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List of works by Qing Nie

11C-CHO PET in optimization of target volume delineation and treatment regimens in postoperative radiotherapy for brain gliomas ⬇️

scientific article published on December 14, 2011

A Binary-Medium Constitutive Model for Artificially Structured Soils Based on the Disturbed State Concept and Homogenization Theory ⬇️

A HYBRID METHOD FOR STIFF REACTION-DIFFUSION EQUATIONS

scientific article published on 01 December 2019

A Robust and Efficient Method for Steady State Patterns in Reaction-Diffusion Systems

scientific article

A combination of multisite phosphorylation and substrate sequestration produces switchlike responses

scientific article

A comparative runtime analysis of heuristic algorithms for satisfiability problems

scientific article published on February 2009

A critical quantity for noise attenuation in feedback systems

scientific article published on 29 April 2010

A delay model for noise-induced bi-directional switching

scientific article

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

scientific article

A hybrid continuous-discrete method for stochastic reaction-diffusion processes

scientific article

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

scientific article

A moment-convergence method for stochastic analysis of biochemical reaction networks

scientific article published on May 2016

A multi-scale model for hair follicles reveals heterogeneous domains driving rapid spatiotemporal hair growth patterning

scientific article published on 11 July 2017

A multiscale hybrid mathematical model of epidermal-dermal interactions during skin wound healing

scientific article published on 01 April 2019

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

scientific article

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

scientific article published on 05 June 2014

A self-enhanced transport mechanism through long noncoding RNAs for X chromosome inactivation

scientific article published on 16 August 2016

A single-cell epigenetic model for parental psychological stress-induced transgenerational reprogramming in offspring

scientific article published on 28 February 2018

A theoretical framework for specificity in cell signaling

scientific article

ADAPTIVE METHODS FOR STOCHASTIC DIFFERENTIAL EQUATIONS VIA NATURAL EMBEDDINGS AND REJECTION SAMPLING WITH MEMORY.

scientific article published in January 2017

Alternative cell polarity behaviours arise from changes in G-protein spatial dynamics

scientific article

An Adaptive Hybrid Algorithm for Global Network Alignment

scientific article published on May 2016

An Integration Factor Method for Stochastic and Stiff Reaction-Diffusion Systems

scientific article published on August 2015

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

scientific article published on 10 November 2015

An Ovol2-Zeb1 transcriptional circuit regulates epithelial directional migration and proliferation

scientific article published on 09 November 2018

An effective method for computing the noise in biochemical networks ⬇️

scientific article published on February 28, 2013

Antimicrobial Resistance and Resistance Genes in Aerobic Bacteria Isolated from Pork at Slaughter

scientific article published in April 2016

Array-representation Integration Factor Method for High-dimensional Systems

scientific article published on February 2014

CA1-projecting subiculum neurons facilitate object-place learning

scientific article published on 23 September 2019

CORRIGENDUM: Nonlinear Growth Kinetics of Breast Cancer Stem Cells: Implications for Cancer Stem Cell Targeted Therapy.

scientific article published on 12 November 2013

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

scientific article

Cell lineage and communication network inference via optimization for single-cell transcriptomics

scientific article published on 01 June 2019

Cell lineages and the logic of proliferative control

scientific article

Cellular retinoic acid-binding proteins are essential for hindbrain patterning and signal robustness in zebrafish

scientific article

Characterization of a transferable bcrABC and cadAC genes-harboring plasmid in Listeria monocytogenes strain isolated from food products of animal origin

scientific article published on 23 October 2015

Circadian control of interferon-sensitive gene expression in murine skin

scientific article published on 04 March 2020

Compact integration factor methods for complex domains and adaptive mesh refinement

scientific article published on August 2010

Compact integration factor methods in high spatial dimensions

scientific article published on January 2008

Complex regulation of cyp26a1 creates a robust retinoic acid gradient in the zebrafish embryo

scientific article

Computational analysis of BMP gradients in dorsal-ventral patterning of the zebrafish embryo

scientific article

Computational modelling of epidermal stratification highlights the importance of asymmetric cell division for predictable and robust layer formation

scientific article

Controlling Stochasticity in Epithelial-Mesenchymal Transition Through Multiple Intermediate Cellular States.

scientific article published in September 2016

Correction: Low-Rank Regularization for Learning Gene Expression Programs

scientific article published on 13 January 2014

Cycling Stem Cells Are Radioresistant and Regenerate the Intestine

scientific article published on 01 July 2020

DNA Methylation and Regulatory Elements during Chicken Germline Stem Cell Differentiation

scientific article published on 17 April 2018

Deciphering principles of morphogenesis from temporal and spatial patterns on the integument

scientific article published on 6 July 2015

Defining Epidermal Basal Cell States during Skin Homeostasis and Wound Healing Using Single-Cell Transcriptomics

scientific article published on 01 March 2020

Development of Vibrio spp. infection resistance related SNP markers using multiplex SNaPshot genotyping method in the clam Meretrix meretrix.

scientific article published on 2 February 2015

Distinct Rab7-related Endosomal-Autophagic-Lysosomal Dysregulation Observed in Cortex and Hippocampus in APPswe/PSEN1dE9 Mouse Model of Alzheimer's Disease

scientific article

Divergent Resistance Mechanisms to Immunotherapy Explain Responses in Different Skin Cancers

scientific article published on 13 October 2020

Diverse feather shape evolution enabled by coupling anisotropic signalling modules with self-organizing branching programme

scientific article

Do morphogen gradients arise by diffusion?

scientific article published in June 2002

Dynamics and precision in retinoic acid morphogen gradients ⬇️

scientific article published on December 19, 2012

EFFECTS OF SOG ON DPP-RECEPTOR BINDING.

scientific article published on January 2005

Editors & Editorial Board

Effects on structure and secretion of pituitary gland in rats after electromagnetic pulse exposure

scientific article published on December 7, 2010

Epithelial Migration and Non-adhesive Periderm Are Required for Digit Separation during Mammalian Development

scientific article published on 27 February 2020

Equal opportunities in stemness

scientific article published on 01 August 2019

Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2

scientific article published on 27 February 2020

Exploring intermediate cell states through the lens of single cells

scientific article published on 02 March 2018

External noise control in inherently stochastic biological systems ⬇️

scientific article published on November 5, 2012

Fast acquisition and reconstruction of optical coherence tomography images via sparse representation.

scientific article published on 03 July 2013

Feedback regulation in multistage cell lineages.

scientific article published on January 2009

Formation of the BMP activity gradient in the Drosophila embryo

scientific article published on June 2005

Free extracellular diffusion creates the Dpp morphogen gradient of the Drosophila wing disc

scientific article published on 22 March 2012

Fus3-triggered Tec1 degradation modulates mating transcriptional output during the pheromone response

scientific article published on 5 August 2008

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

scientific article

Genomic epidemiology of a densely sampled COVID19 outbreak in China

scientific article (preprint)

Graphics processing unit-based alignment of protein interaction networks

scientific article published on August 2015

High resolution molecular and histological analysis of renal disease progression in ZSF1 fa/faCP rats, a model of type 2 diabetic nephropathy

scientific article published on 26 July 2017

Histone Deacetylases Inhibit the Snail2-Mediated EMT During Metastasis of Hepatocellular Carcinoma Cells

scientific article published on 05 August 2020

Human Umbilical Cord Mesenchymal Stem Cells Therapy for Insulin Resistance：A Novel Strategy in Clinical Implication

scientific article published on 01 January 2018

Identification of the MmeHairy gene and expression analysis affected by two SNPs in the 3'-untranslated region in the clam Meretrix meretrix

scientific article

Identifying age-specific gene signatures of the human cerebral cortex with joint analysis of transcriptomes and functional connectomes

scientific article published on 26 December 2020

In vivo kinetics and biodistribution of a Hantaan virus DNA vaccine after intramuscular injection in mice

scientific article published on 6 June 2010

Incorporating existing network information into gene network inference

scientific article

Inference and multiscale model of epithelial-to-mesenchymal transition via single-cell transcriptomic data

scientific article published on 01 September 2020

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

scientific article

Inferring spatial and signaling relationships between cells from single cell transcriptomic data

scientific article published on 29 April 2020

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

scientific article

Interactions and tradeoffs between cell recruitment, proliferation, and differentiation affect CNS regeneration

scientific article published on April 2014

Interdisciplinary Case Study: How Mathematicians and Biologists Found Order in Cellular Noise

scientific article published on 06 October 2018

Intermediate cell states in epithelial-to-mesenchymal transition

scientific article published on 18 January 2019

Keratinocyte-Macrophage Crosstalk by the Nrf2/Ccl2/EGF Signaling Axis Orchestrates Tissue Repair

scientific article published on 01 November 2020

Kernel Differential Subgraph Analysis to Reveal the Key Period Affecting Glioblastoma

scientific article published on 17 February 2020

Kernel differential subgraph reveals dynamic changes in biomolecular networks.

scientific article published on 4 December 2017

Kidney-targeted baicalin-lysozyme conjugate ameliorates renal fibrosis in rats with diabetic nephropathy induced by streptozotocin

scientific article published on 12 May 2020

Landscape reveals critical network structures for sharpening gene expression boundaries.

scientific article

Low-rank regularization for learning gene expression programs

scientific article

Machine learning of swimming data via wisdom of crowd and regression analysis

scientific article

Mathematical analysis of steady-state solutions in compartment and continuum models of cell polarization ⬇️

scientific article published on October 1, 2011

Mathematical model of adult stem cell regeneration with cross-talk between genetic and epigenetic regulation

scientific article published on 05 February 2014

Mathematical models of specificity in cell signaling

scientific article published on 26 February 2007

Mean-Independent Noise Control of Cell Fates via Intermediate States

scientific article published on 11 April 2018

MicroRNA filters Hox temporal transcription noise to confer boundary formation in the spinal cord

scientific article published on 24 March 2017

Modeling Robustness Tradeoffs in Yeast Cell Polarization Induced by Spatial Gradients ⬇️

scientific article published on September 1, 2008

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

scientific article published on 27 November 2018

Modeling spatial population dynamics of stem cell lineage in tissue growth

scientific article published on January 2012

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

scientific article

Mouse cardiac surgery: comprehensive techniques for the generation of mouse models of human diseases and their application for genomic studies.

scientific article published on 13 February 2004

Multiscale Modeling of Inflammation-Induced Tumorigenesis Reveals Competing Oncogenic and Oncoprotective Roles for Inflammation.

scientific article

Multiscale modeling of layer formation in epidermis.

scientific article published on 26 February 2018

Murine interfollicular epidermal differentiation is gradualistic with GRHL3 controlling progression from stem to transition cell states

scientific article published on 28 October 2020

Myocardin expression is regulated by Nkx2.5, and its function is required for cardiomyogenesis

scientific journal article

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

scientific article published on 27 February 2018

Network Topologies That Can Achieve Dual Function of Adaptation and Noise Attenuation

scientific article published on 18 September 2019

Noise Attenuation in the ON and OFF States of Biological Switches ⬇️

scientific article published on June 25, 2013

Noise drives sharpening of gene expression boundaries in the zebrafish hindbrain ⬇️

scientific article published on January 1, 2012

Noise filtering tradeoffs in spatial gradient sensing and cell polarization response

scientific article

Noise modulation in retinoic acid signaling sharpens segmental boundaries of gene expression in the embryonic zebrafish hindbrain

scientific article published on 12 April 2016

Nonessential Sites Improve Phosphorylation Switch ⬇️

scientific article published on September 22, 2010

Nonlinear growth kinetics of breast cancer stem cells: implications for cancer stem cell targeted therapy

scientific article published on January 2013

Nonlinear simulation of tumor growth

scientific article published in March 2003

Numerical Methods for Two-Dimensional Stem Cell Tissue Growth

scientific article published on 25 May 2013

Nursing Management of Severe COVID-19 Patients Undergoing Extracorporeal Membrane Oxygenation Combined with Prone Position Ventilation

scientific article published on 15 June 2020

Operator splitting implicit integration factor methods for stiff reaction–diffusion–advection systems ⬇️

scientific article published on July 1, 2011

Ovol2 suppresses cell cycling and terminal differentiation of keratinocytes by directly repressing c-Myc and Notch1

scientific article

Phylogenetic and phylodynamic analyses of SARS-CoV-2

scientific article published on 17 July 2020

Plasmodium yoelii 17XL infection modified maturation and function of dendritic cells by skewing Tregs and amplificating Th17

scientific article published on 06 April 2020

Predicting transcription factor binding in single cells through deep learning

scientific article published on 18 December 2020

Primary visual cortex shows laminar-specific and balanced circuit organization of excitatory and inhibitory synaptic connectivity.

scientific article published on 4 February 2016

Protein scaffolds can enhance the bistability of multisite phosphorylation systems

scientific article

Quantifying the landscape and kinetic paths for epithelial-mesenchymal transition from a core circuit.

scientific article published on 21 June 2016

ROBUSTNESS OF MORPHOGEN GRADIENTS WITH "BUCKET BRIGADE" TRANSPORT THROUGH MEMBRANE-ASSOCIATED NON-RECEPTORS.

scientific article published on May 2013

ROBUSTNESS OF SIGNALING GRADIENT IN DROSOPHILA WING IMAGINAL DISC.

scientific article published on June 2011

Reduction of ADRs of essential traditional Chinese medicines

scientific article published in January 2016

Regulatory feedback on receptor and non-receptor synthesis for robust signaling

scientific article published on 24 February 2020

Revealing Dynamic Mechanisms of Cell Fate Decisions From Single-Cell Transcriptomic Data

scientific article published on 23 December 2019

Robust and precise morphogen-mediated patterning: trade-offs, constraints and mechanisms

scientific article published in January 2015

Robust spatial sensing of mating pheromone gradients by yeast cells

scientific article

STOCHASTIC DYNAMICS OF CELL LINEAGE IN TISSUE HOMEOSTASIS

scientific article published on 01 August 2019

Safety and efficacy of three-dimensional conformal radiotherapy combined with temozolomide in treatment of diffuse brainstem gliomas

scientific article published on September 1, 2011

Scaling a Dpp Morphogen Gradient through Feedback Control of Receptors and Co-receptors

scientific article published on 01 June 2020

Semi-adaptive response and noise attenuation in bone morphogenetic protein signalling

scientific article published on June 2015

Semi-implicit Integration Factor Methods on Sparse Grids for High-Dimensional Systems

scientific article

Semi-permeable Diffusion Barriers Enhance Patterning Robustness in the C. elegans Germline

scientific article

Semiautomatic Segmentation of Rim Area Focal Hyperautofluorescence Predicts Progression of Geographic Atrophy Due to Dry Age-Related Macular Degeneration.

scientific article published on April 2016

Seroprevalence of antibodies to pertussis and diphtheria among healthy adults in China

scientific article published on August 16, 2011

Shaping organs by a wingless-int/Notch/nonmuscle myosin module which orients feather bud elongation ⬇️

scientific article published on April 16, 2013

Signaling regulated endocytosis and exocytosis lead to mating pheromone concentration dependent morphologies in yeast

scientific article published on 27 October 2012

Single cell transcriptomics of human epidermis identifies basal stem cell transition states

scientific article published on 25 August 2020

Single-cell analysis reveals fibroblast heterogeneity and myeloid-derived adipocyte progenitors in murine skin wounds

scientific article published in Nature Communications

Sparsity based denoising of spectral domain optical coherence tomography images.

scientific article published on 12 April 2012

Spatial dynamics of multistage cell lineages in tissue stratification

scientific article

Spatially distributed morphogen production and morphogen gradient formation

scientific article published in April 2005

Stem Cell Niche Structure as an Inherent Cause of Undulating Epithelial Morphologies ⬇️

scientific article published on January 8, 2013

Stem cells: a window of opportunity in low-dimensional EMT space

Stereotactic body radiotherapy combined with transarterial chemoembolization for hepatocellular carcinoma with portal vein tumor thrombosis

scientific article published on 30 September 2013

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

scientific article published on 19 August 2015

The Msi1-mTOR pathway drives the pathogenesis of mammary and extramammary Paget's disease

scientific article published on 26 May 2020

The measure of success: constraints, objectives, and tradeoffs in morphogen-mediated patterning

scientific article published on July 2009

The role of feedback in the formation of morphogen territories

scientific article published on April 2008

Three isoforms of anti-lipopolysaccharide factor identified from eyestalk cDNA library of swimming crab Portunus trituberculatus ⬇️

scientific article published on December 17, 2010

Three vibrio-resistance related EST-SSR markers revealed by selective genotyping in the clam Meretrix meretrix

scientific article

Transcriptional mechanisms link epithelial plasticity to adhesion and differentiation of epidermal progenitor cells

scientific journal article

Transcriptome analysis of shell color-related genes in the clam Meretrix meretrix.

scientific article published on 14 February 2015

Transcriptomics reveals complex kinetics of dorsal-ventral patterning gene expression in the mandibular arch

scientific article published on 26 December 2018

Ultrasensitive responses and specificity in cell signaling

scientific article

Wingless directly represses DPP morphogen expression via an armadillo/TCF/Brinker complex

scientific article published on 3 January 2007

[Efficacy of whole body gamma-knife radiotherapy combined with thermochemotherapy on locally advanced pancreatic cancer]

scientific article published on 01 November 2008

[Suggestions to strengthen quality management of herbal decoction pieces--based on production chain of herbal decoction pieces]

scientific article published in August 2015

scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles

scientific article published on 03 February 2020

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

scientific article published on 5 February 2018

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

scientific article published on 23 August 2019

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