Qing Nie

According to our database1, Qing Nie authored at least 59 papers between 1998 and 2023.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.



In proceedings 
PhD thesis 


On csauthors.net:


AVIDA: An alternating method for visualizing and integrating data.
J. Comput. Sci., April, 2023

Supervised Optimal Transport.
SIAM J. Appl. Math., December, 2022

AVIDA: Alternating method for Visualizing and Integrating Data.
CoRR, 2022

Continuity scaling: A rigorous framework for detecting and quantifying causality accurately.
CoRR, 2022

DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data.
Briefings Bioinform., 2022

Prediction of Essential Genes in Comparison States Using Machine Learning.
IEEE ACM Trans. Comput. Biol. Bioinform., 2021

Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples.
PLoS Comput. Biol., 2021

Multiple morphogens and rapid elongation promote segmental patterning during development.
PLoS Comput. Biol., 2021

A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development.
PLoS Comput. Biol., 2021

SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration.
Bioinform., 2021

Optimization of the Sino-Europe Transport Networks Under Uncertain Demand.
Asia Pac. J. Oper. Res., 2021

scRCMF: Identification of Cell Subpopulations and Transition States From Single-Cell Transcriptomes.
IEEE Trans. Biomed. Eng., 2020

DNF: A differential network flow method to identify rewiring drivers for gene regulatory networks.
Neurocomputing, 2020

Stability-Optimized High Order Methods and Stiffness Detection for Pathwise Stiff Stochastic Differential Equations.
Proceedings of the 2020 IEEE High Performance Extreme Computing Conference, 2020

Confederated modular differential equation APIs for accelerated algorithm development and benchmarking.
Adv. Eng. Softw., 2019

Modeling craniofacial development reveals spatiotemporal constraints on robust patterning of the mandibular arch.
PLoS Comput. Biol., 2018

Multiscale modeling of layer formation in epidermis.
PLoS Comput. Biol., 2018

Kernel differential subgraph reveals dynamic changes in biomolecular networks.
J. Bioinform. Comput. Biol., 2018

Nanog induced intermediate state in regulating stem cell differentiation and reprogramming.
BMC Syst. Biol., 2018

Landscape reveals critical network structures for sharpening gene expression boundaries.
BMC Syst. Biol., 2018

scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data.
Bioinform., 2018

Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains.
PLoS Comput. Biol., 2017

Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst.
PLoS Comput. Biol., 2017

A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions.
BMC Syst. Biol., 2017

A global biomolecular network alignment method based on network flow model.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

An Adaptive Hybrid Algorithm for Global Network Alignment.
IEEE ACM Trans. Comput. Biol. Bioinform., 2016

Modelling of Yeast Mating Reveals Robustness Strategies for Cell-Cell Interactions.
PLoS Comput. Biol., 2016

A dictionary based survival error compensation for robust adaptive filtering.
Proceedings of the 2016 International Joint Conference on Neural Networks, 2016

An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States.
PLoS Comput. Biol., 2015

The Interplay between Wnt Mediated Expansion and Negative Regulation of Growth Promotes Robust Intestinal Crypt Structure and Homeostasis.
PLoS Comput. Biol., 2015

Semi-implicit integration factor methods on sparse grids for high-dimensional systems.
J. Comput. Phys., 2015

An integration factor method for stochastic and stiff reaction-diffusion systems.
J. Comput. Phys., 2015

Prediction on Performance of Age Group Swimming Using Machine Learning.
Proceedings of the High Performance Computing and Applications, 2015

Numerical Methods for Two-Dimensional Stem Cell Tissue Growth.
J. Sci. Comput., 2014

Array-representation integration factor method for high-dimensional systems.
J. Comput. Phys., 2014

A retinal vessel boundary tracking method based on Bayesian theory and multi-scale line detection.
Comput. Medical Imaging Graph., 2014

Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns.
BMC Syst. Biol., 2014

Fast Acquisition and Reconstruction of Optical Coherence Tomography Images via Sparse Representation.
IEEE Trans. Medical Imaging, 2013

Protein Scaffolds Can Enhance the Bistability of Multisite Phosphorylation Systems.
PLoS Comput. Biol., 2012

A robust and efficient method for steady state patterns in reaction-diffusion systems.
J. Comput. Phys., 2012

A reaction-diffusion mechanism influences cell lineage progression as a basis for formation, regeneration, and stability of intestinal crypts.
BMC Syst. Biol., 2012

Modeling spatial population dynamics of stem cell lineage in tissue growth.
Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2012

Operator splitting implicit integration factor methods for stiff reaction-diffusion-advection systems.
J. Comput. Phys., 2011

Noise filtering tradeoffs in spatial gradient sensing and cell polarization response.
BMC Syst. Biol., 2011

A Critical Quantity for Noise Attenuation in Feedback Systems.
PLoS Comput. Biol., 2010

Compact integration factor methods for complex domains and adaptive mesh refinement.
J. Comput. Phys., 2010

Ultrasensitive Responses and Specificity in Cell Signaling.
BMC Syst. Biol., 2010

Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms.
BMC Syst. Biol., 2010

The Construction of Diversified Learning Platform Based on Bilingual Education - The Teaching Practice of E-commerce Course in SIFT.
Proceedings of the International Conference on E-Business and E-Government, 2010

A high-order boundary integral method for surface diffusions on elastically stressed axisymmetric rods.
J. Comput. Phys., 2009

A comparative runtime analysis of heuristic algorithms for satisfiability problems.
Artif. Intell., 2009

Study on The construction and development of Shanghai E-port system.
Proceedings of the 2009 IEEE/INFORMS International Conference on Service Operations, 2009

Object Recognition Based on Efficient Sub-window Search.
Proceedings of the Artificial Intelligence and Computational Intelligence, 2009

Compact integration factor methods in high spatial dimensions.
J. Comput. Phys., 2008

Contour Based Multi-object Classification Technology.
Proceedings of the Intelligent Robotics and Applications, First International Conference, 2008

Efficient semi-implicit schemes for stiff systems.
J. Comput. Phys., 2006

Effects of Sog on Dpp-Receptor Binding.
SIAM J. Appl. Math., 2005

Singularities in Hele--Shaw Flows Driven by a Multipole.
SIAM J. Appl. Math., 2001

Singularities in Hele-Shaw Flows.
SIAM J. Appl. Math., 1998