Index
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