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| 1 | DTFLOW:Inference and Visualization of Single-cell Pseudotime Trajectory Using Diffusion Propagation显示文摘One of the major challenges in single-cell data analysis is the determination of cellular developmental trajectories using single-cell data.Although substantial studies have been conducted in recent years,more effective methods are still strongly needed to infer the developmental processes accurately.This work devises a new method,named DTFLOW,for determining the pseudotemporal trajectories with multiple branches.DTFLOW consists of two major steps:a new method called Bhattacharyya kernel feature decomposition(BKFD)to reduce the data dimensions,and a novel approach named Reverse Searching on k-nearest neighbor graph(RSKG)to identify the multi-branching processes of cellular differentiation.In BKFD,we first establish a stationary distribution for each cell to represent the transition of cellular developmental states based on the random walk with restart algorithm,and then propose a new distance metric for calculating pseudotime of single cells by introducing the Bhattacharyya kernel matrix.The effectiveness of DTFLOW is rigorously examined by using four single-cell datasets.We compare the efficiency of DTFLOW with the published state-of-the-art methods.Simulation results suggest that DTFLOW has superior accuracy and strong robustness properties for constructing pseudotime trajectories.The Python source code of DTFLOW can be freely accessed at http://gffzz188fe103f8f1460as06f5uwfkwxcq66oq.ffgz.tsg.suse.edu.cn/statway/DTFLOW. | Jiangyong Wei Tianshou Zhou Xinan Zhang Tianhai Tian | 2021 | Genomics, Proteomics & Bioinformatics2021，19，2： | 2 |
| 2 | Communication- induced multistability and multirhythmicity in a synthetic multicelouoar system显示文摘 | Qizhi Yi Tianshou Zhou | 2011 | PRE2011，83，05： | 1 |
| 3 | Chaos synchronization between linearly coupled chaotic sys- tem显示文摘 | LU Jinhu ZHOU Tianshou ZHANG Suochun | 2002 | Chaos Solitons and Fractals2002，20，14： | 1 |
| 4 | ?i’lnikov Chaos in the Generalized Lorenz Canonical Form of Dynamical Systems显示文摘 | Tianshou Zhou Guanrong Chen Sergej ?elikovskY | 2005 | Nonlinear Dynamics2005，，4： | 1 |
| 5 | Dynamical behavior in linearly coupled Oregonators显示文摘 | Zhou Tianshou Zhang Suochun | 2001 | Physical D: Nonlinear Phenomena2001，151，24： | 1 |
| 6 | Promoter-mediated transcrip- tional dynamics 显示文摘 | Zhang Jiajun Zhou Tianshou | 2014 | Biophys J2014，106，2： | 1 |
| 7 | Chaos synchronization between linearly coupled chaotic systems 显示文摘 | Lu Jinhu Zhou Tianshou Zhang Suochun | 2002 | Chaos Solitons and Fractals2002，14，： | 1 |
| 8 | Dynamical analysis of mCAT2 gene models with CTN-RNA nuclear retention 显示文摘 | Wang Qianliang Zhou Tianshou | 2015 | Phys Biol2015，12，01： | 1 |
| 9 | Comment on 'binomial moment equations for chemical reaction net- Norks' 显示文摘 | Zhang Jiajun Huang Lifang Zhou Tianshou | 2014 | Phys Rev Lett2014，112，08： | 1 |
| 10 | Constructing a new chaotic system based on the Silnikov criterion显示文摘 | ZHOU Tianshou CHEN Guanrong YANG Qigui | 2004 | Chaos Solitons and Fractals2004，19，4： | 1 |
| 11 | Quantitative analysis of gene expression systems显示文摘 | Tianshou Zhou Tuoqi Liu | 2015 | Frontiers of Electrical and Electronic Engineering in China2015，10，4： | 1 |
| 12 | Noise-induced coherent switch显示文摘Taking the famous genetic toggle switch as an example,we numerically investigated the effect of noise on bistability.We found that extrinsic noise resulting from stochastic fluctuations in synthesis and degradation rates and from the environmental fluctuation in gene regulatory processes can induce coherent switch,and that there is an optimal noise intensity such that the noise not only can induce this switch,but also can amplify a weak input signal.In addition,we found that the intrinsic noise introduced through the Poisson τ-leap algorithm cannot induce such a switch. | YUAN ZhanJiang ZHANG JiaJun ZHOU TianShou | 2008 | Science China Chemistry2008，51，6： | 1 |
| 13 | Analytical distribution and tunability of noise in a model of promoter progress 显示文摘 | Zhang Jiajun Chen Luonan Zhou Tianshou | 2012 | Biophys J2012，102，6： | 1 |
| 14 | Promoter-mediated transcrip- tional dynamics 显示文摘 | Zhang Jiajun Zhou Tianshou | 2014 | Biophys J2014，106，2： | 1 |
| 15 | Chaos synchronization between linearl coupled chaotic systems 显示文摘 | Jinhu Lü Tianshou Zhou Suochun Zhang | 2002 | Chaos Solitons and Fractals2002，14，： | 1 |
| 16 | Comment onBinomial moment equations for chemical reaction networks显示文摘 | Zhang Jiajun Huang Lifang Zhou Tianshou | 2014 | Phys Rev Lett2014，112，08： | 1 |
| 17 | Physical limits of feedback noise-suppression in biological networks 显示文摘 | Zhang Jiajun Yuan Zhanjiang Zhou Tianshou | 2009 | Phys Biol2009，6，4： | 1 |
| 18 | Physicallimits of feedback noise-suppression in biological networks显示文摘 | Zhang Jiajun Yuan Zhanjiang Zhou Tianshou | 2009 | Phys Biol2009，6，04： | 1 |
| 19 | Classification of Chaos in 3-D Autonomous Quadratic Systems-I显示文摘 | TianShou Zhou GuangrRong Chen | 2006 | Basic Framework And Methods2006，16，9： | 1 |
| 20 | Constructing a new chaotic system based on the Silnnikov criterion显示文摘 | Chen Guanrong Yang Qigui | 2004 | Chaos Solitons and Fractals2004，19，： | 1 |
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