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Bioinformatics analyses for signal transduction networks

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Science china(Life Sciences) 2008年第11期51卷 994-1002页

作者： LIU Wei1,2, LI dong2, ZHU YunPing2 & he fuchu1,2 1 College of Mechanical & Electronic Engineering and Automatization, National University of Defense Technology, Changsha 410073, china 2 state key laboratory of proteomics, beijing proteome research center, beijing institute of radiation medicine, beijing 102206, china College of Mechanical & Electronic Engineering and Automatization National University of Defense Technology Changsha China state key laboratory of proteomics Beijing Proteome Research Center Beijing Institute of Radiation Medicine Beijing China

research in signaling networks contributes to a deeper understanding of organism living activities. With the development of experimental methods in the signal transduction field, more and more mechanisms of signaling pathways have been discovered. This paper introduces such popular bioin-formatics analysis methods for signaling networks as the common mechanism of signaling pathways and database resource on the Internet, summerizes the methods of analyzing the structural properties of networks, including structural Motif finding and automated pathways generation, and discusses the modeling and simulation of signaling networks in detail, as well as the research situation and tendency in this area. Now the investigation of signal transduction is developing from small-scale experiments to large-scale network analysis, and dynamic simulation of networks is closer to the real system. With the investigation going deeper than ever, the bioinformatics analysis of signal transduction would have immense space for development and application.

关键词： signal transduction structural motif automated pathways regeneration dynamics simulation

一种基于基因表达模型识别酵母细胞周期条件特异调控子网的方法(英文)

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生物化学与生物物理进展 2010年第4期37卷 402-415页

作者：刘齐军王正华刘万霖李栋贺福初朱云平国防科学技术大学并行与分布处理国家重点实验室长沙410073 蛋白质组学国家重点实验室北京蛋白质组研究中心军事医学科学院放射与辐射医学研究所北京102206 复旦大学生物医学科学研究所上海200032

由高通量微阵列技术产生的数据集可以用于解释生物系统基因调控的未知机制.生物过程是动态的,所以很有必要关注某些条件下特异的基因调控子网络.细胞周期是一个基本的细胞过程,识别酵母的细胞周期特异调控子网是理解细胞周期过程的基础... 详细信息

由高通量微阵列技术产生的数据集可以用于解释生物系统基因调控的未知机制.生物过程是动态的,所以很有必要关注某些条件下特异的基因调控子网络.细胞周期是一个基本的细胞过程,识别酵母的细胞周期特异调控子网是理解细胞周期过程的基础,并且有助于揭示其他细胞条件的基因调控机理.使用一个基因表达微分方程模型(GEDEM),从静态网络中识别了动态的细胞周期相关调控关系.与已经报道的细胞周期相关调控相互作用相比,该方法识别了更多的真实存在的条件特异调控关系,取得了比当前的方法更好的性能.在大数据集上,GEDEM 识别了具有高敏感性和特异性的调控子网.组合调控的深入分析显示,条件特异调控子网的转录因子之间的相关性呈现出比静态网络中转录因子相关性更强,这说明条件特异网络比静态网络更加接近真实情况.另外,GEDEM 方法还识别更多潜在的共调控转录因子.

关键词：基因调控网络细胞周期基因表达模型条件特异子网微分方程模型

Microbiota enterotoxigenic Bacteroides fragilis-secreted BFT-1 promotes breast cancer cell stemness and chemoresistance through its functional receptor NOD1

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Protein & Cell 2024年第6期15卷 419-440页

作者： Wei Ma Lu Zhang Weilong Chen Zhaoxia Chang Juchuanli Tu Yuanyuan Qin Yuwen Yao Mengxue dong Jiajun Ding Siqin Li Fengkai Li Qiaodan Deng Yifei yang Tingting Feng Fanrong Zhang Xiying Shao Xueyan he Lixing Zhang Guohong Hu Quentin Liu Yi-Zhou jiang Shu Zhu Zhi Xiao Dan Su Tong Liu Suling Liu Fudan University Shanghai Cancer center & institutes of Biomedical Sciences State Key Laboratory of Genetic EngineeringCancer InstitutesDepartment of OncologyKey Laboratory of Breast Cancer in ShanghaiThe Shanghai Key Laboratory of Medical EpigeneticsShanghai Key Laboratory of Radiation OncologyThe International Co-laboratory of Medical Epigenetics and MetabolismMinistry of Science and TechnologyShanghai Medical CollegeFudan UniversityShanghai 200032China Intelligent Pathology institute and Department of Pathology The First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230071China Department of Thyroid Breast and Vascular SurgeryXijing HospitalFourth Military Medical UniversityXi’an 710032China institute of Immunology CAS Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei 230027China Department of Pathology The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital)Institute of Basic Medicine and Cancer (IBMC)Chinese Academy of SciencesHangzhou 310022China Department of Breast Surgery The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital)Institute of Basic Medicine and Cancer (IBMC)Chinese Academy of SciencesHangzhou 310022China Department of Breast Medical Oncology The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital)Institute of Basic Medicine and Cancer (IBMC)Chinese Academy of SciencesHangzhou 310022China Shanghai institute of Nutrition and health University of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China Sun Yat-sen University Cancer center State Key Laboratory of Oncology in South ChinaGuangzhou 510060China Department of Breast Surgery Xiangya HospitalChangsha 410008China Department of Breast Surgery Tumor Hospital of Harbin Medic

Tumor-resident microbiota in breast cancer promotes cancer initiation and malignant ***,targeting microbiota to improve the effects of breast cancer therapy has not been investigated in ***,we evaluated the microbiota composition of breast tumors and found that enterotoxigenic Bacteroides fragilis(ETBF)was highly enriched in the tumors of patients who did not respond to taxane-based neoadjuvant ***,albeit at low biomass,secreted the toxic protein BFT-1 to promote breast cancer cell stemness and *** studies showed that BFT-1 directly bound to NOD1 and stabilized NOD1 ***1 was highly expressed on ALDH+breast cancer stem cells(BCSCs)and cooperated with GAK to phosphorylate NUMB and promote its lysosomal degradation,thereby activating the NOTCH1-heY1 signaling pathway to increase ***1 inhibition and ETBF clearance increase the chemosensitivity of breast cancer by impairing BCSCs.

关键词： NOD1 breast chemotherapy

Frontiers in high entropy alloys and high entropy functional materials

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Rare Metals 2024年第10期43卷 4639-4776页

作者： Wen-Tao Zhang Wen Huang Fu-Jie Yu Qi Zhao Xin-dong Zhu Tao Feng Yao jiang Xiao-Ming Li Xue-Fei Miao he Zhu Si Lan Xue-Qian Wang Bao-Long Shen Zhe Jia Feng-Qi Zhang Wei Wang Qi Liu yang Ren Xun-Li Wang Xiao-Ya Cui Xiao-yang Wang Ya-Nan Chen Bing-Bing Fan Meng-Ru Li Qi-Long Gao Jia-Ming Guo Zeng-Bao Jiao Zhi-Min Guo Yu-Ping Zhao Qian Yu Rui Huang Ling-Kun Zhang Yi-Ping Lu Xu-Bo Li Huai-Jun Lin Yan Ma Wei-Ming yang Zhi-Hua Shen Hai-Yan he Yong-Gang Sun Yong-jiang Huang De-Zhuang Wang Qing-Feng Liu Fei-yang Wang Hui Liu Hong-Hui Wu Li-Qiang Wang yang Lu Nan Wang Tian-Li Wang Wei-Bing Liao Yi-Han Wang Yuan Wu Yu-Zhen Yin Jie Pan Yi Zhang Qing Wang Jian-yang Zhang Tao yang Yasir Sohail Jin-Yu Zhang Hua Ji Qiang Li Wei-Di Liu Zhi-Gang Chen Xiong-Jun Liu Wen Ma Liang Mao Zhen-Duo Wu School of Materials Science and Engineering Nanjing University of Science and Technology jiangsu key laboratory for Advanced Metallic Materials School of Materials Science and Engineering Southeast University Department of Physics City University of Hong Kong School of Materials Science and Engineering Tianjin University School of Physics and Microelectronics Zhengzhou University Department of Mechanical Engineering Research Institute for Advanced Manufacturing The Hong Kong Polytechnic University center of Electron Microscopy and state key laboratory of Silicon Materials School of Materials Science and Engineering Zhejiang University key laboratory of Solidification Control and Digital Preparation Technology (Liaoning Province) School of Materials Science and Engineering Dalian University of Technology institute of Advanced Wear & Corrosion Resistance and Functional Materials Jinan University School of Mechanics and Civil Engineering China University of Mining and Technology School of Physical Sciences Great Bay University School of Materials Science andEngineering Harbin Institute of Technology state key laboratory of Materials-Oriented Chemical Engineering College of Chemical Engineering Nanjing Tech University beijing Advanced Innovation center for Materials Genome Engineering Research Institute for Carbon Neutrality University of Science and Technology Beijing Department of Mechanical Engineering The University of Hong Kong School of Computing Macquarie University key laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province College of Physics and Optoelectronic Engineering Shenzhen University state key laboratory for Advanced Metals and Materials University of Science and Technology Beijing state key laboratory of Materials Processing and Die & Mould Technology School of Materials Science and Engineering Huazhong University of Science and Technology institute of materials Shanghai University Department of Materials Science and Engineering C

Owing to their exceptional properties, high-entropy alloys(heAs) and high-entropy materials have emerged as promising research areas and shown diverse applications. here,the recent advances in the field are comprehensively reviewed,organized into five sections. The first section introduces the background of heAs, covering their definition, significance,application prospects, basic properties, design principles, and microstructure. The subsequent section focuses on cutting-edge high-entropy structural materials, highlighting developments such as nanostructured alloys, grain boundary engineering,eutectic systems, cryogenic alloys, thin films, micro-nano-lattice structures, additive manufacturing, high entropy metallic glasses, nano-precipitate strengthened alloys, composition modulation, alloy fibers, and refractory systems. In the following section, the emphasis shifts to functional materials, exploring heAs as catalysts, magneto-caloric materials, corrosion-resistant alloys, radiation-resistant alloys, hydrogen storage systems, and materials for biomedicine. Additionally, the review encompasses functional high-entropy materials outside the realm of alloys, including thermoelectric, quantum dots, nanooxide catalysts, energy storage materials, negative thermal expansion ceramics,and high-entropy wave absorption materials. The paper concludes with an outlook, discussing future directions and potential growth areas in the field. Through this comprehensive review,researchers, engineers, and scientists may gain valuable insights into the recent progress and opportunities for further exploration in the exciting domains of high-entropy alloys and functional materials.

关键词： Cutting-edge structural materials Cutting-edgefunctional materials High entropy alloys

Plasma biomarker screening for liver fibrosis with the N-terminal isotope tagging strategy

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Science china(Life Sciences) 2011年第5期54卷 393-402页

作者： LI ShuLong LIU Xin WEI Lai WANG HuiFen ZHANG Jiyang WEI Handong QIAN XiaoHong jiang ying he fuchu state key laboratory of proteomics Beijing Proteome Research Center Beijing Institute of Radiation Medicine Beijing 102206 China beijing institute of Biotechnology Beijing 100071 China People 's Hospital of Peking University Beijing 100044 China 302 Military Hospital of china Beijing 100039 China institutes of Biomedical Sciences Fudan University Shanghai 200032 China Central laboratory Yantai Yu-Huang-Ding Hospital Yantai 264000 China

A non-invasive diagnostic approach is crucial for the evaluation of severity of liver disease,treatment decisions,and assessing drug *** study evaluated plasma proteomic profiling via an N-terminal isotope tagging strategy coupled with liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry measurement to detect liver fibrosis *** plasma from different liver fibrosis stages,which were assessed in advance by the current gold-standard of liver biopsy,was quantitatively analyzed.A total of 72 plasma proteins were found to be dysregulated during the fibrogenesis process,and this finding constituted a valuable candidate plasma biomarker bank for follow-up *** results of fibronectin by Western blotting reconfirmed the mass-based *** Pathways Analysis showed four types of metabolic networks for the functional effect of liver fibrosis disease in chronic hepatitis B ***,quantitative proteomics via the N-terminal acetyl isotope labeling technique provides an effective and useful tool for screening plasma candidate biomarkers for liver *** quantitatively monitored the fibrogenesis process in CHB *** discovered many new valuable candidate biomarkers for the diagnosis of liver fibrosis and also partly identified the mechanism involved in liver fibrosis *** results provide a clearer understanding of liver fibrosis pathophysiology and will also hopefully lead to improvement of clinical diagnosis and treatment.

关键词： quantitative proteomics fiver fibrosis biomarker plasma hepatitis B virus

General trends of protein expression and localization reveal the rule of bio-complexity realization

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General trends of protein expression and localization reveal...

A Yeast BiFC-seq Method for Genome-wide Interactome Mapping

第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者：杨冬 Dingchen Li Fan Zhong dong Li ying jiang fuchu he state key laboratory of proteomics Beijing Proteome Research CenterBeijing Institute of Radiation Medicine institutes of Biomedical Sciences and Department of Chemistry Fudan University

Background:During evolution,proteins containing newly emerged domains and the increasing proportion of multi-domain proteins in the full Genome-Encoded proteome(GEP) have substantially contributed to increasing biological ***,it is not known how these two potential structural factors are preferentially utilized at given physiological states,until our most recent study found that multidomain proteins or only older domain- containing proteins are significantly overrepresented in certain-state proteomes(CSPs,i.e., all the proteins expressed at certain physiological states) compared with GEP,which indicates biological complexity under certain conditions is more significantly realized by diverse domain organization than by the emergence of new types of *** further explore the regular utilization pattern in the view of protein spatial distribution at levels ranging from organelles to organs,we investigated the relationships between protein domain characters and protein subcelluar localization width(SLW) or tissue specificity(TS). Methods:To calculate SLW,we collected high confident subcellular location information in Swiss-Prot,GOA,human protein atlas(HPA),MitoP2,Human Liver Organelle proteome(HLOP) and related references and *** identification is based on RPS-BLAST against Pfam and SMART(Ehe number of OTCs (organ,tissue or cell types) in which the gene is expressed. Results:The integrated atlas contains subcellular localization information with high confidence of more than 13000 human proteins,including the subcellular locations for different splice isoforms as complete as *** on this atlas,we found that SLW positively correlates with DN value,while it negatively correlates with DA value,that is, multi-domain proteins or only older domain-containing proteins tend to be localized at more subcellular *** addition,SLW negatively correlate with TS,*** with more subcellular location

关键词： Biological complexity protein domain proteome subcellular localization tissue specificity

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Genomics, proteomics & Bioinformatics 2022年第4期20卷 795-807页

作者： Limin Shang Yuehui Zhang Yuchen Liu Chaozhi Jin Yanzhi Yuan Chunyan Tian Ming Ni Xiaochen Bo Li Zhang dong Li fuchu he Jian Wang state key laboratory of proteomics Beijing Proteome Research CenterNational Center for Protein Sciences(Beijing)Beijing Institute of LifeomicsBeijing 102206China Department of Biotechnology Beijing Institute of Radiation MedicineBeijing 100850China Department of Rehabilitation medicine Nan LouKey Laboratory of Wound Repair and Regeneration of PLACollege of Life SciencesChinese PLA General HospitalBeijing 100853China School of Basic Medical Sciences Anhui Medical UniversityHefei 230032China

Genome-wide physical protein±protein interaction(PPI)mapping remains a major challenge for current ***,we reported a high-efficiency BiFC-seq method,yeastenhanced green fluorescent protein-based bimolecular fluorescence complementation(y EGFPBiFC)coupled with next-generation DNA sequencing,for interactome *** first applied y EGFP-BiFC method to systematically investigate an intraviral network of the Ebola ***-thirds(9/14)of known interactions of EBOV were recaptured,and five novel interactions were ***,we used the BiFC-seq method to map the interactome of the tumor protein *** identified 97 interactors of p53,more than three-quarters of which were ***,in a more complex background,we screened potential interactors by pooling two BiFC libraries together and revealed a network of 229 interactions among 205 *** results show that BiFC-seq is a highly sensitive,rapid,and economical method for genome-wide interactome mapping.

关键词： Bimolecular fluorescence complementation Protein–protein interaction High-throughput Next-generation sequencing

Low operating voltage memtransistors based on ion bombarded p-type GeSe nanosheets for artificial synapse applications

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InfoMat 2023年第12期5卷 54-64页

作者： Jing Wang dong he Rui Chen Hang Xu Hongbo Wang Menghua yang Qi Zhang Changzhong jiang Wenqing Li Xiaoping Ouyang Xiangheng Xiao Department of Physics Wuhan UniversityWuhanHubeithe People's Republic of China state key laboratory of Intense Pulsed radiation Simulation and Effect Northwest Institute of Nuclear TechnologyXi'anShanxithe People's Republic of China Wuhan research center for Infectious Diseases and Cancer Chinese Academy of Medical SciencesWuhanthe People's Republic of China

Two-dimensional(2D)layered materials have many potential applications in memristors owing to their unique atomic structures and electronic *** can overcome the in-memory bottleneck for use in brain-like neuromorphic ***,exploiting additional lateral memtransistors based on 2D layered materials remains *** are few studies on p-type semiconductors that have not been theoretically *** this study,a lateral memtransistor based on p-type GeSe nanosheets is investigated.A threeterminal GeSe memtransistor that modulated the interfacial barrier height was fabricated using low-energy ion irradiation;the memtransistor exhibited a low operating *** memtransistor successfully mimics biological synapse,including neuroplasticity functions,such as short-term plasticity,long-term plasticity,paired-pulse facilitation,and spike-timing-dependent *** mechanism of interfacial modulation was verified by experimental results and theoretical *** results show that it is feasible to modulate the interface of 2D GeSe nanosheets using low-energy ion irradiation to realize a lateral *** may provide promising opportunities for artificial neuromorphic system applications based on 2D layered materials.

关键词： artificial synapses GeSe nanosheet interfacial modulation low-energy ion irradiation memtransistor

RIOX1-demethylated cGAS regulates ionizing radiation-elicited DNA repair

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Bone research 2022年第2期10卷 367-377页

作者： Yanxuan Xiao Jingyi Li Xiaoyu Liao Yumin he Tao he Cuiping yang Lu jiang So Mi Jeon Jong-Ho Lee Yongbin Chen Rui Liu Qianming Chen state key laboratory of Oral Diseases National Clinical Research Center for Oral DiseasesChinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and ManagementWest China Hospital of StomatologySichuan UniversityChengduSichuan 610041China The Second Affiliated Hospital of Chengdu Medical College China National Nuclear Corporation 416 HospitalChengduSichuan 610051China School of Biological Sciences and Technology Chengdu Medical CollegeChengdu 610599China Department of Cardio-thoracic Surgery the Second Affiliated Hospital of Chengdu Medical CollegeChina National Nuclear Corporation 416 HospitalChengduSichuan 610051China key laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences Yunnan Province Kunming Institute of ZoologyKunmingYunnan 650223China Department of health Sciences The Graduate School of Dong-A UniversityBusan 49315Republic of Korea Department of Biological Sciences Dong-A UniversityBusan 49315Republic of Korea center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China

Exposure to radiation causes DNA damage;hence, continuous surveillance and timely DNA repair are important for genome stability. Epigenetic modifications alter the chromatin architecture, thereby affecting the efficiency of DNA repair. However, how epigenetic modifiers coordinate with the DNA repair machinery to modulate cellular radiosensitivity is relatively unknown. here, we report that loss of the demethylase ribosomal oxygenase 1(RIOX1) restores cell proliferation and reduces cell death after exposure to ionizing radiation. Furthermore, RIOX1 depletion enhances homologous recombination(HR) repair but not nonhomologous endjoining(NheJ) repair in irradiated bone marrow cells and oral mucosal epithelial cells. Mechanistic study demonstrates that RIOX1 removes monomethylation at K491 of cyclic GMP-AMP synthase(c GAS) to release c GAS from its interaction with the methyl-lysine reader protein SAGA complex-associated factor 29(SGF29), which subsequently enables c GAS to interact with poly(ADP-ribosyl)ated poly(ADP-ribose) polymerase 1(PARP1) at DNA break sites, thereby blocking PARP1-mediated recruitment of Timeless. High expression of RIOX1 maintains c GAS K491 me at a low level, which impedes HR repair and reduces cellular tolerance to ionizing radiation. This study highlights a novel RIOX1-dependent mechanism involved in the non-immune function of c GAS that is essential for the regulation of ionizing radiation-elicited HR repair.

关键词： thereby repair remove