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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

The Hilbert expansion of the Boltzmann equation in the incompressible Euler level in a channel

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Science China Mathematics 2025年第1期 39-88页

作者： Feimin Huang Weiqiang Wang Yong Wang Feng Xiao academy of Mathematics and Systems Science Chinese Academy of Sciences school of Mathematical sciences University of Chinese Academy of Sciences Key Laboratory of Computing and Stochastic Mathematics (Ministry of Education) School of Mathematics and StatisticsHunan Normal University

The study of the hydrodynamic limit of the Boltzmann equation with physical boundary is a challenging problem due to the appearance of the viscous and Knudsen boundary *** this paper,the hydrodynamic limit from the Boltzmann equation with the specular reflection boundary condition to the incompressible Euler equations in a channel is *** on the multi-scaled Hilbert expansion,the equations with boundary conditions and compatibility conditions for interior solutions,and viscous and Knudsen boundary layers are derived under different scaling,***,some uniform estimates for the interior solutions,and viscous and Knudsen boundary layers are *** the help of the L2-L∞framework and the uniform estimates obtained above,the solutions to the Boltzmann equation are constructed by the truncated Hilbert expansion with multiscales,and hence the hydrodynamic limit in the incompressible Euler level is justified.

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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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Rapid and scalable preparation of highly quaternized polymer networks to achieve efficient simultaneous adsorption of iodide and pertechnetate

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Science China Chemistry 2025年第01期 337-349页

作者： Meiyun Xu Song Gu Fulong Chen Zhe Zhao Peng Liu Daoben Hua State Key Laboratory of Radiation Medicine and Protection School of Radiological and Interdisciplinary Sciences (RAD-X) Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions Soochow University

The efficient separation of fission products,such as TcO4-and I-,holds strategic significance for the management of radioactive wastes and environmental *** this study,we propose an ultrafast strategy for scalable preparation of a highly quaternized organic network to facilitate efficient and synchronous separation of iodide and *** network can be prepared within a few minutes at room temperature,using polyethylenimine and 1,2,4,5-tetrakis（bromomethyl）benzene as building *** chlorine replacement,the network,abundantly decorated with quaternary ammonium groups （Cl@QPN）,exhibits an ultrahigh positive charge density of 7.6 mmol/*** enables the rapid and efficient enrichment of target anions through strong electrostatic Coulomb *** a result,Cl@QPN exhibits significantly higher adsorption rate constants of 0.830 g/（mg min） for ReO4-（a nonradioactive surrogate of TcO4-） and 0.677 g/（mg min） for I-compared to other ***,it possesses high adsorption capacities,reaching 1,681 mg/g for ReO4-and 917.4 mg/g for I-.Cl@QPN also demonstrates good selectivity towards target ions and shows efficient adsorption for99TcO4-.Additionally,Cl@QPN exhibits high dynamic processing capacities,handling up to 3,100 and 7,400 kg of simulated streams per kilogram of material for I-and ReO4-,respectively.

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THE CONSTRUCTION OF DENUMERABLE q-PROCESSES IN RANDOM ENVIRONMENTS SATISFYING (F) OR (B)

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Acta Mathematica Scientia 2008年第4期28卷 975-988页

作者：胡迪鹤胡晓予 school of Mathematics and statistics Yunnan University school of Mathematics and statistics Wuhan University Graduate school Chinese Academy of Sciences

This article is a continuation of[9].Based on the discussion of random Kolmogorov forward（backward）equations,for any given q-matrix in random environment, Q（θ）=（q（θ;x,y）,x,y∈X）,an infinite class of q-processes in random environments satisfying the random Kolmogorov forward（backward）equation is ***, under some conditions,all the q-processes in random environments satisfying the random Kolmogorov forward（backward）equation are constructed.

关键词： Markov process in random environment q-matrix in random environment,q-process in random environment

Multiplicative forms on Poisson groupoids

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Science China Mathematics 2025年第1期 169-206页

作者： Zhuo Chen Honglei Lang Zhangju Liu Department of Mathematical sciences Tsinghua University College of Science China Agricultural University school of Mathematics and statistics Henan University

First,we prove a decomposition formula for any multiplicative differential form on a Lie groupoid ***,we prove that if G is a Poisson Lie groupoid,then the space ?mult·（G） of multiplicative forms on G has a differential graded Lie algebra（DGLA） ***,when combined with ?·（M）,which is the space of forms on the base manifold M of G,?mult·（G） forms a canonical DGLA crossed *** supplements a previously known fact that multiplicative multi-vector fields on G form a DGLA crossed module with the Schouten algebra Γ（∧·A） stemming from the Lie algebroid A of G.

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Joint Analysis of Recurrent Event Data with a Dependent Terminal Event

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Journal of Systems Science & Complexity 2017年第6期30卷 1443-1458页

作者： YE Peng DAI Jiajia ZHU Jun school of statistics University of International Business and Economics school of Mathematics and statistics Guizhou University Institute of Applied Mathematics Academy of Mathematics and Systems Science Chinese Academy of Sciences

Recurrent event data frequently occur in many longitudinal studies, and the observation on recurrent events could be stopped by a terminal event such as death. This paper considers joint modeling and analysis of recurrent event and terminal event data through a common subject-specific frailty, in which the proportional intensity model is used for modeling the recurrent event process and the additive hazards model is used for modeling the terminal event time. Estimating equation approaches are developed for parameter estimation and asymptotic properties of the resulting estimators are established. In addition, some procedures are presented for model checking. The finite sample behavior of the proposed estimators is evaluated through simulation studies, and an application to a heart failure study is provided.

关键词： Additive hazards model estimating equation frailty recurrent events terminal event

Generalized Profile LSE in Varying-Coefficient Partially Linear Models with Measurement Errors

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Acta Mathematicae Applicatae Sinica 2013年第3期29卷 477-490页

作者： Yun-bei MA Jin-hong YOU Yong ZHOU school of statistics Southwestern University of Finance and Economics school of statistics and Management Shanghai University of Finance and Economics academy of Mathematics and System sciences Chinese Academy of Sciences

This paper is concerned with the estimating problem of a semiparametric varying-coefficient partially linear errors-in-variables model Yi=Xτiβ＋Zτiα（Ui）＋εi , Wi=Xi＋ξi,i=1, · · · , n. Due to measurement errors, the usual profile least square estimator of the parametric component, local polynomial estimator of the nonparametric component and profile least squares based estimator of the error variance are biased and inconsistent. By taking the measurement errors into account we propose a generalized profile least squares estimator for the parametric component and show it is consistent and asymptotically normal. Correspondingly, the consistent estimation of the nonparametric component and error variance are proposed as well. These results may be used to make asymptotically valid statistical inferences. Some simulation studies are conducted to illustrate the finite sample performance of these proposed estimations.

关键词： Semiparametric modeling varying-coefficient measurement error local polynomial profile least squares asymptotic normality

FUNCTIONAL COEFFICIENT AUTOREGRESSIVE CONDITIONAL ROOT MODEL

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Journal of Systems Science & Complexity 2012年第5期25卷 998-1013页

作者： Jianjun ZHOU Min CHEN school of Mathematics and statistics Yunnan University academy of Mathematics and Systems Science Chinese Academy of Sciences

This paper proposes an extended model based on ACR nmdel： Functional coefficient autoregressive conditional root model （FCACR）. Under some assumptions, the authors show that the process is geometrically ergodic, stationary and all moments of the process exist. The authors use the polynomial spline function to approximate the functional coefficient, and show that the estimate is consistent with the rate of convergence Op（hv＋1 ＋ n-1/3）. By simulation study, the authors discover the proposed method can approximate well the real model. Furthermore, the authors apply the model to real exchange rate data analysis.

关键词： Ergodicity functional coefficient polynomial spline function.