蛋白结构域语义注解数据库

  工具概括

      研发了基于蛋白质超家族结构域（superfamily）的语义注解信息数据库dcGO（Nucleic Acids Research 2013）与开源分析软件dcGOR（PLoS Computational Biology 2014）,构建了基于结构域组学进化树并开展基因功能的进化研究（Biochimie 2015）。作为首个蛋白质结构域语义注解数据库与开源分析工具软件，该资源收录于维基百科全书条目（https://en.wikipedia.org/wiki/dcGO），其独立IP地址访问量为2千多次/月（数据出自ClustrMaps）。


  论文发表

    The dcGO domain-centric ontology database in 2023: new website and extended annotations for protein structural domains

    Journal of Molecular Biology 2023

    DOI: 10.1016/j.jmb.2023.168093

    Hypothesis-free phenotype prediction within a genetics-first framework

    Nature Communications 2023

    DOI: 10.1038/s41467-023-36634-6

    The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

    Genome Biology 2019

    DOI: 10.1186/s13059-019-1835-8

    An expanded evaluation of protein function prediction methods shows an improvement in accuracy

    Genome biology 2016

    DOI: 10.1186/s13059-016-1037-6

    XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits
    Access the recommendation on F1000Prime

    Genome Medicine 2016

    DOI: 10.1186/s13073-016-0384-y

    Evolution of the calcium-based intracellular signalling system

    Genome Biology and Evolution 2016

    DOI: 10.1093/gbe/evw139

    Function-selective domain architecture plasticity potentials in eukaryotic genome evolution

    Biochimie 2015

    DOI: 10.1016/j.biochi.2015.05.003

    A proteome quality index

    Environmental Microbiology 2015

    DOI: 10.1111/1462-2920.12622

    The SUPERFAMILY 1.75 database in 2014: a doubling of data

    Nucleic Acids Research 2015

    DOI: 10.1093/nar/gku1041

    The ‘dnet’ approach promotes emerging research on cancer patient survival

    Genome Medicine 2014

    DOI: 10.1186/s13073-014-0064-8

    The Evolution of Human Cells in Terms of Protein Innovation

    Molecular Biology and Evolution 2014

    DOI: 10.1093/molbev/mst139

    dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations

    PLoS Computational Biology 2014

    DOI: 10.1371/journal.pcbi.1003929

    A large-scale evaluation of computational protein function prediction

    Nature Methods 2013

    DOI: 10.1038/nmeth.2340

    A disease-drug-phenotype matrix inferred by walking on a functional domain network

    Molecular BioSystems 2013

    DOI: 10.1039/c3mb25495j

    A daily-updated tree of (sequenced) life as a reference for genome research

    Scientific Reports 2013

    DOI: 10.1038/srep02015

    A domain-centric solution to functional genomics via dcGO Predictor

    BMC Bioinformatics 2013

    DOI: 10.1186/1471-2105-14-S3-S9

    dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more

    Nucleic Acids Research 2013

    DOI: 10.1093/nar/gks1080

    SUPERFAMILY 1.75 including a domain-centric gene ontology method

    Nucleic Acids Research 2011

    DOI: 10.1093/nar/gkq1130