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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)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

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Blocking the PD-1 signal transduction by occupying the phosphorylated ITSM recognition site of SHP-2

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Science China(life sciences) 2025年第1期68卷 189-203页

作者： Wenjie Li Wenyi Mei Hewei Jiang Jie Wang Xiaoli Li Lina Quan Yanyan Diao Yanni Ma Sisi Fan Zhuwei Xie Mengdie Gong Huan Zhu Dewen Bi Feng Zhang Lei Ma Jian Zhang Yufeng Gao Aris Paschalidis Honghuang Lin Fangfang Liu Kangdong Liu Mingliang Ye Zhenjiang Zhao Yajun Duan Zhuo Chen Yufang Xu Weilie Xiao Shengce Tao Lili Zhu Honglin Li shanghai Key Laboratory of New Drug Design School of PharmacyEast China University of Science&TechnologyShanghai 200237China shanghai center for Systems Biomedicine Key Laboratory of Systems Biomedicine(Ministry of Education)Shanghai Jiao Tong UniversityShanghai 200240China Key Laboratory of Medicinal Chemistry for Natural Resource Ministry of EducationYunnan Characteristic Plant Extraction LaboratoryYunnan Provincial Center for Research&Development of Natural ProductsState Key Laboratory for Conservation and Utilization of Bio-Resources in YunnanSchool of Pharmacy and School of Chemical Science and TechnologyYunnan UniversityKunming650500China CAS Key Laboratory of Separation sciences for Analytical Chemistry National Chromatographic R&A CenterDalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023China department of Cardiology The First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230027China department of Infectious Diseases The First Affiliated Hospital of Anhui Medical UniversityHefei 230022China department of Medicine University of Massachusetts Chan Medical SchoolWorcester MA 01655USA department of Pathophysiology School of Basic Medical SciencesAcademy of Medical ScienceCollege of MedicineZhengzhou UniversityZhengzhou 450001China Innovation center for AI and Drug Discovery East China Normal UniversityShanghai 200062China Lingang Laboratory Shanghai 200031China

Targeting the PD-1/PD-L1 axis with small-molecular inhibitors is a promising approach for ***,we identify a natural pentacyclic triterpenoid,Pygenic Acid A(PA),as a PD-1 signaling *** exerts anti-tumor activity in hPD-1 knock-in C57BL/6 mice and enhances effector functions of T cells to promote immune responses by disrupting the PD-1 signaling ***,we identify SHP-2 as the direct molecular target of PA for inhibiting the PD-1 signaling ***,mechanistic studies suggest that PA binds to a new druggable site in the phosphorylated PD-1 ITSM recognition site of SHP-2,inhibiting the recruitment of SHP-2 by *** together,our findings demonstrate that PA has a potential application in cancer immunotherapy and occupying the phosphorylated ITSM recognition site of SHP-2 may serve as an alternative strategy to develop PD-1 signaling *** addition,our success in target recognition provides a paradigm of target identification and confirmation for natural products.

关键词： pygenic acid A programmed death-1 immunoreceptor tyrosine-based switch motif SH2 domain-containing protein-tyrosine phosphatase-2 target identification site recognition

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Interaction of Magnesium Ion and Acetate Anion in Bulk Water:Toward High-Level Machine Learning Potential

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Chinese Journal of Chemical physics 2025年第1期38卷 95-101,I0056页

作者： Jiaying Gu Jin Xiao Xingyu Wu Xi Zhu Huimin Chen John ZHZhang Tong Zhu Ya Gao Zhixiang Yin School of Mathematics Physics and StatisticsShanghai University of Engineering ScienceShanghai 201620China shanghai Engineering Research center of Molecular Therapeutics&New Drug Development School of Chemistry and Molecular EngineeringEast China Normal UniversityShanghai 200062China CAS Key Laboratory of quantitative Engineering Biology Shenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China NYU-ECNU center for Computational Chemistry at NYU shanghai Shanghai 200062China department of Chemistry New York UniversityNew York 10003USA Collaborative Innovation center of Extreme Optics Shanxi UniversityTaiyuan 030006China shanghai Frontiers Science Research center for Druggability of Cardiovascular Noncoding RNA Shanghai 201620China

Metal ions play crucial roles in various biologi-cal functions,in-cluding maintain-ing homeostasis,regulating mus-cle contraction,and facilitating enzyme ***,accurately simulating the interaction between metal ions and amino acid side chain analogs using high-level wave function theories remains challenging due to the significant computational costs *** this study,deep potential molecular dynamics(DeePMD)simulation was employed to investigate the solvation structure of the Mg^(2+)-Ac^(−)ion pair in aqueous *** address the computational bottleneck associated with expensive quan-tum mechanics(QM)methods,the Deep Kohn-Sham(DeePKS)approach was utilized,which allows us to generate highly accurate self-consistent energy functionals while significantly re-ducing computational *** root mean square error and mean absolute error of energies and atomic forces indicate close agreement between DeePKS predictions and QM strongly constrained and appropriately normed(SCAN)***,the neural network potential(NNP)generated using the SCAN-level dataset predicted by DeePKS exhibits high-er accuracy compared to previous work,which employed a moderate BLYP *** potential of mean force for the Mg^(2+)-Ac−system was further examined,revealing a prefer-ence for monodentate coordination of Mg^(2+)with a~5.8 kcal/mol energy barrier between bidentate and monodentate ***,this work provides a comprehensive,precise,and reliable methodology for investigating metal ions’properties in aqueous solutions.

关键词： Molecular dynamics simulation Umbrella sampling Neural network potential Machine learning

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Integrating operando spectroscopies and transient analysis for dynamic catalytic insights

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Science China Chemistry 2025年

作者： Xiao Kong Yue Chen Xinhe Bao Yifeng Zhu School of Material and Chemistry University of Shanghai for Science and Technology shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Department of Chemistry Fudan University State Key Laboratory of Catalysis National Laboratory for Clean Energy Collaborative Innovation Center of Chemistry for Energy Materials Dalian Institute of Chemical Physics Chinese Academy of Sciences

Catalysis, which is central to the energy and chemical industries, constitutes a dynamic process that involves multiple stages,ranging from activation and deactivation to rapid catalytic cycles. Comprehending these dynamic processes is crucial for optimizing catalytic reactions and developing innovative catalytic systems. This review centers on the integration of operando spectroscopies with transient analysis to acquire quantitative dynamic information directly from spectroscopic investigations of catalytic processes. Operando spectroscopies facilitate real-time observations of dynamic changes occurring during catalysis,while transient experiments yield insights that extend beyond steady-state kinetics by examining catalysts' responses to and recovery from dynamic conditions. This review aims to underscore the significance of integrating multiple spectroscopic techniques and transient methodologies to yield quantitative insights into catalytic processes, elucidating in real time the relationships between active structures, surface intermediates, and catalytic kinetics.

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Is philosophy of any use for scientists？

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Science Bulletin 2018年第16期63卷 1017-1018页

作者： Ping Ao shanghai center for quantitative life sciences and department of physics Shanghai University.Shanghai 200444 China

This is a question which would certainly divide physicists in particular and scientists in *** aware of that,here I would like to take the successful career path of an excellent physicist as a positive example,supplemented by my own humble and negligible experience.I do hope that a bit of such discussion would be useful in the current rash state of scientific research in China.

关键词：科学家哲学物理学家科学研究

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Efficient transfer of metallophosphor excitons via confined polaritons in organic nanocrystals

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Chinese physics B 2023年第10期32卷 503-508页

作者：芦文斌陈永聪杨旭云敖平 shanghai center for quantitative life sciences&physics department Shanghai UniversityShanghai 200444China College of Biomedical Engineering Sichuan UniversitySichuan 610064China

We investigate the transfer of phosphorescent energy between co-assembled metallophosphors in crystalline nanostructures [Angew. Chem. Int. Ed. 57 7820(2018) and J. Am. Chem. Soc. 140 4269(2018)]. Neither Dexter's nor Forster's mechanism of resonance energy transfer(RET) could account fully for the observed rates, which exceed 85% with significant temperature dependence. But there exists an alternative pathway on RET mediated by intermediate states of resonantly confined exciton–polaritons. Such a mechanism was used to analyze artificial photosynthesis in organic fluorescents [***. Lett. 122 257402(2019)]. For metallophosphors, the confined modes act as extended states lying between the molecular S_(1) and T_(1) states, offering a bridge for the long-lived T_(1) excitons to migrate from donors to acceptors. Population dynamics with parameters taken entirely based on experiments fits the observed lifetimes of phosphorescence across a broad range of doping and temperature.

关键词： organic nanocrystals phosphorescent emission resonance energy transfer exciton–polariton

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Stochastic Gradient Descent and Anomaly of Variance-Flatness Relation in Artificial Neural Networks

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Chinese physics Letters 2023年第8期40卷 6-10页

作者：熊霞陈永聪石春晓敖平 shanghai center for quantitative life sciences and physics department Shanghai UniversityShanghai 200444China Colloge of Biomedical Engineering Sichuan UniversityChengdu 610065China

Stochastic gradient descent(SGD),a widely used algorithm in deep-learning neural networks,has attracted continuing research interests for the theoretical principles behind its success.A recent work reported an anomaly(inverse)relation between the variance of neural weights and the landscape flatness of the loss function driven under SGD[Feng Y and Tu Y *** 118 e2015617118(2021)].To investigate this seeming violation of statistical physics principle,the properties of SGD near fixed points are analyzed with a dynamic decomposition *** approach recovers the true“energy”function under which the universal Boltzmann distribution *** differs from the cost function in general and resolves the paradox raised by the the *** study bridges the gap between the classical statistical mechanics and the emerging discipline of artificial intelligence,with potential for better algorithms to the latter.

关键词： neural bridges holds

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Cryo-EM Data Statistics and Theoretical Analysis of KaiC Hexamer

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Chinese physics Letters 2022年第7期39卷 24-29页

作者： Xu Han Zhaolong Wu Tian Yang Qi Ouyang department of physics Peking UniversityBeijing 100871China center for quantitative Biology and Peking-Tsinghua center for life sciences AAICPeking UniversityBeijing 100871China

Cryo-electron microscopy(cryo-EM) provides a powerful tool to resolve the structure of biological macromolecules in natural state. One advantage of cryo-EM technology is that different conformation states of a protein complex structure can be simultaneously built, and the distribution of different states can be measured. This provides a tool to push cryo-EM technology beyond just to resolve protein structures, but to obtain the thermodynamic properties of protein machines. Here, we used a deep manifold learning framework to get the conformational landscape of Kai C proteins, and further obtained the thermodynamic properties of this central oscillator component in the circadian clock by means of statistical physics.

关键词： Cryo-EM Data Statistics and Theoretical Analysis of KaiC Hexamer

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High density gas state at water/graphite interface studied by molecular dynamics simulation

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Chinese physics B 2008年第7期17卷 2646-2654页

作者：王春雷李朝霞李敬源修鹏胡钧方海平 shanghai Institute of Applied physics Chinese Academy of Sciences Graduate School of the Chinese Academy of sciences department of physics Zhejiang University School of physics and Microelectronics Shandong University Bio-X life sciences Research center College of Life Science and TechnologyShanghai Jiaotong University

In this paper molecular dynamics simulations are performed to study the accumulation behaviour of N2 and H2 at water/graphite interface under ambient temperature and pressure. It finds that both N2 and H2 molecules can accumulate at the interface and form one of two states according to the ratio of gas molecules number to square of graphite surface from our simulation results： gas films （pancake-like） for a larger ratio and nanobubbles for a smaller ratio. In addition, we discuss the stabilities of nanobubbles at different environment temperatures. Surprisingly, it is found that the density of both kinds of gas states can be greatly increased, even comparable with that of the liquid N2 and liquid H2. The present results are expected to be helpful for the understanding of the stable existence of gas film （pancake-like） and nanobubbles.

关键词： nanobubbles and gas film hydrophobic interface molecular dynamics simulations high density

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Humidity Effects on Imaging and Nanomanipulation of Individual DNA Molecules on HOPG Surface

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Chinese physics Letters 2007年第9期24卷 2692-2695页

作者：周星飞张益王化斌牛冬校王培卿胡钧 department of physics College of Sciences Ningbo University Ningbo 315211 shanghai Institute of Applied physics Chinese Academy of Sciences Shanghai 201800 Bio-X life Science Research center Shanghai Jiao Tong University Shanghai 200240

Single DNA molecules are aligned on highly ordered pyrolytic graphite （HOPG） surface in ambient air. It is shown that environmental humidity has a remarkable influence on the measured height of DNA by atomic force microscopy （AFM）, probably due to the conformation transition of DNA. We also demonstrate that DNA molecules deposited on HOPG surface can be ＇pushed＇ much more easily by AFM tip at high humidity than at 10W one.

关键词： coated conductor buffer layer self-epitaxy CeO2

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