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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

Unraveling brain aging through the lens of oral microbiota

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Neural Regeneration Research 2025年第7期20卷 1930-1943页

作者： Qinchao Hu Si Wang Weiqi Zhang Jing Qu Guang-Hui Liu State key laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijingChina Hospital of Stomatology Guanghua School of StomatologyGuangdong Provincial Key Laboratory of StomatologySun Yat-sen UniversityGuangzhouGuangdong ProvinceChina Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders Xuanwu HospitalCapital Medical UniversityBeijingChina Aging Translational medicine Center International Center for Aging and CancerBeijing Municipal Geriatric Medical Research CenterXuanwu HospitalCapital Medical UniversityBeijingChina CAS key laboratory of Genomic and precision medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina University of Chinese Academy of Sciences BeijingChina Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijingChina Aging Biomarker Consortium BeijingChina State key laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijingChina Beijing Institute for Stem Cell and Regenerative medicine BeijingChina

The oral cavity is a complex physiological community encompassing a wide range of *** of oral microbiota can lead to various oral infectious diseases,such as periodontitis and tooth decay,and even affect systemic health,including brain aging and neurodegenerative *** studies have highlighted how oral microbes might be involved in brain aging and neurodegeneration,indicating potential avenues for intervention *** this review,we summarize clinical evidence demonstrating a link between oral microbes/oral infectious diseases and brain aging/neurodegenerative diseases,and dissect potential mechanisms by which oral microbes contribute to brain aging and *** also highlight advances in therapeutic development grounded in the realm of oral microbes,with the goal of advancing brain health and promoting healthy aging.

关键词： Alzheimer's disease brain aging multiple sclerosis neurodegeneration neurodegenerative diseases oral microbiota Parkinson's disease periodontitis bacteria Porphyromonas gingivalis

Integration of Electrical Properties and Polarization Loss Modulation on Atomic Fe–N‑RGO for Boosting Electromagnetic Wave Absorption

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Nano-Micro Letters 2025年第2期17卷 517-532页

作者： Kaili Zhang Yuefeng Yan Zhen Wang Guansheng Ma Dechang Jia Xiaoxiao Huang Yu Zhou State key laboratory of precision Welding&Joining of Materials and Structures Harbin Institute of TechnologyHarbin 150001People’s Republic of China School of Materials Science and Engineering Harbin Institute of TechnologyHarbin 150001People’s Republic of China MIIT key laboratory of Advanced Structural‑Functional Integration Materials&Green Manufacturing Technology Harbin Institute of TechnologyHarbin 150001People’s Republic of China

Developing effective strategies to regulate graphene’s conduction loss and polarization has become a key to expanding its application in the electromagnetic wave absorption(EMWA)*** on the unique energy band structure of graphene,regulating its bandgap and electrical properties by introducing heteroatoms is considered a feasible ***,metal-nitrogen doping reduced graphene oxide(M–N-RGO)was prepared by embedding a series of single metal atoms M–N_(4) sites(M=Mn,Fe,Co,Ni,Cu,Zn,Nb,Cd,and Sn)in RGO using an N-coordination atom-assisted *** composites had adjustable conductivity and polarization to optimize dielectric loss and impedance matching for efficient EMWA *** results showed that the minimum reflection loss(RL_(min))of Fe–N-RGO reaches−74.05 dB(2.0 mm)and the maximum effective absorption bandwidth(EAB_(max))is 7.05 GHz(1.89 mm)even with a low filler loading of only 1 wt%.Combined with X-ray absorption spectra(XAFS),atomic force microscopy,and density functional theory calculation analysis,the Fe–N_(4) can be used as the polarization center to increase dipole polarization,interface polarization and defect-induced polarization due to d-p orbital hybridization and structural ***,electron migration within the Fe further leads to conduction loss,thereby synergistically promoting energy *** study demonstrates the effectiveness of metal-nitrogen doping in regulating the graphene′s dielectric properties,which provides an important basis for further investigation of the loss mechanism.

关键词： Electromagnetic wave absorption Fe-N-RGO Dipole polarization Conduction loss Impedance matching

Anomalous quality factor evolution of induced transparency in a virtualized coupled-oscillator system

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 148-155页

作者： Yunhan Yang Han Jia Tuo Liu Yuzhen Yang Jun Yang key laboratory of Noise and Vibration Research Institute of Acoustics Chinese Academy of Sciences University of Chinese Academy of Sciences State key laboratory of Acoustics Institute of Acoustics Chinese Academy of Sciences

The phenomenon of induced transparency, characterized by a high quality(Q) factor, holds significant importance in the fields of high-precision sensing, energy storage and wave manipulation. Conventional transparency systems are often constrained by the limited experimentally accessible parameter space and the lack of independent control over intrinsic parameters, thereby hindering advanced research on high-Q effects. Here we propose a virtualized coupled-oscillator system that enables reconfigurable induced transparency in the reflection spectrum. By virtually incorporating a pair of coupled oscillators into an individual acoustic meta-atom, we achieve the manipulation of induced transparency in a decoupled, wide-ranging, and elaborate manner. Exploiting the diverse evolutions across the intrinsic parameter space, we show experimentally a counter-intuitive increase in the Q-factor of the transparency window, which is attributed to the enhanced dissipation of the bright ***, a constant group delay at the center frequency is observed accompanying this evolution. Our work demonstrates an intriguing platform as well as a novel strategy to engineer high-Q induced transparency phenomenon, and paves the way towards applications in programmable acoustic sensors, filters and slow-wave devices.

关键词： induced transparency acoustic meta-atom high quality-factor scattering programmable intrinsic parameter

Advances in Graphene‑Based Electrode for Triboelectric Nanogenerator

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Nano-Micro Letters 2025年第1期17卷 378-403页

作者： Bin Xie Yuanhui Guo Yun Chen Hao Zhang Jiawei Xiao Maoxiang Hou Huilong Liu Li Ma Xin Chen Chingping Wong State key laboratory of precision Electronic Manufacturing Technology and Equipment Guangdong University of TechnologyGuangzhou 510006People’s Republic of China School of Electromechanical Engineering Guangdong University of TechnologyGuangzhou 510006People’s Republic of China School of Materials Science and Engineering Georgia Institute of TechnologyAtlantaGA 30332USA

With the continuous development of wearable electronics,wireless sensor networks and other micro-electronic devices,there is an increasingly urgent need for miniature,flexible and efficient nanopower generation *** nanogenerator(TENG)technology can convert small mechanical energy into electricity,which is expected to address this *** the core component of TENG,the choice of electrode materials significantly affects its *** metal electrode materials often suffer from problems such as durability,which limits the further application of ***,as a novel electrode material,shows excellent prospects for application in TENG owing to its unique structure and excellent electrical *** review systematically summarizes the recent research progress and application prospects of TENGs based on graphene *** precision processing methods of graphene electrodes are introduced,and the applications of graphene electrode-based TENGs in various scenarios as well as the enhancement of graphene electrodes for TENG performance are *** addition,the future development of graphene electrode-based TENGs is also prospectively discussed,aiming to promote the continuous advancement of graphene electrode-based TENGs.

关键词： Triboelectric nanogenerator precision processing Graphene electrode Self-powered sensor

The priming induction regimen of HAG as a low dose chemotherapy strategy in AML clonal evolution

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Science China(Life Sciences) 2015年第12期58卷 1302-1305页

作者： CHEN AiLi YANG JingYi HU ShaoYan WANG Qian-Fei key laboratory of Genomic and precision medicine Beijing Institute of Genomics Chinese Academy of Sciences The Children's Hospital of Soochow University

Chemotherapy employs chemical substances to interfere with the growth of cancer cells,and is a major treatment strategy in human cancer including acute myeloid leukemia（AML）.Although they often effectively kill fast... 详细信息

关键词： regimen chemotherapy clonal interfere myeloid dividing subgroup induction clone relapse

Phylogeny of genera Laminaria and Saccharina(Laminariales, Phaeophyceae) based on three molecular markers

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Acta Oceanologica Sinica 2014年第9期33卷 139-151页

作者： CHI Shan QIAN Hao LI Tianyong WANG Xumin LIU Cui REN Lei TANG Xuexi LIU Tao Ocean University of China Beijing key laboratory of Functional genomics for Dao-di Herbs Beijing Institute of Genomics Chinese Academy of Sciences Chinese Academy of Sciences key laboratory of Genome Sciences and Information Beijing Key Laboratory of Genome and Precision Medicine Technologies Beijing Institute of Genomics Chinese Academy of Sciences

In the past two decades, many studies have focused on the classification within genus Laminaria, ultimately trying to divide it into two subgroups or genera： Laminaria and Saccharina. A significant debate still surrounds the question of its division, as the conflicting phylogenetic hypotheses that have resulted from the classification studies are based on different taxon sampling, molecular markers, or analysis methods. It is aimed at elucidate the molecular phylogeny within Laminaria and Saccharina. The nine species of Lami- nariales are sampled from northern Asia and Europe, and 23 new sequences in the nuclear, plastid, and mitochondrial genomes are determined to identify their taxonomic status. The phylogenetic analyses of 71 species are performed, including representatives from six of the seven families of the order Laminariales, based on three separate data sets. An evidence is provided to strongly support a clear split that maintains the two recognized genera, Laminaria and Saccharina, with Laminaria appearing to be the ancestor group. Further, analyses indicate that all taxa in Saccharina and Laminaria did not form a monophyletic lineage, instead Laminariaceae and Lessoniaceae grouped together interlacedly, and Costariaceae appeared as the sister taxon of the Lessoniaceae-Laminariaceae clade. In the phylogenetic analysis, mitochondrial c oxi- dase I （COI） sequences appeared to be the most credible molecular marker which was more befitting than nuclear encoded internal transcribed spacer （ITS） and plastid encoded rbcL for establishment of Laminariales systematics. It is the most comprehensive phylogeny of the order Laminariales, and contributes to an enhanced understanding and estimation of the phylogenetic relationships for the economically important seaweeds, Laminaria and Saccharina.

关键词： Saccharina Laminaria phylogeny COI rbcL ITS

Comparative analysis of four essential Gracilariaceae species in China based on whole transcriptomic sequencing

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Acta Oceanologica Sinica 2014年第2期33卷 54-62页

作者： XU Jiayue SUN Jing YIN Jinlong WANG Liang WANG Xumin LIU Tao CHI Shan LIU Cui REN Lufeng WU Shuangxiu YU Jun CAS key laboratory of Genome Sciences and Information Beijing Key Laboratory of Genome and Precision Medicine TechnologiesBeijing Institute of GenomicsChinese Academy of Sciences Beijing key laboratory of Functional genomics for Dao-di Herbs Beijing Institute of GenomicsChinese Academy of Sciences University of Chinese Academy of Sciences Changchun University of Chinese medicine College of Marine Life Science Ocean University of China

Three Gracilaria species, G. chouae, G. blodgettii, G. vermiculophylla and a close relative species, Gracilari-opsis lemaneiformis which is now nominated as Gracilaria lemaneiformis, are the typically indigenous spe-cies which are important resources for the production of special proteins, phycobilisomes, special carbo-hydrates, and agar in China. In this study, de novo transcriptome sequencing on these four species using the next generation sequencing technology was performed for the first time. Functional annotations on assembled sequencing reads showed that the transcriptomic profiles were quite different between G. lema-neiformis and other three Gracilaria species. Comparative analysis of differential gene expression related to carbohydrate and phycobiliprotein metabolisms also showed that the expression profiles of these essential genes were different in four species. The genes encoding allophycocyanin, phycocyanin and phycoerythrin were further examined in four species and their deduced amino acid sequences were used for phylogenetic analysis to confirm that G. lemaneiformis had close relationship to genus Gracilaria, as well as that within genus Gracilaria, G. chouae had closer relationship to G. vermiculophylla rather than to G. blodgettii. The de novo transcriptome study on four species provided a valuable genomic resource for further understanding and analysis on biological and evolutionary study among marine algae.

关键词： Gracilaria chouae Gracilaria blodgettii Gracilaria vermiculophylla Gracilariopsis lemaneiformis transcriptome sequencing phycobiliprotein phylogeny

Transcriptome sequencing of essential marine brown and red algal species in China and its significance in algal biology and phylogeny

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Acta Oceanologica Sinica 2014年第2期33卷 1-12页

作者： WU Shuangxiu SUN Jing CHI Shan WANG Liang WANG Xumin LIU Cui LI Xingang YIN Jinlong LIU Tao YU Jun CAS key laboratory of Genome Sciences and Information Beijing Key Laboratory of Genome and Precision Medicine TechnologiesBeijing Institute of GenomicsChinese Academy of Sciences Beijing key laboratory of Functional genomics for Dao-di Herbs Beijing Institute of GenomicsChinese Academy of Sciences University of Chinese Academy of Sciences College of Marine Life Science Ocean University of China

Most phaeophytes （brown algae） and rhodophytes （red algae） dwell exclusively in marine habitats and play important roles in marine ecology and biodiversity. Many of these brown and red algae are also important resources for industries such as food, medicine and materials due to their unique metabolisms and me-tabolites. However, many fundamental questions surrounding their origins, early diversification, taxonomy, and special metabolisms remain unsolved because of poor molecular bases in brown and red algal study. As part of the 1 000 Plant Project, the marine macroalgal transcriptomes of 19 Phaeophyceae species and 21 Rhodophyta species from China＇s coast were sequenced, covering a total of 2 phyla, 3 classes, 11 orders, and 19 families. An average of 2 Gb per sample and a total 87.3 Gb of RNA-seq raw data were generated. Approxi-mately 15 000 to 25 000 unigenes for each brown algal sample and 5 000 to 10 000 unigenes for each red algal sample were annotated and analyzed. The annotation results showed obvious differences in gene expres-sion and genome characteristics between red algae and brown algae;these differences could even be seen between multicellular and unicellular red algae. The results elucidate some fundamental questions about the phylogenetic taxonomy within phaeophytes and rhodophytes, and also reveal many novel metabolic pathways. These pathways include algal CO2 fixation and particular carbohydrate metabolisms, and related gene/gene family characteristics and evolution in brown and red algae. These findings build on known algal genetic information and significantly improve our understanding of algal biology, biodiversity, evolution, and potential utilization of these marine algae.

关键词： Phaeophyceae brown algae Rhodophyta red algae marine macroalgae transcriptome sequencing secondary generation sequencing