检索结果-南通市图书馆

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

在线全文

学校读者我要写书评

暂无评论

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

Marine Metagenome as A Resource for Novel Enzymes

在线全文

同方期刊数据库

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2015年第5期13卷 290-295页

作者： Amani D.Alma'abadi Takashi Gojobori Katsuhiko Mineta computational Bioscience research center (cbrc) King Abdullah University of Science and Technology (KAUST)

More than 99% of identified prokaryotes, including many from the marine environment, cannot be cultured in the laboratory. This lack of capability restricts our knowledge of microbial genetics and community ecology. Metagenomics, the culture-independent cloning of environmental DNAs that are isolated directly from an environmental sample, has already provided a wealth of information about the uncultured microbial world. It has also facilitated the discovery of novel bio- catalysts by allowing researchers to probe directly into a huge diversity of enzymes within natural microbial communities. Recent advances in these studies have led to a great interest in recruiting microbial enzymes for the development of environmentally-friendly industry. Although the metage- nomics approach has many limitations, it is expected to provide not only scientific insights but also economic benefits, especially in industry. This review highlights the importance of metagenomics in mining microbial lipases, as an example, by using high-throughput techniques. In addition, we dis- cuss challenges in the metagenomics as an important part of bioinformatics analysis in big data.

关键词： Microbial diversity Culture-independent studies Catalysis Lipase Biotechnology

Toward understanding the role of genomic repeat elements in neurodegenerative diseases

在线全文

学校读者我要写书评

暂无评论

Neural Regeneration research 2025年第3期20卷 646-659页

作者： Zhengyu An Aidi Jiang Jingqi Chen Institute of Science and Technology for Brain-Inspired Intelligence Fudan UniversityShanghaiChina MOE Frontiers center for Brain Science Fudan UniversityShanghaiChina MOE Key Laboratory of computational Neuroscience and Brain-Inspired Intelligence Fudan UniversityShanghaiChina Zhangjiang Fudan International Innovation center ShanghaiChina

Neurodegenerative diseases cause great medical and economic burdens for both patients and society;however, the complex molecular mechanisms thereof are not yet well understood. With the development of high-coverage sequencing technology, researchers have started to notice that genomic repeat regions, previously neglected in search of disease culprits, are active contributors to multiple neurodegenerative diseases. In this review, we describe the association between repeat element variants and multiple degenerative diseases through genome-wide association studies and targeted sequencing. We discuss the identification of disease-relevant repeat element variants, further powered by the advancement of long-read sequencing technologies and their related tools, and summarize recent findings in the molecular mechanisms of repeat element variants in brain degeneration, such as those causing transcriptional silencing or RNA-mediated gain of toxic function. Furthermore, we describe how in silico predictions using innovative computational models, such as deep learning language models, could enhance and accelerate our understanding of the functional impact of repeat element variants. Finally, we discuss future directions to advance current findings for a better understanding of neurodegenerative diseases and the clinical applications of genomic repeat elements.

关键词： Alzheimer's disease ataxia deep learning long-read sequencing neurodegeneration neurodegenerative diseases Parkinson's disease repeat element structural variant

Single-cell technologies: current and near future

在线全文

学校读者我要写书评

暂无评论

Science China Life Sciences 2025年第01期 1-4页

作者： Chenfei Wang Qi Liu Xiaohui Fan Tieliu Shi Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration Ministry of EducationOrthopedics 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 Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University 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 Key Laboratory of Advanced Theory and Application in Statistics and Data Science (MOE) School of StatisticsEast China Normal University

Single-cell technologies enable the indepth exploration of multiple biological hierarchies at the scale of individual cells,which have deepened our knowledge of cellular diversity, tissue organization, and overall organism function(Sun et al.,2024). In 2009, single-cell RNA sequencing(sc RNA-seq) was first developed as a powerful tool to dissect gene expression and uncover transcriptional *** the rapid advancement of technology, single-cell approaches have expanded to encompass other omics, such as genomics, epigenomics, proteomics,and metabolomics.

关键词：

同方期刊数据库

Deciphering fungal metabolon coupling tandem inverse-electrondemand Diels-Alder reaction and semipinacol rearrangement for the biosynthesis of spiro polycyclic alkaloids

在线全文

学校读者我要写书评

暂无评论

Science China Chemistry 2025年第01期 288-296页

作者： Shuai Liu Wen-Qiang Xu Ying-Tong Di Man-Cheng Tang Ding-Kang Chen Ming-Ming Cao Yao-Wen Chang Hong-Yu Tang Chun-Mao Yuan Jun-Bo Yang Zhi-Li Zuo Han Guo Zi-Fei Xu Ying Zeng Yun-Dong Wu Xiao-Jiang Hao Key Laboratory of Phytochemistry and Natural Medicines (Chinese Academy of Sciences) Kunming Institute of Botany Chinese Academy of Sciences University of Chinese Academy of Sciences Lab of computational Chemistry and Drug Design State Key Laboratory of Chemical Oncogenomics Peking University Shenzhen Graduate School Shenzhen Bay Laboratory State Key Laboratory of Microbial Metabolism School of Life Sciences & Biotechnology Shanghai Jiao Tong University State Key Laboratory of Functions and Applications of Medicinal Plants Guizhou Medical University Molecular biology Experimental center Germplasm Bank of Wild Species in Southwest China Kunming Institute of Botany Chinese Academy of Sciences Yunnan Key Laboratory for Wild Plant Resources Kunming Institute of Botany Chinese Academy of Sciences research Unit of Chemical biology of Natural Anti-Virus Products Chinese Academy of Medical Sciences

In the intricate process of natural product biosynthesis, a metabolon can enhance metabolic flux by associating sequential enzymes. A fungal metabolon, comprising of flavin-dependent monooxygenase Spe F and P450 monooxygenase Spe G, is identified in the biosynthesis of spiro polycyclic alkaloids(+)-notoamide B and its diastereomer(+)-versicolamide B. Using notoamide E as a substance, Spe F/Spe G metabolon can control the stereoselectivity of its 2,3-epoxidation, followed by hydrogen atom ion at C-17 to generate reactive epoxide tau-m A with dienyl iminium unit. Subsequently,(+)-notoamide B and(+)-versicolamide B are produced via tandem nonenzymatic inverse-electron-demand Diels-Alder reaction and semipinacol rearrangement. This provides the first example of metabolon in the biosynthesis of spiro-prenylated indole alkaloids.

关键词：

同方期刊数据库

Deep Learning Deepens the Analysis of Alternative Splicing

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2019年第2期17卷 219-221页

作者： Xudong Zou Xin Gao Wei Chen Department of biology Southern University of Science and Technology Shenzhen 518055 China computational Bioscience research center (cbrc) Computer Electrical and Mathematical Sciences and Engineering (CEMSE) Division King Abdullah University of Science and Technology (KAUST) Thuwal 23955 Saudi Arabia

The ever-increasing high-volume and high-dimensional geno-mics data on the one hand challenge traditional data analysis approaches,and on the other hand provide ample opportuni-ties for developing novel analytic strat... 详细信息

关键词： Deep Learning Deepens the Analysis Alternative Splicing

First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2015年第5期13卷 304-309页

作者： Andr Antunes Intikhab Alam Marta Filipa Simoes Camille Daniels Ari J.S.Ferreira Rania Siam Hamza El-Dorry Vladimir B.Bajic computational Bioscience research center (cbrc) ComputerElectrical and Mathematical Sciences and Engineering Division (CEMSE)King Abdullah University of Science and Technology (KAUST) Red Sea research center (RSRC) Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST) biology Department American University in Cairo

The deep-sea brines of the Red Sea include some of the most extreme and unique envi- ronments on Earth. They combine high salinities with increases in temperature, heavy metals, hydrostatic pressure, and anoxic conditions, creating unique settings for thriving populations of novel extremophiles. Despite a recent increase of studies focusing on these unusual biotopes, their viral communities remain unexplored. The current survey explores four metagenomic datasets obtained from different brine-seawater interface samples, focusing specifically on the diversity of their viral communities. Data analysis confirmed that the particle-attached viral communities present in the brine-seawater interfaces were diverse and generally dominated by Candovirales, yet appearing distinct from sample to sample. With a level of caution, we report the unexpected finding of Phycodnaviridae, which infects algae and plants, and trace amounts of insect-infecting Iridoviridae. Results from Kebrit Deep revealed stratification in the viral communities present in the interface： the upper-interface was enriched with viruses associated with typical marine bacteria, while the lower-interface was enriched with haloviruses and halophages. These results provide first insights into the unexplored viral communities present in deep-sea brines of the Red Sea, represent- ing one of the first steps for ongoing and future sampling efforts and studies.

关键词： Viral diversity Metagenomics Brine-seawater interface Caudovirales Red Sea

Theoretical Elucidation on Different Lipid-Oxidation Potentials of Aminoxyl Antioxidants

在线全文

学校读者我要写书评

暂无评论

Chinese Journal of Chemistry 2003年第12期21卷 1669-1672页

作者：王兰芬张红雨 Laboratory for computational biology Shandong Provincial Research Center for Bioinformatic Engineering and TechniqueShandong University of Technology

To elucidate the different lipid-oxidation potentials of aminoxylantioxidants, a kind of combined density functional theory (DFT) method was employed to calculateC―H bond dissociation enthalpies (BDEs) of a model linoleic acid (LH) and O―H BDEs of hydrogenatedaminoxyls. The higher the O―H BDE is, the more potent the aminoxyl to abstract the H-atom from LHand the stronger the LH-oxidation potential. Accordingly, the prooxidant activity differences ofaminoxyls were elucidated by the different O―H BDEs of hydrogenated aminoxyls, which were furtherclarified in terms of distinct electronic effects of the substituents.

关键词： AM1 aminoxyl antioxidant density functional theory H-abstraction reaction lipid oxidation O―H bond dissociation enthalpy

Accuracy and Consistency of the Explicit-Invariant Energy Quadratization Approach for the Cahn-Hilliard Equation

在线全文

学校读者我要写书评

暂无评论

Journal of Mathematical research with Applications 2025年第1期 84-104页

作者： Jun ZHANG Fangying SONG Yu ZHANG computational Mathematics research center Guizhou University of Finance and Economics School of mathematics and statistics Guizhou University of Finance and Economics School of Mathematics and Stastistics Fuzhou University

It is well known that the explicit-invariant energy quadratization (EIEQ) approach can generate fully decoupled, linear and unconditionally energy-stable numerical schemes, so it is favored by many researchers. However, the undeniable fact is that the numerical method obtained by EIEQ approach preserves the “modified” energy law instead of the original *** is mainly due to the introduction of some auxiliary variables in EIEQ scheme, and the truncation error will make the auxiliary variables deviate from the original definition in the process of numerical calculation. The primary objective of this paper is to address this gap by providing the accuracy and consistency of the EIEQ method in the context of the CahnHilliard equation. We introduce a relaxation technique for auxiliary variables and construct two numerical schemes based on EIEQ. The analysis results show that the newly constructed schemes are not only unconditionally energy stable, linear and fully decoupled, but also can effectively correct the errors introduced by auxiliary variables and follow the original energy ***, several 2D and 3D numerical examples illustrate the accuracy and efficiency of the newly constructed numerical schemes.

关键词：