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

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

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A Discrete Spectral Problem and Related Hierarchy of Discrete Hamiltonian Lattice Equations

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Communications in Theoretical Physics 2007年第8期48卷 193-198页

作者： XU Xi-Xiang college of science,shandong Uniersity of science and technology,Qingdao 266510,ChinaCAO Wei-Li college of science,Uniersity of Shanghai for science and technology,Shanghai 200093,China college of science Shandong University of Science and Technology college of science University of Shanghai for Science and Technology

Staring from a discrete matrix spectral problem,a hierarchy of lattice soliton equations is presentedthough discrete zero curvature *** resulting lattice soliton equations possess non-local Lax *** structures are esta... 详细信息

关键词： lattice soliton equation zero curvature representation Hamiltonian structure Liouville integrability

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Variable-sampling-period dependent global stabilization of delayed memristive neural networks based on refined switching event-triggered control

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science China(Information sciences) 2020年第11期63卷 159-174页

作者： Zhilian YAN Xia HUANG Jinde CAO college of Electrical Engineering and Automation Shandong University of Science and Technology School of mathematics Southeast University

This paper studies the stabilization problem of delayed memristive neural networks under eventtriggered control. A refined switching event-trigger scheme that switches between variable sampling and continuous event-trigger can be designed by introducing an exponential decay term into the threshold function. Compared with the existing mechanisms, the proposed scheme can enlarge the interval between two successively triggered events and therefore can reduce the amount of triggering times. By constructing a time-dependent and piecewise-defined Lyapunov functional, a less-conservative criterion can be derived to ensure global stability of the closed-loop system. Based on matrix decomposition, equivalent conditions in linear matrix inequalities form of the above stability criterion can be established for the co-design of both the trigger matrix and the feedback gain. A numerical example is provided to demonstrate the effectiveness of the theoretical analysis and the advantages of the refined switching event-trigger scheme.

关键词： event-triggered control delayed memristive neural networks global stabilization time-dependent Lyapunov functional variable sampling

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Community Detection by Neighborhood Similarity

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Chinese Physics Letters 2012年第4期29卷 244-247页

作者： LIU Xu XIE Zheng YI Dong-Yun Department of mathematics and systems science College of ScienceNational University of Defense TechnologyChangsha 410073

Detection of the community structure in a network is important for understanding the structure and dynamics of the *** exploring the neighborhood of vertices,a local similarity metric is proposed,which can be quickly *** resulting similarity matrix retains the same support as the adjacency *** on local similarity,an agglomerative hierarchical clustering algorithm is proposed for community *** algorithm is implemented by an efficient max-heap data structure and runs in nearly linear time,thus is capable of dealing with large sparse networks with tens of thousands of *** on synthesized and real-world networks demonstrate that our method is efficient to detect community structures,and the proposed metric is the most suitable one among all the tested similarity indices.

关键词： similarity networks structure

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The Spectrum and Automorphism Group of the Set-Inclusion Graph

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Algebra Colloquium 2021年第3期28卷 497-506页

作者： Xueyi Huang Qiongxiang Huang Jianfeng Wang Department of mathematics East China University of Science and Technology Shanghai 200237China college of mathematics and systems science Xinjiang University UrumqiXinjiang 830046China School of mathematics and Statistics Shandong University of Technology ZiboShandong 255049China

Let n,k and l be integers with 1≤k 详细信息

Let n,k and l be integers with 1≤k

关键词： set-inclusion graph spectrum automorphism group

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A new eight-dimensional Lie superalgebra and two corresponding hierarchies of evolution equations

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Chinese Physics B 2010年第1期19卷 7-12页

作者：王新赠董焕河 college of Information science and Engineering Shandong University of Science and Technology

A new eight-dimensional Lie superalgebra is constructed and two isospectral problems with six potentials are designed. Corresponding hierarchies of nonlinear evolution equations, as well as super-AKNS and super-Levi, are derived. Their super-Hamiltonian structures are established by making use of the supertrace identity, and they are integrable in the sense of Liouville.

关键词： Lie superalgebra supertrace identity superintegrable system super-Hamiltonian structure

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Bargmann Symmetry Constraint for a Family of Liouville Integrable Differential-Difference Equations

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Communications in Theoretical Physics 2012年第6期57卷 953-960页

作者：徐西祥 college of science Shandong University of Science and Technology

A family of integrable differential-difference equations is derived from a new matrix spectral problem. The Hamiltonian forms of obtained differential-difference equations are constructed. The Liouville integrability for the obtained integrable family is proved. Then, Bargmann symmetry constraint of the obtained integrable family is presented by binary nonliearization method of Lax pairs and adjoint Lax pairs. Under this Bargmann symmetry constraints, an integrable symplectic map and a sequences of completely integrable finite-dimensional Hamiltonian systems in Liouville sense are worked out, and every integrable differential-difference equations in the obtained family is factored by the integrable symplectie map and a completely integrable tinite-dimensionai Hamiltonian system.

关键词： differential-difference equation Lax pair Hamiltonian form Binary nonliearization Bargmannsymmetry constraint integrable symplectic map

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Higher-Dimensional Lie Algebra and New Integrable Coupling of Discrete KdV Equation

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Communications in Theoretical Physics 2010年第7期54卷 7-15页

作者：李欣越宋宏伟 college of science Shandong University of Science and Technology

Based on semi-direct sums of Lie subalgebra G, a higher-dimensional 6 × 6 matrix Lie algebra sμ（6） is constructed. A hierarchy of integrable coupling KdV equation with three potentials is proposed, which is derived from a new discrete six-by-six matrix spectral problem. Moreover, the Hamiltonian forms is deduced for lattice equation in the resulting hierarchy by means of the discrete variational identity -- a generalized trace identity. A strong symmetry operator of the resulting hierarchy is given. Finally, we prove that the hierarchy of the resulting Hamiltonian equations is Liouville integrable discrete Hamiltonian systems.

关键词： semi-direct sums of Lie subalgebra integrable couplings discrete variational identity Liouvilleintegrability

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A Family of Integrable Rational Semi-Discrete systems and Its Reduction

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Communications in Theoretical Physics 2010年第2期53卷 205-210页

作者：徐西祥 college of science Shandong University of Science and Technology

Within framework of zero curvature representation theory, a family of integrable rational semi-discrete systems is derived from a matrix spectral problem. The Hamiltonian forms of obtained semi-discrete systems are constructed by means of the discrete trace identity. The Liouville integrability for the obtained family is demonstrated. In the end, a reduced family of obtained semi-discrete systems and its Hamiltonian form are worked out.

关键词： semi-discrete system discrete zero curvature equation Lax pair Hamiltonian form Liouville integrability

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An easy CTAB-assisted path towards bayberry-like Ni–Co–Mn ternary hydroxide with enhancing supercapacitor performance

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Progress in Natural science:Materials International 2023年第4期33卷 433-441页

作者： Huiling Zhu Kai Wang Yao Qi Ruixin Li Jianxu Ding Rui Liu School of Materials science and Engineering Shandong University of Science and Technology college of Energy and Mining Engineering Shandong University of Science and Technology

In this study, we synthesized a bayberry-like Ni–Co–Mn ternary hydroxide with a secondary nanoneedle structure using a modified and cost-effective hydrothermal process assisted by the surfactant cetyltrimethylammonium bromide(CTAB). The incorporation of CTAB and graphene in the preparation process significantly enhances the electrochemical performance of NiCoMn–OH. The achieved results are truly impressive, with a high specific capacity of 1450 F g-1and an outstanding capacity retention of 52.57% over 5000 cycles. The superior performance could be attributed to the specific bayberry-like microstructure with high effective specific surface area,which allowed for facile and rapid transport of ions and electrons. Moreover, the synergistic effect of CTAB and graphene proved to be crucial in stabilizing the Co2+and Mn2+ions within the ternary hydroxide structure. We developed a hybrid capacitor using a NiCoMn–OH-CTAB/Graphene composite electrode and an active electrode,which delivered a superior energy density of 50.79 Wh kg-1at a power density of 400 W kg-1and a cycling stability of 60.37% after 10000 cycles. These results indicate that the NiCoMn–OH-CTAB/Graphene composite electrode has great potential as an electrode material for energy storage devices.

关键词： Bayberry-like microstructure CTAB Graphene Ni–Co–Mn ternary hydroxide Supercapacitors

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