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  • Oxford University Press (OUP)  (4)
  • Biology  (4)
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  • Oxford University Press (OUP)  (4)
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  • Biology  (4)
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  • 1
    Online Resource
    Online Resource
    Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024
    Oxford University Press (OUP) ; 2024
    In:  Nucleic Acids Research Vol. 52, No. D1 ( 2024-01-05), p. D18-D32
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 52, No. D1 ( 2024-01-05), p. D18-D32
    Abstract: The National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support the global academic and industrial communities. With the rapid accumulation of multi-omics data at an unprecedented pace, CNCB-NGDC continuously expands and updates core database resources through big data archiving, integrative analysis and value-added curation. Importantly, NGDC collaborates closely with major international databases and initiatives to ensure seamless data exchange and interoperability. Over the past year, significant efforts have been dedicated to integrating diverse omics data, synthesizing expanding knowledge, developing new resources, and upgrading major existing resources. Particularly, several database resources are newly developed for the biodiversity of protists (P10K), bacteria (NTM-DB, MPA) as well as plant (PPGR, SoyOmics, PlantPan) and disease/trait association (CROST, HervD Atlas, HALL, MACdb, BioKA, BioKA, RePoS, PGG.SV, NAFLDkb). All the resources and services are publicly accessible at https://ngdc.cncb.ac.cn.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkad1078
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 186809-3
    detail.hit.zdb_id: 1472175-2
    SSG: 12
    Location Call Number Limitation Availability
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    Online Resource
  • 2
    Online Resource
    Online Resource
    Aging Atlas: a multi-omics database for aging biology
    Oxford University Press (OUP) ; 2021
    In:  Nucleic Acids Research Vol. 49, No. D1 ( 2021-01-08), p. D825-D830
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 49, No. D1 ( 2021-01-08), p. D825-D830
    Abstract: Organismal aging is driven by interconnected molecular changes encompassing internal and extracellular factors. Combinational analysis of high-throughput ‘multi-omics’ datasets (gathering information from genomics, epigenomics, transcriptomics, proteomics, metabolomics and pharmacogenomics), at either populational or single-cell levels, can provide a multi-dimensional, integrated profile of the heterogeneous aging process with unprecedented throughput and detail. These new strategies allow for the exploration of the molecular profile and regulatory status of gene expression during aging, and in turn, facilitate the development of new aging interventions. With a continually growing volume of valuable aging-related data, it is necessary to establish an open and integrated database to support a wide spectrum of aging research. The Aging Atlas database aims to provide a wide range of life science researchers with valuable resources that allow access to a large-scale of gene expression and regulation datasets created by various high-throughput omics technologies. The current implementation includes five modules: transcriptomics (RNA-seq), single-cell transcriptomics (scRNA-seq), epigenomics (ChIP-seq), proteomics (protein–protein interaction), and pharmacogenomics (geroprotective compounds). Aging Atlas provides user-friendly functionalities to explore age-related changes in gene expression, as well as raw data download services. Aging Atlas is freely available at https://bigd.big.ac.cn/aging/index.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkaa894
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 186809-3
    detail.hit.zdb_id: 1472175-2
    SSG: 12
    Location Call Number Limitation Availability
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    Online Resource
  • 3
    Online Resource
    Online Resource
    Combinations of Ghd7 , Ghd8 , and Hd1 determine strong heterosis of commercial rice hybrids in diverse ecological regions
    Oxford University Press (OUP) ; 2021
    In:  Journal of Experimental Botany Vol. 72, No. 20 ( 2021-10-26), p. 6963-6976
    Details
    In: Journal of Experimental Botany, Oxford University Press (OUP), Vol. 72, No. 20 ( 2021-10-26), p. 6963-6976
    Abstract: Heterosis of grain yield is closely associated with heading date in crops. Gene combinations of the major heading date genes Ghd7, Ghd8, and Hd1 play important roles in enhancing grain yield and adaptation to ecological regions in rice. However, the predominant three-gene combinations for a specific ecological region remain unclear in both three-line and two-line hybrids. In this study, we sequenced these three genes of 50 cytoplasmic male sterile/maintainer lines, 31 photo-thermo-sensitive genic male sterile lines, and 109 restorer lines. Sequence analysis showed that hybrids carrying strong functional alleles of Ghd7 and Hd1 and non-functional Ghd8 are predominant in three-line hybrids and are recommended for rice production in the subtropics around 30°N/S. Hybrids carrying strong functional Ghd7 and Ghd8 and non-functional Hd1 are predominant in two-line hybrids and are recommended for low latitude areas around 23.5°N/S rich in photothermal resources. Hybrids carrying strong functional Ghd7 and Ghd8 and functional Hd1 were not identified in commercial hybrids in the middle and lower reaches of the Yangtze River, but they have high yield potential in tropical regions because they have the strongest photoperiod sensitivity. Based on these findings, two genic sterile lines, Xiangling 628S and C815S, whose hybrids often head very late, were diagnosed with these three genes, and Hd1 was targeted to be knocked out in Xiangling 628S and replaced with hd1 in C815S. The hybrids developed from both modified sterile lines in turn had appropriate heading dates and significantly improved grain yield. This study provides new insights for breeding design to develop hybrids for various regions.
    Type of Medium: Online Resource
    ISSN: 0022-0957 , 1460-2431
    URL: Article
    DOI: 10.1093/jxb/erab344
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2976-2
    detail.hit.zdb_id: 1466717-4
    SSG: 12
    Location Call Number Limitation Availability
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    Online Resource
  • 4
    Online Resource
    Online Resource
    HALL: a comprehensive database for human aging and longevity studies
    Oxford University Press (OUP) ; 2024
    In:  Nucleic Acids Research Vol. 52, No. D1 ( 2024-01-05), p. D909-D918
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 52, No. D1 ( 2024-01-05), p. D909-D918
    Abstract: Diverse individuals age at different rates and display variable susceptibilities to tissue aging, functional decline and aging-related diseases. Centenarians, exemplifying extreme longevity, serve as models for healthy aging. The field of human aging and longevity research is rapidly advancing, garnering significant attention and accumulating substantial data in recent years. Omics technologies, encompassing phenomics, genomics, transcriptomics, proteomics, metabolomics and microbiomics, have provided multidimensional insights and revolutionized cohort-based investigations into human aging and longevity. Accumulated data, covering diverse cells, tissues and cohorts across the lifespan necessitates the establishment of an open and integrated database. Addressing this, we established the Human Aging and Longevity Landscape (HALL), a comprehensive multi-omics repository encompassing a diverse spectrum of human cohorts, spanning from young adults to centenarians. The core objective of HALL is to foster healthy aging by offering an extensive repository of information on biomarkers that gauge the trajectory of human aging. Moreover, the database facilitates the development of diagnostic tools for aging-related conditions and empowers targeted interventions to enhance longevity. HALL is publicly available at https://ngdc.cncb.ac.cn/hall/index.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkad880
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 186809-3
    detail.hit.zdb_id: 1472175-2
    SSG: 12
    Location Call Number Limitation Availability
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    Online Resource
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