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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)Wuhu 241000China Pharmaceutical informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration(Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji UniversityShanghai 200092China Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Research Institute of Intelligent Computing Zhejiang LabHangzhou 311121China Shanghai Research Institute for Intelligent Autonomous Systems Shanghai 201210China Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of MedicineShanghai 200025China National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314103China Center for Bioinformatics and computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Beijing Institutes of Life Science Chinese Academy of SciencesBeijing 100101China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology(CQB)Peking UniversityBeijing 100871China Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women’s HospitalZhejiang University School of MedicineHangzhou 310006China Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal U

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular *** 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 *** the inception of the first single-cell RNA technology,technologies related to single-cell sequencing have experienced rapid advancements in recent *** 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 scRNA-seq and CRISPR ***-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases,including ***,we comprehensively summarize recent advances in single-cell omics technologies,with a specific focus on the methodology *** 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

Orbit Classification of Qutrit via the Gram Matrix

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Chinese Physics Letters 2008年第6期25卷 1923-1926页

作者：郑万安 Hishamuddin Zainuddin Department of Physics Faculty of Science Universiti Putra Malaysia 43400 UPM Serdang Selangor Malaysia Laboratory of computational Science and informatics Institute for Mathematical Research Universiti Putra Malaysia 43400 UPM Serdang Selangor Malaysia

We classify the orbits generated by unitary transformation on the density matrices of the three-state quantum systems （qutrits） via the Gram matrix. The Gram matrix is a real symmetric matrix formed from the Hilbert- Schmidt scalar products of the vectors lying in the tangent space to the orbits. The rank of the Gram matrix determines the dimensions of the orbits, which fall into three classes for qutrits.

关键词： QUANTUM COMMUNICATION SYSTEMS SU(3) GEOMETRY

Application of computational Biology to Decode Brain Transcriptomes

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Genomics, Proteomics & Bioinformatics 2019年第4期17卷 367-380页

作者： Jie Li Guang-Zhong Wang CAS Key Laboratory of computational Biology CAS-MPG Partner Institute for Computational BiologyShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200031China University of Chinese Academy of Sciences Beijing 100049China

The rapid development of high-throughput sequencing technologies has generated massive valuable brain transcriptome atlases,providing great opportunities for systematically investigating gene expression characteristics across various brain regions throughout a series of developmental *** studies have revealed that the transcriptional architecture is the key to interpreting the molecular mechanisms of brain ***,our knowledge of brain transcriptional characteristics remains very *** the immense efforts to generate high-quality brain transcriptome atlases,new computational approaches to analyze these highdimensional multivariate data are greatly *** this review,we summarize some public resources for brain transcriptome atlases and discuss the general computational pipelines that are commonly used in this field,which would aid in making new discoveries in brain development and disorders.

关键词： Brain transcriptome atlas computational analysis Spatiotemporal pattern Coexpression analysis Single-cell analysis

TESTING k-EDGE-CONNECTIVITY OF DIGRAPHS

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Journal of Systems Science & Complexity 2010年第1期23卷 91-101页

作者： Yuichi YOSHIDA.HiroI TO School of informatics Kyoto University

This paper presents an algorithm that tests whether a given degree-bounded digraph is k-edge-connected or E-far from k-edge-connectivity. This is the first testing algorithm for k-edge- connectivity of digraphs whose running time is independent of the number of vertices and edges. A digraph of n vertices with degree bound d is ε-far from k-edge-connectivity if at least εdn edges have to be added or deleted to make the digraph k-edge-connected, preserving the degree bound. Given a constant error parameter ε and a degree bound d, our algorithm always accepts all k-edge-connected digraphs and reiects all digraphs that is ε-far from k-edge-connectivity with orobabilitv at least 2/*** runs in O（d（εd^-c）^k logεd^-1O）（c〉1 is a constant）time when input digraphs are restricted to be （k-1）-edge connected and runs in O（d（εd^-ck）^klogεd^-kO）（c〉1 is a constant）time for general digraphs.

关键词： Digraph graph k-edge-connectivity property testing.

Small Alfvén number limit for incompressible magneto-hydrodynamics in a domain with boundaries

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Science China Mathematics 2019年第11期62卷 2229-2248页

作者： Song Jiang Qiangchang Ju Xin Xu Institute of Applied Physics and computational Mathematics

For any fixed Alfvén number, the local well-posedness is proved for the equations of threedimensional ideal incompressible magneto-hydrodynamics in a domain with boundaries. Under appropriate conditions, a smooth solution is shown to exist in a time interval independent of the Alfvén number, and the solutions of the original system tend to the solutions of a two-dimensional Euler flow coupled with a linear transport equation as the Alfvén number goes to zero.

关键词： MHD equations vanishing Alfvén number limit small Mach number uniform estimates

Studying Validity of Single-Fluid Model in Inertial Confinement Fusion

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Communications in Theoretical Physics 2014年第3期61卷 370-376页

作者：谷建法范证锋戴振生叶文华裴文兵朱少平 Institute of Applied Physics and computational Mathematics

The validity of single-fluid model in inertial confinement fusion simulations is studied by comparing the results of the multi- and single-fluid models. The multi-fluid model includes the effects of collision and interpenetration between fluid species. By simulating the collision of fluid species, steady-state shock propagation into the thin DT gas and expansion of hohlraum Au wall heated by lasers, the results show that the validity of single-fluid model is strongly dependent on the ratio of the characteristic length of the simulated system to the particle mean free path. When the characteristic length L is one order larger than the mean free path A, the single-fluid model＇s results are found to be in good agreement with the multi-fluid model＇s simulations, and the modeling of single-fluid remains valid. If the value of L/A is lower than 10, the interpenetration between fluid species is significant, and the single-fluid simulations show some unphysical results; while the multi-fluid model can describe well the interpenetration and mix phenomena, and give more reasonable results.

关键词： multi-fluid model interpenetration mixing inertial confinement fusion

Review on the Methods of Automatic Liver Segmentation from Abdominal Images

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Journal of Computer and Communications 2014年第2期2卷 1-7页

作者： Suhuai Luo Xuechen Li Jiaming Li The CSIRO computational informatics Australia The University of Newcastle Australia

Automatic liver segmentation from abdominal images is challenging on the aspects of segmentation accuracy, automation and robustness. There exist many methods of liver segmentation and ways of categorisingthem. In this paper, we present a new way of summarizing the latest achievements in automatic liver segmentation. We categorise a segmentation method according to the image feature it works on, therefore better summarising the performance of each category and leading to finding an optimal solution for a particular segmentation task. All the methods of liver segmentation are categorized into three main classes including gray level based method, structure based method and texture based method. In each class, the latest advance is reviewed with summary comments on the advantages and drawbacks of each discussed approach. Performance comparisons among the classes are given along with the remarks on the problems existed and possible solutions. In conclusion, we point out that liver segmentation is still an open issue and the tendency is that multiple methods will be employed together to achieve better segmentation performance.

关键词： Liver Segmentation Image Feature Performance Comparison Review Survey

Optimization of the Doped Ablator Layers for the Plastic Ignition Capsule

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Communications in Theoretical Physics 2015年第2期63卷 236-242页

作者：谷建法戴振生李永升宋鹏叶文华邹士阳郑无敌朱少平 Institute of Applied Physics and computational Mathematics

The paper investigates theoretically the optimization of the doped ablator layers for the plastic ignition capsule. The high-resolved one-dimensional implosion simulations show that the inner pure CFI layer of the Si-doped design is excessively preheated by the hard x-ray, leading to the unstable ablator-fuel interface compared to the Ge-doped capsule. This is because that the Si K-shell absorption edge （1.8 keV） is higher than the Ge L-edge （1.3 keV）, and Si dopant makes more hard x-ray penetrate through the doped ablator layers to preheat the inner pure CH layer. So an optimization of the doped ablator layers （called ＂Si/Ge capsule＂） is performed： an Si-doped CH layer is placed next to the outer pure CH layer to keep the high implosion velocity; next to the Si-doped layer is a thin Ge-doped layer, in order to absorb the hard x-ray and protect the inner undoped CH-layer from excessively preheating. The simulations show that the Si/Ge capsule can effectively improve hydrodynamic stability at the ablator-fuel interface while keeping the high implosion velocity.

关键词： doped ablator tayer optimization ablator-fuel interface hydrodynamic instability ignition capsuleimplosion

Numerical Simulation of 2-D Radiation-Drive Ignition Implosion Process

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Communications in Theoretical Physics 2013年第6期59卷 737-744页

作者：勇珩宋鹏翟传磊康洞国谷建法杭旭登古培俊江松 Institude of Applied Physics and computational Mathematics

A Lagrangian compatible radiation hydrodynamic algorithm and the nuclear dynamics computing module are developed and implemented in the LARED Integration code, which is a radiation hydrodynamic code based on the 2-D cylindrical coordinates for the numerical simulation of the indirect-drive Inertial Confined Fusion. A number of 1-D and 2-D ignition implosion numerical simulations by using the improved LARED Integration code (ILARED) are presented which show that the 1-D numerical results are consistent with those computed by the 1-D radiation hydrodynamic code RDMG, while the simulation results of the 2-D low-mode radiative asymmetry and hydrodynamic instability growth,according to the physical analysis and anticipation, are satisfactory. The capsules driven by the sources from SGII experiments are also simulated by ILARED, and the fuel shapes agree well with the experimental results. The numerical simulations demonstrate that ILARED can be used in the simulation of the 1-D and 2-D ignition capsule implosion using the multi-group diffusion model for radiation.

关键词： LARED Integration code ignition implosion capsule spherical symmetry Lagrangian compatibleradiation hydrodynamic algorithm