Investigating the genetic and developmental characteristics,infection transmission attributes,and epidemiological trends of pathogens using genomic data represents the foundation for pathogen surveillance and is a cru...Investigating the genetic and developmental characteristics,infection transmission attributes,and epidemiological trends of pathogens using genomic data represents the foundation for pathogen surveillance and is a crucial prerequisite for guaranteeing global health security.To meet the analytical demands of research relating to pathogen prevention and control,we designed a secure visualization system capable of pathogen genome assembly,annotation,species identification,sequence typing,antibiotic resistance and virulence analysis,genomic mobile element and transferable resistance gene annotation,and phylogenetic tree reconstruction.For highly pathogenic organisms requiring complete data protection,we have developed a secure computing tool that utilizes a trusted execution environment,is combined with blockchain and privacy computing technologies,and is specifically designed for nucleotide basic local alignment search tool(BLASTn)comparison analysis.This technological advancement offers scientific support for in‐depth investigations into pathogen transmission and epidemiological mechanisms,environmental adaptability,evolutionary trends,and immune evasion mechanisms,as well as the identification of new or emerging pathogen strains.This,in turn,aids efforts in infectious disease prevention,treatment,and research.展开更多
Background of database.Organ degeneration refers to the gradual decline in organ function and structure deterioration that occurs during aging,which represents the greatest risk factor for various degenerative disease...Background of database.Organ degeneration refers to the gradual decline in organ function and structure deterioration that occurs during aging,which represents the greatest risk factor for various degenerative diseases,including cardiovascular diseases,neurodegenerative diseases,and osteoarthritis,etc.(Aging Biomarker et al.,2023;Becker et al.,2018;Cai et al.,2022).展开更多
Advanced satellite tracking technologies provide biologists with long-term location sequence data to understand movement of wild birds then to find explicit correlation between dynamics of migratory birds and the spre...Advanced satellite tracking technologies provide biologists with long-term location sequence data to understand movement of wild birds then to find explicit correlation between dynamics of migratory birds and the spread of avian influenza. In this paper, we propose a hierarchical clustering algorithm based on a recursive grid partition and kernel density estimation （KDE） to hierarchically identify wild bird habitats with different densities. We hierarchically cluster the GPS data by taking into account the following observations： 1） the habitat variation on a variety of geospatial scales; 2） the spatial variation of the activity patterns of birds in different stages of the migration cycle. In addition, we measure the site fidelity of wild birds based on clustering. To assess effectiveness, we have evaluated our system using a large-scale GPS dataset collected from 59 birds over three years. As a result, our approach can identify the hierarchical habitats and distribution of wild birds more efficiently than several commonly used algorithms such as DBSCAN and DENCLUE.展开更多
Impact Statement We present a method of mapping data from publicly available genomics and publication resources to the Resource Description Framework(RDF)and implement a server to publish linked open data(LOD).As one ...Impact Statement We present a method of mapping data from publicly available genomics and publication resources to the Resource Description Framework(RDF)and implement a server to publish linked open data(LOD).As one of the largest and most comprehensive semantic databases about coronaviruses,the resulted gcCov database demonstrates the capability of using data in the LOD framework to promote correlations between genotypes and phenotypes.These correlations will be helpful for future research on fundamental viral mechanisms and drug and vaccine designs.展开更多
基金supported by National Key Research and Development Program of China,China(2021YFC2300900).
文摘Investigating the genetic and developmental characteristics,infection transmission attributes,and epidemiological trends of pathogens using genomic data represents the foundation for pathogen surveillance and is a crucial prerequisite for guaranteeing global health security.To meet the analytical demands of research relating to pathogen prevention and control,we designed a secure visualization system capable of pathogen genome assembly,annotation,species identification,sequence typing,antibiotic resistance and virulence analysis,genomic mobile element and transferable resistance gene annotation,and phylogenetic tree reconstruction.For highly pathogenic organisms requiring complete data protection,we have developed a secure computing tool that utilizes a trusted execution environment,is combined with blockchain and privacy computing technologies,and is specifically designed for nucleotide basic local alignment search tool(BLASTn)comparison analysis.This technological advancement offers scientific support for in‐depth investigations into pathogen transmission and epidemiological mechanisms,environmental adaptability,evolutionary trends,and immune evasion mechanisms,as well as the identification of new or emerging pathogen strains.This,in turn,aids efforts in infectious disease prevention,treatment,and research.
基金This work was supported by the National Key Research and Development Program of China(2020YFA0112200,2020YFA0804000,2022YFA1103700,the STI2030-Major Projects-2021ZD0202400,2021YFF1201000)the National Natural Science Foundation of China(81921006,82125011,92149301)+9 种基金the Informatization Plan of Chinese Academy of Sciences(CAS-WX2022SDC-XK14,CASWX2021SF-0301,CAS-WX2021SF-0101)the National Natural Science Foundation of China(92168201,91949209,92049304,82271600,82322025,32000500,92049116,32121001,82192863,82122024,82071588)CAS Project for Young Scientists in Basic Research(YSBR-076,YSBR-012)the Program of the Beijing Natural Science Foundation(Z230011)New Cornerstone Science Foundation through the XPLORER PRIZE(2021-1045)Young Elite Scientists Sponsorship Program by CAST(2021QNRC001)Youth Innovation Promotion Association of CAS(2022083,E1CAZW0401)Excellent Young Talents Program of Capital Medical University(12300927)The Project for Technology Development of Beijing-affiliated Medical Research Institutes(11000023T000002036310)Excellent Young Talents Training Program for the Construction of Beijing Municipal University Teacher Team(BPHR202203105).
文摘Background of database.Organ degeneration refers to the gradual decline in organ function and structure deterioration that occurs during aging,which represents the greatest risk factor for various degenerative diseases,including cardiovascular diseases,neurodegenerative diseases,and osteoarthritis,etc.(Aging Biomarker et al.,2023;Becker et al.,2018;Cai et al.,2022).
文摘Advanced satellite tracking technologies provide biologists with long-term location sequence data to understand movement of wild birds then to find explicit correlation between dynamics of migratory birds and the spread of avian influenza. In this paper, we propose a hierarchical clustering algorithm based on a recursive grid partition and kernel density estimation （KDE） to hierarchically identify wild bird habitats with different densities. We hierarchically cluster the GPS data by taking into account the following observations： 1） the habitat variation on a variety of geospatial scales; 2） the spatial variation of the activity patterns of birds in different stages of the migration cycle. In addition, we measure the site fidelity of wild birds based on clustering. To assess effectiveness, we have evaluated our system using a large-scale GPS dataset collected from 59 birds over three years. As a result, our approach can identify the hierarchical habitats and distribution of wild birds more efficiently than several commonly used algorithms such as DBSCAN and DENCLUE.
基金supported by the National Key Research Program of China(grant no.2019YFE0191000)the 13th Five-year Informatization Plan of the Chinese Academy of Sciences(grant nos.XXH13506,XXH13505)the National Science Foundation for Young Scientists of China(grant no.31701157).
文摘Impact Statement We present a method of mapping data from publicly available genomics and publication resources to the Resource Description Framework(RDF)and implement a server to publish linked open data(LOD).As one of the largest and most comprehensive semantic databases about coronaviruses,the resulted gcCov database demonstrates the capability of using data in the LOD framework to promote correlations between genotypes and phenotypes.These correlations will be helpful for future research on fundamental viral mechanisms and drug and vaccine designs.
