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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

Understanding super-enhancers

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Science China(Life Sciences) 2016年第3期59卷 277-280页

作者： Hao Cheng Xiaoyang Dou jing-Dong j.han Key Laboratory of Computational Biology CAS Center for Excellence in Molecular Cell Science Collaborative Innovation Center for Genetics and Developmental Biology Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences

Super-enhancers are defined as cluster of enhancers with dense TF binding, which can activate proximal cell-identity gene expression. Here we review the identification, func- tional significance of super-enhancers, and their relation- ships with cancer. With the current intense interests in su- per-enhancers, more super-enhancers will be defined and studied in different cell types and tissues and in different developmental and biological contexts to reveal molecular mechanisms of their functions.

关键词：超促进剂基因表达分子机制生物环境定义细胞激活

Facile autoreduction synthesis of core-shell Bi-Bi2O3/CNT with 3-dimensional neural network structure for high-rate performance supercapacitor

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journal of Materials Science & Technology 2020年第12期47卷 169-176页

作者： han Wu jingdong Guo De'an Yang Key Laboratory of Advanced Ceramics and Machining Technology of Ministry of Education School of Materials Science and EngineeringTianjin University300072China

Core-shell Bi-Bi2 O3/CNT(carbon nanotube) with 3-dimensional neural network structure where Bi-Bi2O3 nanospheres act as cell bodies supported by a 3-dimensional network of CNTs acting as synapses is designed and prepared by simple solvothermal method and subsequent annealing autoreduction treatment,and this structure facilitates the efficient transport of *** can provide two electron transfer paths due to the double contact of Bi2O3 shell with CNT and metal Bi core which enhances the efficiency of the electrochemical *** Bi-Bi2 O3/CNT electrode shows a high gravimetric capacitance of 850 F g-1(1 A g-1),and the specific capacitance of Bi-Bi2O3/CNT can be still 714 F g-1 at 30 A g-1 indicating excellent rate *** asymmetric supercapacitor is assembled with Bi-Bi2 O3/CNT as the negative electrode and Ni(OH)2/CNT as the positive electrode,delivering a high energy density of 36.7 Wh kg-1 and a maximum power density of 8000 W ***,the core-shell Bi-Bi2O3/CNT with 3-dimensional neural network structure as the negative electrode of supercapacitor shows great potential in the field of energy storage in the future.

关键词： Electrochemical energy-storage Asymmetric supercapacitor 3-Dimensional neural network structure Core-shell structure Bismuth oxide Bismuth metal Carbon nanotube

Targeting Ageing to Decrease Complex Non-Communicable Human Diseases

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journal of Genetics and Genomics 2014年第9期41卷 457-458页

作者： jing-Dong j.han john R.Speakman Chinese Academy of Sciences Key Laboratory of Computational Biology Chinese Academy of Sciences-Max Planck Partner Institute for Computational BiologyShanghai Institutes for Biological SciencesChinese Academy of Sciences State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental BiologyChinese Academy of Sciences Institute of Biological and Environmental Sciences University of Aberdeen

During the last two centuries, there have been many spectacular advances in medical science, the main consequence of which has been the dramatically reduced burden of infectious diseases. While in the 1800s many people died before reaching adult- hood, nowadays most people survive. Hence average life ex- pectancy in 1800s was around 30-40, which was barely higher than it had been in Greek and Roman times （Finch, 2010）, but nowadays life expectancy in most modernised economies is around 75 - 80. This demographic shift, which has happened in only 200 years, has created a dramatic change in the causes of mortality. The major killers in the modern world are non- communicable diseases （NCDs）： principally cardiovascular disease, cancer and neurodegenerative disorders such as Alz- heimer＇s disease. A major factor that influences susceptibility to all these diseases is age. As we get older, our risk of developing these NCDs increases enormously. For example, the rate of breast cancer in females at age 15-19 is less than 10 per 100,000 population, but this increases to 100 at age 40-44, 275 at age 55--59 and 450 at age 85 ＋（http：//***/ cancer-info/cancerstats/types/breast/incidence/#age）. Ageing has consequently become a major medical, social and economic burden to many countries.

关键词： Targeting Ageing to Decrease Complex Non-Communicable Human Diseases

How should bioinformatics Pls run wet-labs?

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Quantitative Biology 2022年第4期10卷 301-306页

作者： Miaomiao Tian jing-Dong j.han Sci-Tech journal Centre Higher Education PressBejing.100029China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology(CQB)Peking UniversityBeijing 100871China

With the rapid development of biotechnology,data-driven bioinformatics research is increasingly dependent on data generation from biological *** the same time,to gain in-depth knowledge of various biological systems,conventional biology laboratories have become more reliant on the establishment and optimization of advanced bioinformatics *** bioinformatics labs are debating whether to build their own wet-bench or to seek collaborations,while many wet-bench labs are also confused over whether they should build their own dry-labs or likewise seek collaborations.

关键词： methods. own fused

Application of Bayesian networks on large-scale biological data

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Frontiers in Biology 2010年第2期5卷 98-104页

作者： Yi LIU jing-Dong j.han Chinese Academy of Sciences Key Laboratory of Molecular Developmental Biology Center for Molecular Systems BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China

The investigation of the interplay between genes,proteins,metabolites and diseases plays a central role in molecular and cellular *** genome sequencing has made it possible to examine the behavior of all the genes in a genome by high-throughput experimental techniques and to pinpoint molecular interactions on a genome-wide scale,which form the backbone of systems *** particular,Bayesian network(BN)is a powerful tool for the ab-initial identification of causal and non-causal relationships between biological factors directly from experimental ***,scalability is a crucial issue when we try to apply BNs to infer such *** this paper,we not only introduce the Bayesian network formalism and its applications in systems biology,but also review recent technical developments for scaling up or speeding up the structural learning of BNs,which is important for the discovery of causal knowledge from large-scale biological ***,we highlight the basic idea,relative pros and cons of each technique and discuss possible ways to combine different algorithms towards making BN learning more accurate and much faster.

关键词： Bayesian networks(BN) large-scale biological data

Coordinate-wise monotonic transformations enable privacy-preserving age estimation with 3D face point cloud

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Science China(Life Sciences) 2024年第7期67卷 1489-1501页

作者： Xinyu Yang Runhan Li Xindi Yang Yong Zhou Yi Liu jing-Dong j.han School of Life Sciences Peking UniversityBeijing 100871China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology(CQB)Peking UniversityBeijing 100871China Beijing Key Lab of Traffic Data Analysis and Mining School of Computer and Information TechnologyBeijing Jiaotong UniversityBeijing 100044China Clinical Research Institute Shanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai 200025China

The human face is a valuable biomarker of aging,but the collection and use of its image raise significant privacy *** we present an approach for facial data masking that preserves age-related features using coordinate-wise monotonic *** first develop a deep learning model that estimates age directly from non-registered face point clouds with high accuracy and *** show that the model learns a highly indistinguishable mapping using faces treated with coordinate-wise monotonic transformations,indicating that the relative positioning of facial information is a low-level biomarker of facial *** visual perception tests and computational3D face verification experiments,we demonstrate that transformed faces are significantly more difficult to perceive for human but not for machines,except when only the face shape information is *** study leads to a facial data protection guideline that has the potential to broaden public access to face datasets with minimized privacy risks.

关键词： face point cloud age estimation face verification privacy coordinate-wise monotonic transformation

Structure-based protein-protein interaction networks and drug design

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Frontiers of Electrical and Electronic Engineering in China 2013年第3期8卷 183-191页

作者： Hammad Naveed jingdong j. han Chinese Academy of Sciences Key Laboratory of Computational Biology Chinese Academy of Sciences-Max Planck PartnerInstitute for Computational Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai200031 China

Proteins carry out their functions by interacting with other proteins and small molecules, forming a complex interaction network. In this review, we briefly introduce classical graph theory based protein-protein interaction networks. We also describe the commonly used experimental methods to construct these networks, and the insights that can be gained from these networks. We then discuss the recent transition from graph theory based networks to structure based protein-protein interaction networks and the advantages of the latter over the former, using two networks as examples. We further discuss the usefulness of structure based protein-protein interaction networks for drug discovery, with a special emphasis on drug repositioning.

关键词： protein-protein interaction network structure-based drug design drug reposition

A digitized catalog of COVID-19 epidemiology data

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Quantitative Biology 2021年第1期9卷 23-46页

作者： Wanyu Tao Zhengqing Yu jing-Dong j.han Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology(CQB)Peking UniversityBeijing 100871China

COVID-19 is now rapidly spreading *** the majority of COVID-19 patients show only mild or moderate symptoms,some could deteriorate quickly and may succumb to a sudden *** is therefore important to identify who will be more likely to develop severe outcomes and be treated with particular or preventive *** in this literature survey,we collected epidemiologic and clinical data from 36 articles on 51,270 patients with different severity of COVID-19,aiming to characterize the population that are prone to severe condition and bad *** data reveal that old males and those with high BMI or underlying diseases,especially cardiovascular disease,hypertension and diabetes,are overrepresented among severe *** leukocyte and lymphopenia are common features in severe and critical *** deterioration of the disease,both CD4^(+) and CD8^(+)T cells are decreased,while almost all serum cytokines,especially pro-inflammatory cytokines,increased.

关键词： COVID-19 severity epidemiology immune cells cytokine