{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T00:37:08Z","timestamp":1774053428572,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,8,12]],"date-time":"2021-08-12T00:00:00Z","timestamp":1628726400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2017YFC1200205"],"award-info":[{"award-number":["2017YFC1200205"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32070667"],"award-info":[{"award-number":["32070667"]}],"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":["31671366"],"award-info":[{"award-number":["31671366"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>We present HoPhage (Host of Phage) to identify the host of a given phage fragment from metavirome data at the genus level. HoPhage integrates two modules using a deep learning algorithm and a Markov chain model, respectively. HoPhage achieves 47.90% and 82.47% mean accuracy at the genus and phylum levels for \u223c1-kb long artificial phage fragments when predicting host among 50 genera, representing 7.54\u201320.22% and 13.55\u201324.31% improvement, respectively. By testing on three real virome samples, HoPhage yields 81.11% mean accuracy at the genus level within a much broader candidate host range.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>HoPhage is available at http:\/\/cqb.pku.edu.cn\/ZhuLab\/HoPhage\/data\/<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab585","type":"journal-article","created":{"date-parts":[[2021,8,10]],"date-time":"2021-08-10T15:12:02Z","timestamp":1628608322000},"page":"543-545","source":"Crossref","is-referenced-by-count":28,"title":["HoPhage: an\n                    <i>ab initio<\/i>\n                    tool for identifying hosts of phage fragments from metaviromes"],"prefix":"10.1093","volume":"38","author":[{"given":"Jie","family":"Tan","sequence":"first","affiliation":[{"name":"State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering and Center for Quantitative Biology, Peking University , Beijing 100871, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhencheng","family":"Fang","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering and Center for Quantitative Biology, Peking University , Beijing 100871, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shufang","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering and Center for Quantitative Biology, Peking University , Beijing 100871, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qian","family":"Guo","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering and Center for Quantitative Biology, Peking University , Beijing 100871, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoqing","family":"Jiang","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering and Center for Quantitative Biology, Peking University , Beijing 100871, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6376-218X","authenticated-orcid":false,"given":"Huaiqiu","family":"Zhu","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering and Center for Quantitative Biology, Peking University , Beijing 100871, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,8,12]]},"reference":[{"key":"2023020108414234800_btab585-B1","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1093\/nar\/gkw1002","article-title":"Alignment-free d2* oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences","volume":"45","author":"Ahlgren","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023020108414234800_btab585-B2","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1007\/s00239-008-9068-6","article-title":"Codon bias is a major factor explaining phage evolution in translationally biased hosts","volume":"66","author":"Carbone","year":"2008","journal-title":"J. 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