{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:42:47Z","timestamp":1753875767455,"version":"3.41.2"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2024,7,2]],"date-time":"2024-07-02T00:00:00Z","timestamp":1719878400000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National key research and development program of China","doi-asserted-by":"publisher","award":["2022YFC2602400"],"award-info":[{"award-number":["2022YFC2602400"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Accurately detecting pathogenic microorganisms requires effective primers and probe designs. Literature-derived primers are a valuable resource as they have been tested and proven effective in previous research. However, manually mining primers from published texts is time-consuming and limited in species scop.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To address these challenges, we have developed MiPRIME, a real-time Microbial Primer Mining platform for primer\/probe sequences extraction of pathogenic microorganisms with three highlights: (i) comprehensive integration. Covering &amp;gt;40 million articles and 548\u00a0942 organisms, the platform enables high-frequency microbial gene discovery from a global perspective, facilitating user-defined primer design and advancing microbial research. (ii) Using a BioBERT-based text mining model with 98.02% accuracy, greatly reducing information processing time. (iii) Using a primer ranking score, PRscore, for intelligent recommendation of species-specific primers. Overall, MiPRIME is a practical tool for primer mining in the pan-microbial field, saving time and cost of trial-and-error experiments.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The web is available at {{https:\/\/www.ai-bt.com}}.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae429","type":"journal-article","created":{"date-parts":[[2024,7,2]],"date-time":"2024-07-02T23:50:16Z","timestamp":1719964216000},"source":"Crossref","is-referenced-by-count":0,"title":["MiPRIME: an integrated and intelligent platform for mining primer and probe sequences of microbial species"],"prefix":"10.1093","volume":"40","author":[{"given":"Zhiming","family":"Zhang","sequence":"first","affiliation":[{"name":"Research and Development Department, Coyote Bioscience (Beijing) Co., Ltd. , Building 22, Zone 3, Gaolizhang Road, Haidian District , Beijing, 10095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-4495-3136","authenticated-orcid":false,"given":"Jing","family":"Ren","sequence":"additional","affiliation":[{"name":"Research and Development Department, Coyote Bioscience (Beijing) Co., Ltd. , Building 22, Zone 3, Gaolizhang Road, Haidian District , Beijing, 10095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lili","family":"Ren","sequence":"additional","affiliation":[{"name":"Equipment technology research institute, Science and Technology Research Center of China Customs , Tianshuiyuan street No. 6, Chaoyang District , Beijing, 100026, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lanying","family":"Zhang","sequence":"additional","affiliation":[{"name":"Research and Development Department, Coyote Diagnostics Lab (Beijing) Co., Ltd. , Building 22, Zone 3, Gaolizhang Road, Haidian District , Beijing, 100095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qubo","family":"Ai","sequence":"additional","affiliation":[{"name":"Research and Development Department, Coyote Bioscience (Beijing) Co., Ltd. , Building 22, Zone 3, Gaolizhang Road, Haidian District , Beijing, 10095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haixin","family":"Long","sequence":"additional","affiliation":[{"name":"Research and Development Department, Coyote Diagnostics Lab (Beijing) Co., Ltd. , Building 22, Zone 3, Gaolizhang Road, Haidian District , Beijing, 100095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Ren","sequence":"additional","affiliation":[{"name":"Research and Development Department, Coyote Bioscience (Beijing) Co., Ltd. , Building 22, Zone 3, Gaolizhang Road, Haidian District , Beijing, 10095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kun","family":"Yang","sequence":"additional","affiliation":[{"name":"Research and Development Department, Coyote Bioscience (Beijing) Co., Ltd. , Building 22, Zone 3, Gaolizhang Road, Haidian District , Beijing, 10095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huiying","family":"Feng","sequence":"additional","affiliation":[{"name":"Research and Development Department, Coyote Bioscience (Beijing) Co., Ltd. , Building 22, Zone 3, Gaolizhang Road, Haidian District , Beijing, 10095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sabrina","family":"Li","sequence":"additional","affiliation":[{"name":"Research and Development Department, Coyote Bioscience (Beijing) Co., Ltd. , Building 22, Zone 3, Gaolizhang Road, Haidian District , Beijing, 10095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5294-1062","authenticated-orcid":false,"given":"Xu","family":"Li","sequence":"additional","affiliation":[{"name":"Research and Development Department, Coyote Bioscience (Beijing) Co., Ltd. , Building 22, Zone 3, Gaolizhang Road, Haidian District , Beijing, 10095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,7,2]]},"reference":[{"key":"2024071321123632700_btae429-B1","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2024071321123632700_btae429-B2","first-page":"D517","article-title":"CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database","volume":"48","author":"Alcock","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2024071321123632700_btae429-B3","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1186\/1471-2105-9-465","article-title":"QuantPrime\u2014a flexible tool for reliable high-throughput primer design for quantitative PCR","volume":"9","author":"Arvidsson","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2024071321123632700_btae429-B4","doi-asserted-by":"crossref","first-page":"D36","DOI":"10.1093\/nar\/gks1195","article-title":"GenBank","volume":"41","author":"Benson","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2024071321123632700_btae429-B5","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1038\/s41587-018-0010-1","article-title":"Ultrafast search of all deposited bacterial and viral genomic data","volume":"37","author":"Bradley","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2024071321123632700_btae429-B6","doi-asserted-by":"crossref","first-page":"D325","DOI":"10.1093\/nar\/gki008","article-title":"VFDB: a reference database for bacterial virulence factors","volume":"33","author":"Chen","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2024071321123632700_btae429-B7","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/s41586-021-04384-4","article-title":"Streptococcal pyrogenic exotoxin B cleaves GSDMA and triggers pyroptosis","volume":"602","author":"Deng","year":"2022","journal-title":"Nature"},{"key":"2024071321123632700_btae429-B8","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1186\/1471-2105-11-410","article-title":"A method for automatically extracting infectious disease-related primers and probes from the literature","volume":"11","author":"Garc\u00eda-Remesal","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2024071321123632700_btae429-B9","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/j.watres.2019.06.009","article-title":"Literature-based, manually-curated database of PCR primers for the detection of antibiotic resistance genes in various environments","volume":"161","author":"Gorecki","year":"2019","journal-title":"Water Res"},{"key":"2024071321123632700_btae429-B10","doi-asserted-by":"crossref","first-page":"D586","DOI":"10.1093\/nar\/gkv1232","article-title":"probeBase\u2014an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016","volume":"44","author":"Greuter","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2024071321123632700_btae429-B11","doi-asserted-by":"crossref","first-page":"W5","DOI":"10.1093\/nar\/gkn201","article-title":"NCBI BLAST: a better web interface","volume":"36","author":"Johnson","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2024071321123632700_btae429-B12","doi-asserted-by":"crossref","first-page":"D475","DOI":"10.1093\/nar\/gkw1095","article-title":"MRPrimerV: a database of PCR primers for RNA virus detection","volume":"45","author":"Kim","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2024071321123632700_btae429-B13","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1093\/bioinformatics\/btm091","article-title":"Enhancements and modifications of primer design program Primer3","volume":"23","author":"Koressaar","year":"2007","journal-title":"Bioinformatics"},{"key":"2024071321123632700_btae429-B14","doi-asserted-by":"crossref","first-page":"1234","DOI":"10.1093\/bioinformatics\/btz682","article-title":"BioBERT: a pre-trained biomedical language representation model for biomedical text mining","volume":"36","author":"Lee","year":"2020","journal-title":"Bioinformatics"},{"key":"2024071321123632700_btae429-B15","doi-asserted-by":"crossref","first-page":"3991","DOI":"10.1021\/acs.accounts.1c00498","article-title":"Development of integrated systems for on-Site infection detection","volume":"54","author":"Lee","year":"2021","journal-title":"Acc Chem Res"},{"key":"2024071321123632700_btae429-B16","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1039\/D2CS00594H","article-title":"Amplification-free CRISPR\/Cas detection technology: challenges, strategies, and perspectives","volume":"52","author":"Li","year":"2023","journal-title":"Chem Soc Rev"},{"key":"2024071321123632700_btae429-B17","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/s41587-021-01006-2","article-title":"Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis","volume":"40","author":"Lohoff","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2024071321123632700_btae429-B18","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1093\/nar\/gkg016","article-title":"probeBase: an online resource for rRNA-targeted oligonucleotide probes","volume":"31","author":"Loy","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2024071321123632700_btae429-B19","doi-asserted-by":"crossref","first-page":"D800","DOI":"10.1093\/nar\/gkl856","article-title":"probeBase\u2014an online resource for rRNA-targeted oligonucleotide probes: new features 2007","volume":"35","author":"Loy","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2024071321123632700_btae429-B20","doi-asserted-by":"crossref","first-page":"e185","DOI":"10.1016\/S1473-3099(22)00723-X","article-title":"Advancing detection and response capacities for emerging and re-emerging pathogens in Africa","volume":"23","author":"Nachega","year":"2023","journal-title":"Lancet Infect Dis"},{"key":"2024071321123632700_btae429-B21","doi-asserted-by":"crossref","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation","volume":"44","author":"O'Leary","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2024071321123632700_btae429-B22","doi-asserted-by":"crossref","first-page":"baaa062","DOI":"10.1093\/database\/baaa062","article-title":"NCBI taxonomy: a comprehensive update on curation, resources and tools","volume":"2020","author":"Schoch","year":"2020","journal-title":"Database"},{"key":"2024071321123632700_btae429-B23","doi-asserted-by":"crossref","first-page":"D792","DOI":"10.1093\/nar\/gkp1005","article-title":"PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification","volume":"38","author":"Spandidos","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2024071321123632700_btae429-B24","first-page":"365","article-title":"Primer3 on the WWW for general users and for biologist programmers","volume":"132","author":"Rozen","year":"2000","journal-title":"Methods Mol Biol (Clifton, N.J.)"},{"key":"2024071321123632700_btae429-B25","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1038\/s41586-020-03126-2","article-title":"Integrated spatial genomics reveals global architecture of single nuclei","volume":"590","author":"Takei","year":"2021","journal-title":"Nature"},{"key":"2024071321123632700_btae429-B26","doi-asserted-by":"crossref","first-page":"e115","DOI":"10.1093\/nar\/gks596","article-title":"Primer3\u2014new capabilities and interfaces","volume":"40","author":"Untergasser","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2024071321123632700_btae429-B27","doi-asserted-by":"crossref","first-page":"W610","DOI":"10.1093\/nar\/gkz351","article-title":"MFEprimer-3.0: quality control for PCR primers","volume":"47","author":"Wang","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2024071321123632700_btae429-B28","doi-asserted-by":"crossref","first-page":"D1144","DOI":"10.1093\/nar\/gkr1013","article-title":"PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update","volume":"40","author":"Wang","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2024071321123632700_btae429-B29","doi-asserted-by":"crossref","first-page":"918710","DOI":"10.1155\/2015\/918710","article-title":"GNormPlus: an integrative approach for tagging genes, gene families, and protein domains","volume":"2015","author":"Wei","year":"2015","journal-title":"Biomed Res Int"},{"key":"2024071321123632700_btae429-B30","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1186\/1471-2105-13-134","article-title":"Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction","volume":"13","author":"Ye","year":"2012","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae429\/58394184\/btae429.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/7\/btae429\/58536799\/btae429.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/7\/btae429\/58536799\/btae429.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,13]],"date-time":"2024-07-13T22:01:51Z","timestamp":1720908111000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae429\/7703287"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2024,7,1]]},"references-count":30,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2024,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae429","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2024,7]]},"published":{"date-parts":[[2024,7,1]]},"article-number":"btae429"}}