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REMARKS ON NETWORK COMMUNITY PROPERTIES

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Journal of Systems Science & Complexity 2008年第4期21卷 637-644页

作者： jiguang wang Yuqing QIU Ruisheng wang Xiangsun ZHANG Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 China Graduate University of the Chinese Academy of Sciences Beijing 100049 China. School of Information Renmin University of China Beijing 100872 China. Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 China.

This paper discusses a popular community definition in complex network research in terms of the conditions under which a community is minimal, that is, the community cannot be split into several smaller communities or split and reorganized with other network elements into new communities. The result provides a base on which further optimization computation of the quantitative measure for community identification can be realized.

关键词： Community complex network modularity modularity density.

RECOGNITION OF STRUCTURE SIMILARITIES IN PROTEINS

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Journal of Systems Science & Complexity 2008年第4期21卷 665-675,F0003页

作者： Lin wang Yuqing QIU jiguang wang Xiangsun ZHANG Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 China Graduate School of the Chinese Academy of Sciences Beijing 100049 China. Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 China.

Protein fold structure is more conserved than its amino acid sequence and closely associated with biological function, so calculating the similarity of protein structures is a fundamental problem in structural biology and plays a key role in protein fold classification, fold function inference, and protein structure prediction. Large progress has been made in recent years in this field and many methods for considering structural similarity have been proposed, including methods for protein structure comparison, retrieval of protein structures from databases, and ligand binding site comparison. Most of those methods can be available on the World Wide Web, but evaluation of all the methods is still a hard problem. This paper summarizes some popular methods and latest methods for structure similarities, including structure alignment, protein structure retrieval, and ligand binding site alignment.

关键词： Binding site alignment circular permutations flexible alignment protein structure alignment protein structure retrieval.

Depressing defocusing effect in microscopy by bi-orthogonal wavelet transform

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Particuology 2012年第5期10卷 644-647页

作者： Hequan Sun jiguang wang Ruoli Shao Department of Military Oceanography Dalian Naval AcademyDalian 116018China Design Institute of Civil Engineering and Architecture Dalian University of TechnologyDalian 116023China

For different dimensions, heights and irregular shapes, small and large particles cannot be viewed simultaneously as sharp images under the microscope due to optical defocusing effects. Bi-orthogonal wavelet transform is used in this paper to depress such defocusing effect by merging the wavelet coefficients of the image series. The algorithm is presented in detail, using SWE（13,7） and CDF（2,2）, and a few particle images are provided to validate the proposed method.

关键词： Defocusing effectWavelet transformBi-orthogonal waveletCDF(2.2)SWE( 13 7 )

Deciphering Brain Complexity Using Single-cell Sequencing

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Genomics, Proteomics & Bioinformatics 2019年第4期17卷 344-366页

作者： Quanhua Mu Yiyun Chen jiguang wang Department of Chemical and Biological Engineering Division of Life Science Center for Systems Biology and Human Health and State Key Laboratory of Molecular Neuroscience The Hong Kong University of Science and Technology

The human brain contains billions of highly differentiated and interconnected cells that form intricate neural networks and collectively control the physical activities and high-level cognitive functions,such as memory,decision-making,and social *** data is required to decipher the complexity of cell types,as well as connectivity and functions of the *** newly developed single-cell sequencing technology,which provides a comprehensive landscape of brain cell type diversity by profiling the transcriptome,genome,and/or epigenome of individual cells,has contributed substantially to revealing the complexity and dynamics of the brain and providing new insights into brain development and brain-related *** this review,we first introduce the progresses in both experimental and computational methods of single-cell sequencing *** of single-cell sequencing-based technologies in brain research,including cell type classification,brain development,and brain disease mechanisms,are then elucidated by representative ***,we provided our perspectives into the challenges and future developments in the field of single-cell *** summary,this mini review aims to provide an overview of how big data generated from single-cell sequencing have empowered the advancements in neuroscience and shed light on the complex problems in understanding brain functions and diseases.

关键词： Neuroscience Single-cell RNA-seq Cell type Brain development Brain diseases

Real-world gaseous emission characteristics of natural gas heavy-duty sanitation trucks

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Journal of Environmental Sciences 2022年第5期34卷 319-329页

作者： jiguang wang Huaqiao Gui Zhiwen Yang Tongzhu Yu Xiaowen Zhang Jianguo Liu Key Laboratory of Environmental Optics and Technology Anhui Institute of Optics and Fine MechanicsChinese Academy of SciencesHefei 230031China University of Science and Technology of China Hefei 230026China China Automotive Technology and Research Center Co. LtdTianjin 300300China Innovation excellence center for urban atmospheric environment Institute of Urban EnvironmentChinese Academy of SciencesXiamen 361021China

As compared to conventional diesel heavy-duty vehicles,natural gas vehicles have been proved to be more eco-friendly due to their lower production of greenhouse gas and pollu-tant emissions,which are causing enormous adverse effects on global warming and air ***,natural gas vehicles were rarely studied before,especially through on-road *** this study,a portable emission measurement system(PEMS)was em-ployed to investigate the real-world emissions of nitrogen oxides(NO_(x))(nitrogen monoxide(NO),nitrogen dioxide(NO_(2))),total hydrocarbons(THC),carbon monoxide(CO),and carbon dioxide(CO_(2))from two liquified natural gas(LNG)China V heavy-duty cleaning sanitation trucks with different *** with the more aggressive driving behaviors,the ve-hicle with lower weight exhibited higher CO_(2)(3%)but lower NO_(x)(48.3%)(NO_(2)(78.2%)and NO(29.4%)),CO(44.8%),and THC(3.7%)emission *** driving behaviors were also favorable to the production of THC,especially those in the medium-speed range but sig-nificantly negative to the production of CO and NO_(2),especially those in the low-speed range with high engine *** particular,the emission rate ratio of NO_(2)/NO decreased with the increase of speed/scaled tractive power in different speed ranges.

关键词： Natural gas sanitation vehicle PEMS Gaseous pollutant emission

Intratumor heterogeneity,microenvironment,and mechanisms of drug resistance in glioma recurrence and evolution

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Frontiers of Medicine 2021年第4期15卷 551-561页

作者： Zhaoshi Bao Yongzhi wang Qiangwei wang Shengyu Fang Xia Shan jiguang wang Tao Jiang Beijing Neurosurgical Institute Capital Medical UniversityBeijing 100050China Department of Neurosurgery Beijing Tiantan HospitalCapital Medical UniversityBeijing 100050China Divison of Life Science Department of Chemical and Biological EngineeringCenter for Systems Biology and Human Healthand State Key Laboratory of Molecular NeuroscienceThe Hong Kong University of Science and TechnologyHong KongChina China National Clinical Research Center for Neurological Diseases Beijing 100050China Division of Life Science Hong Kong University of Science and TechnologyHong KongChina Center of Brain Tumor Beijing Institute for Brain DisordersBeijing 100069China Department of Radiotherapy Beijing Tiantan HospitalCapital Medical UniversityBeijing 100050China

Glioma is the most common lethal tumor of the human *** median survival of patients with primary World Health Organization grade IV glioma is only 14.6 *** World Health Organization classification of tumors of the central nervous system categorized gliomas into lower-grade gliomas and *** primary glioblastoma that usually develop de novo in the elderly,secondary glioblastoma enriched with an isocitrate dehydrogenase mutant typically progresses from lower-grade glioma within 5-10 years from the time of *** on various evolutional trajectories brought on by clonal and subclonal alterations,the evolution patterns of glioma vary according to different *** important features distinguish the normal brain from other tissues,e.g.,the composition of the microenvironment around the tumor cells,the presence of the blood-brain barrier,and *** underlying mechanism of glioma recurrence and evolution patterns of glioma are different from those of other types of *** studies correlated tumor recurrence with tumor heterogeneity and the immune ***,the detailed reasons for the progression and recurrence of glioma remain *** this review,we introduce the different mechanisms involved in glioma progression,including tumor heterogeneity,the tumor microenvironment and drug resistance,and their pre-clinical implements in clinical *** review aimed to provide new insights into further clinical strategies for the treatment of patients with recurrent and secondary glioma.

关键词： glioma evolution mechanism strategies tumor heterogeneity secondary glioma

An information theoretic method to identify combinations of genomic alterations that promote glioblastoma

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Journal of Molecular Cell Biology 2015年第3期7卷 203-213页

作者： Rachel D.Melamed jiguang wang Antonio Iavarone Raul Rabadan Department of Systems Biology Columbia University College of Physicians and SurgeonsNew YorkNYUSA Department of Biomedical Informatics Columbia University College of Physicians and SurgeonsNew YorkNYUSA Institute for Cancer Genetics Columbia University College of Physicians and SurgeonsNew YorkNYUSA Department of Pathology and Cell Biology Columbia University College of Physicians and SurgeonsNew YorkNYUSA Department of Neurology Columbia University College of Physicians and SurgeonsNew YorkNYUSA

Tumors are the result of accumulated genomic alterations that cooperate synergistically to produce uncontrollable cell *** identifying recurrent alterations among large collections of tumors provides a way to pinpoint genes that endow a selective advantage in oncogenesis and progression,it fails to address the genetic interactions behind this selection process.A non-random pattern of co-mutated genes is evidence for selective forces acting on tumor cells that harbor combinations of these genetic *** existing methods have successfully identified mutually exclusive gene sets,no current method can systematically discover more general genetic *** develop Genomic Alteration Modules using Total Correlation(GAMToC),an information theoretic frameworkthat integrates copynumberandmutation datato identify genemodules with any non-randompattern of joint ***,wepresent theSeed-GAMToCprocedure,which uncoversthe mutational context of any putative cancer *** software is publicly *** to glioblastoma multiforme samples,GAMToC results show distinct subsets of co-occurring mutations,suggesting distinct mutational routes to cancer and providing new insight into mutations associated with proneural,proneural/G-CIMP,and classical types of the *** results recapitulate known relationships such as mutual exclusive mutations,place these alterations in the context of other mutations,and find more complex relationships such as conditional mutual exclusivity.

关键词： genomics sequencing entropy copy number cancer cancer genetics

Optimal decision-making considering inter-supply-chain competition and negative-spillover from environmental effort

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Regional Sustainability 2022年第4期3卷 319-334页

作者： wang jiguang HU Yushang WU Yucai School of Economics and Management Shanxi UniversityTaiyuan030006China School of Business Administration Shanxi University of Finance and EconomicsTaiyuan030006China

Focusing on negative-spillover from environmental effort,this paper explores the issues of competition and optimal decision-making based on two competing two-stage manufacturer-dominated supply chains:centralized and *** develop the Stackelberg competition models according to four identified competition scenarios(pure centralized structure-CC,mixed structure-DC,mixed structure-CD,and pure decentralized structure-DD).By comparing the results of the four scenarios,we find that negative-spillover from environmental effort negatively impacts environmental-effort providers and reduces the optimal profit of the manufacturer who provide the environmental effort,which in turn reduces the profit of the entire supply *** inter-supply-chain competition also produces a negative incentive for environmental-effort providers but provides a free riding effect on the non-provider,and this effect increases as competition *** terms of network externality,the structural change of a supply chain from centralized to decentralized is altruistic,which generates a double-marginalization(i.e.,the network externality enhances competitor performance).Furthermore,the leader supply chain with a centralized structure is more willing to provide greater environmental effort,whereas when the leader supply chain structure remains unchanged,its environmental effort depends on the negative-spillover effect and the follower supply chain ***,excessive supply chain competition should be avoided,and the negative-spillover effect of environmental effort should be reduced to motivate environmental-effort providers to increase their environmental efforts and promote the development of sustainable green supply *** research should examine retailer-dominated supply chain competition and compare the results with the conclusions of this study.

关键词： Supply chain management Environmental effort Negative-spillover effect Inter-supply-chain competition Manufacturer-dominated supply chain Centralized Decentralized Stackelberg game

CELLO:a longitudinal data analysis toolbox untangling cancer evolution

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Quantitative Biology 2020年第3期8卷 256-266页

作者： Biaobin Jiang Dong Song Quanhua Mu jiguang wang Department of Chemical and Biological Engineering The Hong Kong University of Science and Tech no logyHong KongChina Division of Life Science The Hong Kong University of Science and TechnologyHong KongChina Center of Systems Biology and Human Health The Hong Kong University of Science and TechnologyHong KongChina State Key Laboratory of Molecular Neuroscienee The Hong Kong University of Science and TechnologyHong KongChina

The complex pattern of cancer evolution poses a huge challenge to precision *** sequencing of tumor samples allows us to monitor the dynamics of mutations that occurred during this clonal evolution ***,we present a versatile toolbox,namely CELLO(Cancer EvoLution for Longitudinal data),accompanied with a step-by-step tutorial,to exemplify how to profile,analyze and visualize the dynamic change of somatic mutational landscape using longitudinal genomic sequencing ***,we customize the hypermutation detection module in CELLO to adapt targeted-DNA and whole-transcriptome sequencing data,and verify the extensive applicability of CELLO in published longitudinal datasets from brain,bladder and breast *** entire tutorial and reusable programs in MATLAB,R and docker versions are open access at https://***/WaiigLabHKUST/CELLO.

关键词： cancer evolution genomics longitudinal sequencing bioinformatics