{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T07:09:55Z","timestamp":1771484995208,"version":"3.50.1"},"reference-count":64,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,3,30]],"date-time":"2024-03-30T00:00:00Z","timestamp":1711756800000},"content-version":"vor","delay-in-days":3,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Science & Technology Fundamental Resources Investigation Program","award":["2022FY101100"],"award-info":[{"award-number":["2022FY101100"]}]},{"name":"National Science Fund for Distinguished Young Scholars of China","award":["62325308"],"award-info":[{"award-number":["62325308"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170114"],"award-info":[{"award-number":["32170114"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31770152"],"award-info":[{"award-number":["31770152"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Predicting interactions between microbes and hosts plays critical roles in microbiome population genetics and microbial ecology and evolution. How to systematically characterize the sophisticated mechanisms and signal interplay between microbes and hosts is a significant challenge for global health risks. Identifying microbe-host interactions (MHIs) can not only provide helpful insights into their fundamental regulatory mechanisms, but also facilitate the development of targeted therapies for microbial infections. In recent years, computational methods have become an appealing alternative due to the high risk and cost of wet-lab experiments. Therefore, in this study, we utilized rich microbial metagenomic information to construct a novel heterogeneous microbial network (HMN)-based model named KGVHI to predict candidate microbes for target hosts. Specifically, KGVHI first built a HMN by integrating human proteins, viruses and pathogenic bacteria with their biological attributes. Then KGVHI adopted a knowledge graph embedding strategy to capture the global topological structure information of the whole network. A natural language processing algorithm is used to extract the local biological attribute information from the nodes in HMN. Finally, we combined the local and global information and fed it into a blended deep neural network (DNN) for training and prediction. Compared to state-of-the-art methods, the comprehensive experimental results show that our model can obtain excellent results on the corresponding three MHI datasets. Furthermore, we also conducted two pathogenic bacteria case studies to further indicate that KGVHI has excellent predictive capabilities for potential MHI pairs.<\/jats:p>","DOI":"10.1093\/bib\/bbae119","type":"journal-article","created":{"date-parts":[[2024,3,31]],"date-time":"2024-03-31T02:41:05Z","timestamp":1711852865000},"source":"Crossref","is-referenced-by-count":9,"title":["A microbial knowledge graph-based deep learning model for predicting candidate microbes for target hosts"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4993-298X","authenticated-orcid":false,"given":"Jie","family":"Pan","sequence":"first","affiliation":[{"name":"Key Laboratory of Resources Biology and Biotechnology in Western China , Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, , Xi\u2019an 710069 , China"},{"name":"College of Life Sciences, Northwest University , Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, , Xi\u2019an 710069 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhen","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Resources Biology and Biotechnology in Western China , Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, , Xi\u2019an 710069 , China"},{"name":"College of Life Sciences, Northwest University , Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, , Xi\u2019an 710069 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of Resources Biology and Biotechnology in Western China , Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, , Xi\u2019an 710069 , China"},{"name":"College of Life Sciences, Northwest University , Ministry of Education, Provincial Key Laboratory of Biotechnology of 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Laboratory of Resources Biology and Biotechnology in Western China , Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, , Xi\u2019an 710069 , China"},{"name":"College of Life Sciences, Northwest University , Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, , Xi\u2019an 710069 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shixu","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Resources Biology and Biotechnology in Western China , Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, , Xi\u2019an 710069 , China"},{"name":"College of Life Sciences, Northwest University , Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, , Xi\u2019an 710069 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Minghui","family":"Zhu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Resources Biology and Biotechnology in Western China , Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, , Xi\u2019an 710069 , China"},{"name":"College of Life Sciences, Northwest University , Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, , Xi\u2019an 710069 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fengzhi","family":"Ren","sequence":"additional","affiliation":[{"name":"North China Pharmaceutical Group , Shijiazhuang 050015, Hebei , China"},{"name":"National Microbial Medicine Engineering & Research Center , Shijiazhuang 050015, Hebei , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xuexia","family":"Zhang","sequence":"additional","affiliation":[{"name":"North China Pharmaceutical Group , Shijiazhuang 050015, Hebei , China"},{"name":"National Microbial Medicine Engineering & Research Center , Shijiazhuang 050015, Hebei , 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