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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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Tuning electrospinning hierarchically porous nanowires anode for enhanced bioelectrocatalysis in microbial fuel cells

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Nano Research 2022年第6期15卷 5089-5097页

作者： Shiwei Qian Xiaoshuai Wu Zhuanzhuan Shi Xiaofen Li Xin Sun Yongjia Ma Wei Sun Chunxian Guo ChangMing Li institute for advanced cross-field science and college of life science Qingdao UniversityQingdao 266071China institute of Materials science and Devices School of Materials Science and EngineeringSuzhou University of Science and TechnologySuzhou 215011China college of Chemistry and Chemical Engineering Hainan Normal UniversityHaikou 571158China

Pore structure plays critical roles in electrode kinetics but very challenging to tailor porous nanowires with rationally distributed pore sizes in a bioelectrochemical *** a hierarchically porous nanowires-material is delicately tuned for an optimal pore structure by adjusting the weight percentage of SiO_(2)-hard template in an electrospinning precursor *** asprepared optimal electrospinning nanowires further used as an anode of microbial fuel cells(MFCs),delivering a maximum output power density of 1,407.42 mW·m^(−2)with 4.24 and 10 times higher than that of the non-porous fiber and carbon cloth anode,*** great enhancement is attributed to the rational pore structure which offers the largest surface area while the rich-mesopores well match with the size of electron mediators for a high density of catalytic *** work provides thoughtful insights to design of hierarchical porous electrode for high-performance MFCs and other bioelectrochemical system devices.

关键词： hierarchically porous nanowires microbial fuel cells interfacial electron transfer biofilm

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2-D/2-D heterostructured biomimetic enzyme by interfacial assembling Mn_(3)(PO_(4))_(2) and MXene as a flexible platform for realtime sensitive sensing cell superoxide

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Nano Research 2021年第3期14卷 879-886页

作者： Shen Fei Zhao Fang Xin Hu Zhuan Zhuan Shi Jing Jing Fu Yue Chen Fang Yin Dai Chun Xian Guo Chang Ming Li institute of Materials science and Devices Suzhou University of Science and TechnologySuzhou215009China institute for Clean Energy and advanced Materials Southwest UniversityChongqing400715China State Key Laboratory of Silkworm Genome Biology Southwest UniversityChongqing400715China institute for advanced cross-field science&college of life science Qingdao UniversityQingdao200671China

It is critical for fabricating flexible biosensors with both high sensitivity and good selectivity to realize real-time monitoring superoxide anion(O_(2)^(·−)),a specific reactive oxygen species that plays critical roles in various biological *** work delicately designs a Mn_(3)(PO_(4))_(2)/MXene heterostructured biomimetic enzyme by assembling two-dimensional(2-D)Mn_(3)(PO_(4))_(2) nanosheets with biomimetic activity and 2-D MXene nanosheets with high conductivity and abundant functional *** 2-D nature of the two components with strong interfacial interaction synergistically enables the heterostructure an excellent flexibility with retained 100%of the response when to reach a bending angle up to 180°,and 96%of the response after 100 bending/relaxing *** is found that the surface charge state of the heterostructure promotes the adsorption of O_(2)^(·−),while the high-energy active site improves electrochemical oxidation of O_(2)^(·−).The Mn_(3)(PO_(4))_(2)/MXene as a sensing platform towards O2•−achieves a high sensitivity of 64.93µA·µM^(−1)·cm^(−2),a wide detection range of 5.75 nM to 25.93µM,and a low detection limit of 1.63 ***,the flexible heterostructured sensing platform realizes real-time monitoring of O_(2)^(·−)in live cell assays,offering a promising flexible biosensor towards exploring various biological processes.

关键词： two-dimensional(2-D)nanosheets assembled heterostructure interface flexible biosensor real-time monitoring

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A core-shell copper oxides-cobalt oxides heterostructure nanowire arrays for nitrate reduction to ammonia with high yield rate

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Green Energy & Environment 2023年第6期8卷 1619-1629页

作者： Hui Liu Jingsha Li Feng Du Luyun Yang Shunyuan Huang Jingfeng Gao Changming Li Chunxian Guo institute of advanced cross-field science College of Life ScienceQingdao UniversityQingdao266071China institute of Materials science and Devices School of Materials Science and EngineeringSuzhou University of Science and TechnologySuzhou215011China Jiangsu Key Laboratory for Micro and Nano Heat Fluid Flow Technology and Energy Application Collaborative Innovation Center of Water Treatment Technology&MaterialChina

Electrochemical nitrate reduction to ammonia(NRA) can realize the green synthesis of ammonia(NH3) at ambient conditions, and also remove nitrate contamination in water. However, the current catalysts for NRA still face relatively low NH3yield rate and poor stability. We present here a core-shell heterostructure comprising cobalt oxide anchored on copper oxide nanowire arrays(CuO NWAs@Co_(3)O_(4)) for efficient NRA. The CuO NWAs@Co_(3)O_(4)demonstrates significantly enhanced NRA performance in alkaline media in comparison with plain CuO NWAs and Co_(3)O_(4)flocs. Especially, at-0.23 V vs. RHE, NH_(3) yield rate of the CuO NWAs@Co_(3)O_(4)reaches 1.915 mmol h^(-1)cm^(-2),much higher than those of CuO NWAs(1.472 mmol h^(-1)cm^(-2)), Co_(3)O_(4)flocs(1.222 mmol h^(-1)cm^(-2)) and recent reported Cu-based *** is proposed that the synergetic effects of the heterostructure combing atom hydrogen adsorption and nitrate reduction lead to the enhanced NRA performance.

关键词： Electrocatalytic nitrate reduction Ammonia production Core–shell heterostructure Copper oxides nanowire arrays Cobalt oxidesﬂocs

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An investigation on the wind profiles and gravity wave dynamics in MLT region based on the meteor radars from the Meridian Project

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Earth and Planetary Physics 2025年第1期9卷 29-38页

作者： Tai Liu Zhe Wang MengXi Shi Willie Soon ShiCan Qiu Department of Geophysics College of the Geology Engineering and GeomaticsChang’an UniversityXi’an 710054China Center for Environmental Research and Earth sciences(CERES) SalemMA 01970USA institute of Earth Physics and Space science(ELKH EPSS) 9400SopronHungary

The meteor radar can detect the zenith angle,azimuth,radial velocity,and altitude of meteor trails so that one can invert the wind profiles in the mesosphere and low thermosphere(MLT)region,based on the Interferometric and Doppler *** this paper,the horizontal wind field,gravity wave(GW)disturbance variance,and GW fluxes are analyzed through the meteor radar observation from 2012−2022,at Mohe(53.5°N,122.4°E)and Zuoling(30.5°N,114.6°E)stations of the(Chinese)Meridian *** Lomb−Scargle periodogram method has been utilized to analyze the periodic variations for time series with observational data *** results show that the zonal winds at both stations are eastward dominated,while the meridional winds are southward *** variance of GW disturbances in the zonal and meridional directions increases gradually with height,and there is a strong pattern of annual *** zonal momentum flux of GW changes little with height,showing weak annual *** meridional GW flux varies gradually from northward to southward with height,and the annual periodicity is *** both stations,the maximum values of zonal and meridional wind occur close to the peak heights of GW flux,with opposite *** observational evidence is consistent with the filtering *** horizontal wind velocity,GW flux,and disturbance variance of the GW at Mohe are overall smaller than those at Zuoling,indicating weaker activities in the MLT at *** power spectral density(PSD)calculated by the Lomb−Scargle periodogram shows that there are 12-month period and 6-month period in horizontal wind field,GW disturbance variance and GW flux at both stations,and especially there is also a 4-month cycle in the disturbance *** PSD of the 12-month and 6-month cycles exhibits maximum values below 88 km and above 94 km.

关键词： meteor radar wind field gravity wave Lomb−Scargle method

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Algorithm for complex network diameter based on distance matrix

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Journal of Systems Engineering and Electronics 2018年第2期29卷 336-342页

作者： CHEN Bin ZHU Weixing LIU Ying institute of Command Information System PLA University of Science and Technology college of Computer science and Engineering Sanjiang University institute of field Engineering PLA University of Science and Technology

The network diameter is an important characteristic parameter of a complex network. Calculation for a large-scale complex network’s diameter has been an important subject in the study of complex networks. If the network diameter is calculated directly, the problem mainly exists in efficiency for searching and counting the shortest paths. If the network diameter is calculated indirectly by studying the statistical function about the relationship between the network diameter and parameters affecting the diameter, the problems not only exist in the efficiency of statistic, but also exist in the function which may be not applicable to all kinds of networks. An algorithm for the complex network diameter based on the k order distance matrix is proposed with a matrix multiplication approach, and a mathematical proof for the algorithm correctness is given as well. Furthermore, some relevant propositions and deductions for reducing the complexity of this algorithm are put forward. With a good theoretical basis and a simple calculation process, this algorithm can be used to calculate the diameter of a large-scale complex network with small-world effect more accurately and efficiently. Two cases about the advanced research projects agency(ARPA) network model and the Chinese airline network model are adopted to verify the effect of this algorithm.

关键词： complex network network diameter distance matrix

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Calcium-organic frameworks cathode for high-stable aqueous Zn/organic batteries

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Chinese Chemical Letters 2023年第7期34卷 289-293页

作者： Wenshan Gou Tian Jiang Wei Wang Qi Fan Yan Zhang institute of advanced cross-field science College of Life SciencesQingdao UniversityQingdao 200671China School of Materials science and Engineering Jiulonghu CampusSoutheast UniversityNanjing 211189China China State Key Laboratory of Materials-Oriented Chemical Engineering College of Chemical EngineeringNanjing Tech UniversityNanjing 210009China

Rechargeable aqueous zinc-ion batteries(AZIBs) are attracting tremendous attention because of their intrinsic merits such as high safety and low cost. Cathode plays a critical role in enhancing the electrochemical performance of AZIBs. However, it is difficult to design a robust and high-efficiency cathode material and further implement the commercialization of AZIBs. Metal-organic frameworks(MOFs) electroactive compounds are attractive to serve as the cathode of AZIBs due to their unique porosity and crystal structures, resource renewability and structural diversity. In this work, a calcium-pure terephthalates acid framework(Ca-PTA·3H_(2)O) was synthesized by facile hydrolysis and cationic exchange method,then explored as a novel cathode for AZIBs. The results highlight a high specific capacity of 431 mAh/g(0.51 mAh/cm^(2)) at a current density of 50 mA/g, and excellent cycle performance with capacity retention of ~90% after 2700 cycles at 500 m A/g. The following up characterizations investigate the reversible zinc storage mechanism in detail. This experiment made a specific contribution to the exploration of the new MOF as a competitive cathode for AZIBs.

关键词： Aqueous zinc-ion battery Metal-organic frameworks Cathode material Excellent cycle performance Zinc storage mechanism

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Recent progress on photoactive nonprecious transition-metal complexes

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science China Chemistry 2025年第1期 46-95页

作者： Zhong-Liang Gong Hong-Jie Zhang Yan Cheng Jianxun Liu Yuhan Ai Yaqin Li Zhihui Feng Qiong Zhang Shaolong Gong Yong Chen Chang-Jiang Yao Yuan-Yuan Zhu Liang-Jin Xu Yu-Wu Zhong CAS Key Laboratory of Photochemistry Institute of Chemistry Chinese Academy of Sciences State Key Laboratory of Structural Cemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences School of Chemistry and Chemical Engineering Anhui Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringHefei University of Technology State Key Laboratory of Explosion science and Safety Protection School of Mechatronical Engineering Beijing Institute of Technology college of Chemistry and Molecular sciences Hubei Key Lab on Organic and Polymeric Optoelectronic Materials Wuhan University School of Chemistry and Chemical Engineering Anhui University Key Laboratory of Photochemical Conversion and Optoelectronic Materials & CAS-HKU Joint Laboratory on New Materials Technical Institute of Physics and Chemistry Chinese Academy of Sciences

Photoactive complexes of nonprecious transition metals, mainly including those in the first-row and partially the second-row of the Periodic table of elements, have received increasing attention in view of their low cost and long-term sustainability. They are recognized as promising alternatives to noble transition metal complex congeners that have been extensively studied in optoelectronic devices, artificial photosynthesis, photocatalysis, biodiagnostics, and therapeutics, etc. This review is devoted to a comprehensive summary on the classical and recent advances on photoactive nonprecious transition metal complexes, including photoactive Zr, V, Cr, Mo, and W complexes, Mn complexes and hybrids, Fe, Co, Ni, and Cu complexes, and Zn and Cd complexes and hybrids. A particular focus is given on the molecular design, modulation of photophysical and photochemical properties, and applications of the representative and lately-developed nonprecious metal complexes. In addition, a perspective on the future development in this field is provided at the end of this review.

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Three dimension simulation analysis of the interpass stress and deformation during multipass welding

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China Welding 2008年第2期17卷 72-78页

作者：张华军张广军张秀兰蔡春波高洪明 State Key Laboratory of advanced Welding Production Technology Harbin Institute of Technology Daqing Oil field Limited Company college of Material science and Engineering Harbin University of Science and Technology

It has been widely studied about the final residual stress and deformation in muhipass welding of thick weldments. But there is a lack of a clear understanding of the interrelationship of interpass stress and deformation during multipass welding. In this study, a three dimension numerical model of a sixteen-pass double V-groove welded joint with 50 mm plate is developed to compute the stress field and deformation by using multiple CPU parallel processing technology. The following factors such as the non-linear of temperature, heat radiation, filling of material step by step and so on are considered. Distribution and evolution law of welding stress in the transverse and longitudinal section is analyzed in this paper, and the interpnss stresses are studied also. At the same time the evolution course of angular deformation amount is analyzed, and the experimental results show that the calculated resuhs accord with the measured results of angular deformation.

关键词： interpass stress multipass welding three-dimensional stress field angular deformation numerical simulation

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Relationship between the Thickness of β-FeSi_2 Thin Film and the Solar Photo Wavelength

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Chinese Journal of Mechanical Engineering 2012年第2期25卷 315-319页

作者： XIONG Xicheng XIE Quan YAN Wanjun institute of advanced Optoelectronic Materials and Technology College of ScienceGuizhou UniversityGuiyang 550025China

The β-FeSi2 thin film has been applied in the research field of the solar cell,and the thickness of β-FeSi2 absorption layer was chosen through the ***,Up to now neither the optimal thickness of β-FeSi2 absorption layer nor the relationship between the thickness of β-FeSi2 absorption layer and the solar photo wavelength has been theoretically *** this paper,the relationship between the thickness of the absorption layer of β-FeSi2 thin film solar cell and the solar photo wavelength is calculated and analyzed by *** results show that the thickness of the absorption layer of β-FeSi2 is at least 200 nm when the optical absorption efficiency of the solar energy reaches 90%,and that the optimal thickness range is from 200 nm to 250 nm,and that the optimal wavelength of the photon absorbed by β-FeSi2 thin film solar cell is from 0.46 μm？0.6 μ***,two formulas are put forward to indicate the relationship between the thickness of the absorption layer of β-FeSi2 thin film solar cell and the solar photo *** thickness of the absorption layer of β-FeSi2 thin film solar cell increases linearly with the solar photo wavelength within the optimal photo *** formulas provide a reliable theoretical basis of determining the thickness of the β-FeSi2 thin film in the solar cell.

关键词： β-FeSi2 solar cell absorption layer thickness

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