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Single-cell omics: experimental workflow, data analyses and applications

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Science China Life sciences 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi Department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical Informatics institute College of Pharmaceutical SciencesZhejiang University Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research institute of Intelligent Computing Zhejiang Lab Shanghai Research institute for Intelligent Autonomous Systems Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua Center for Life sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women's HospitalZhejiang University School of Medicine Key Laboratory of Advanced Theory and Application in statistics and Data Science-MOE School of StatisticsEast China Normal University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial sc RNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

A General Comparison Theorem for 1-dimensional Anticipated BSDEs

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Acta Mathematicae Applicatae Sinica 2016年第2期32卷 343-348页

作者： Xiao-ming XU institute of finance and statistics School of Mathematical Sciences Nanjing Normal University

Anticipated backward stochastic differential equation （ABSDE） studied the first time in 2007 is a new type of stochastic differential equations. In this paper, we establish a general comparison theorem for ABSDEs.

关键词： anticipated backward stochastic differential equation backward stochastic differential equation comparison theorem

Single-cell technologies: current and near future

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Science China Life sciences 2025年第01期 1-4页

作者： Chenfei Wang Qi Liu Xiaohui Fan Tieliu Shi Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration Ministry of EducationOrthopedics DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research institute of Intelligent Computing Zhejiang Lab Pharmaceutical Informatics institute College of Pharmaceutical SciencesZhejiang University National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Key Laboratory of Advanced Theory and Application in statistics and Data Science (MOE) School of StatisticsEast China Normal University

Single-cell technologies enable the indepth exploration of multiple biological hierarchies at the scale of individual cells,which have deepened our knowledge of cellular diversity, tissue organization, and overall organism function(Sun et al.,2024). In 2009, single-cell RNA sequencing(sc RNA-seq) was first developed as a powerful tool to dissect gene expression and uncover transcriptional *** the rapid advancement of technology, single-cell approaches have expanded to encompass other omics, such as genomics, epigenomics, proteomics,and metabolomics.

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Dynamic Asset Allocation with Loss Aversion in a Jump-diffusion Model

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Acta Mathematicae Applicatae Sinica 2015年第2期31卷 557-566页

作者： Hui MI Xiu-chun BI Shu-guang ZHANG school of mathematical sciences and institute of finance and statistics Nanjing Normal University Department of statistics and finance University of Science and Technology of China

This paper investigates a dynamic asset allocation problem for loss-averse investors in a jumpdiffusion model where there are a riskless asset and N risky assets. Specifically, the prices of risky assets are governed by jump-diffusion processes driven by an m-dimensional Brownian motion and a（N- m）-dimensional Poisson process. After converting the dynamic optimal portfolio problem to a static optimization problem in the terminal wealth, the optimal terminal wealth is first solved. Then the optimal wealth process and investment strategy are derived by using the martingale representation approach. The closed-form solutions for them are finally given in a special example.

关键词： jump-diffusion process loss aversion asset allocation martingale

Fully Coupled Forward-Backward Stochastic Functional Differential Equations and Applications to Quadratic Optimal Control

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Journal of Systems Science & Complexity 2020年第6期33卷 1886-1902页

作者： XU Xiaoming institute of finance and statistics School of Mathematical SciencesNanjing Normal UniversityNanjing210023China

This paper considers the fully coupled forward-backward stochastic functional differential equations(FBSFDEs) with stochastic functional differential equations as the forward equations and the generalized anticipated backward stochastic differential equations as the backward equations. The authors will prove the existence and uniqueness theorem for FBSFDEs. As an application, we deal with a quadratic optimal control problem for functional stochastic systems, and get the explicit form of the optimal control by virtue of FBSFDEs.

关键词： Forward-backward stochastic functional differential equation functional stochastic system generalized anticipated backward stochastic differential equation quadratic optimal control stochastic functional differential equation

STRONG N-DISCOUNT AND FINITE-HORIZON OPTIMALITY FOR CONTINUOUS-TIME MARKOV DECISION PROCESSES

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Journal of Systems Science & Complexity 2014年第5期27卷 1045-1063页

作者： ZHU Quanxin GUO Xianping school of mathematical sciences and institute of finance and statistics Nanjing Normal University school of Mathematics and Computational Science Zhongshan University

This paper studies the strong n(n =—1,0)-discount and finite horizon criteria for continuoustime Markov decision processes in Polish *** corresponding transition rates are allowed to be unbounded,and the reward rates may have neither upper nor lower *** mild conditions,the authors prove the existence of strong n(n =—1,0)-discount optimal stationary policies by developing two equivalence relations:One is between the standard expected average reward and strong—1-discount optimality,and the other is between the bias and strong 0-discount *** authors also prove the existence of an optimal policy for a finite horizon control problem by developing an interesting characterization of a canonical triplet.

关键词： Continuous-time Markov decision process expected average reward criterion finite-horizon optimality Polish space strong n-discount optimality

Approximation to the Distribution of the Least Squares Estimators in Two Dimensional Cosine Models by Randomly Weighted Bootstrap

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Acta Mathematicae Applicatae Sinica 2013年第4期29卷 765-776页

作者： Yuan-yuan ZHAO Rui-xing MING Yao-hua WU Department of statistics and finance University of Science and Technology of China school of mathematical sciences Nanjing Normal University institute of finance and statistics Nanjing Normal University school of statistics and Mathematics Zhejiang Gongshang University

Recently, Kundu and Gupta （Metrika, 48：83 C 97, 1998） established the asymptotic normality of the least squares estimators in the two dimensional cosine model. In this paper, we give the approximation to the general least squares estimators by using random weights which is called the Bayesian bootstrap or the random weighting method by Rubin （Annals of statistics, 9：130 C 134, 1981） and Zheng （Acta Math. Appl. Sinica （in Chinese）, 10（2）： 247 C 253, 1987）. A simulation study shows that this approximation works very well.

关键词： two dimensional model least squares estimator Bayesian bootstrap random weighting method

The inviscid limit for the Landau-Lifshitz-Gilbert equation in the critical Besov space

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Science China Mathematics 2017年第11期60卷 2155-2172页

作者： GUO ZiHua HUANG ChunYan school of mathematical sciences Monash University school of statistics and Mathematics Central University of Finance and Economics

We prove that in dimensions three and higher the Landau-Lifshitz-Gilbert equation with small initial data in the critical Besov space is globally well-posed in a uniform way with respect to the Gilbert damping parameter. Then we show that the global solution converges to that of the Schr¨odinger maps in the natural space as the Gilbert damping term vanishes. The proof is based on some studies on the derivative Ginzburg-Landau equations.

关键词： Landau-Lifshitz-Gilbert equation Schrdinger maps inviscid limit critical Besov space

Trimmed and Winsorized Transformed Means Based on a Scaled Deviation

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Acta Mathematicae Applicatae Sinica 2015年第2期31卷 475-492页

作者： Si-yang WANG Heng-jian CUI school of statistics and Mathematics Central University of Finance and Economics Department statistics School of Mathematical Sciences Capital Normal University

This paper introduces the Tukey trimmed and Winsorized means for the transformed data based on a scaled deviation. The trimmed and Winsorized means and scale based on a scaled deviation are as special cases. Meanwhile, the trimmed and Winsorized skewness and kurtosis based on a scaled deviation are ***, some of their robust properties（influence function, breakdown points） and asymptotic properties（asymptotic representation and limiting distribution） are also obtained.

关键词： trimmed and Winsorized transformed means influence function skewness kurtosis