{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T01:24:06Z","timestamp":1774401846833,"version":"3.50.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2025,9,7]],"date-time":"2025-09-07T00:00:00Z","timestamp":1757203200000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100014188","name":"MSIT","doi-asserted-by":"publisher","award":["RS-2023-00217123"],"award-info":[{"award-number":["RS-2023-00217123"]}],"id":[{"id":"10.13039\/501100014188","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009647","name":"Ministry of Health","doi-asserted-by":"publisher","award":["RS-2023-KH135226"],"award-info":[{"award-number":["RS-2023-KH135226"]}],"id":[{"id":"10.13039\/100009647","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012264","name":"NIH","doi-asserted-by":"publisher","award":["2023ER210902"],"award-info":[{"award-number":["2023ER210902"]}],"id":[{"id":"10.13039\/501100012264","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,9,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Mobile genetic elements (MGEs) play an important role in facilitating the acquisition of antibiotic resistance genes (ARGs) within microbial communities, significantly impacting the evolution of antibiotic resistance. Understanding the mechanism and trajectory of ARG acquisition requires a comprehensive analysis of the ARG-carrying mobilome\u2014a collective set of MGEs carrying ARGs. However, identifying the mobilome within complex microbiomes poses considerable challenges. Existing MGE prediction methods, designed primarily for single genomes, exhibit substantial limitations when applied to metagenomic data, often producing high false positive rates in identifying target MGEs from metagenome sequencing data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To address these challenges, we developed DeepMobilome, a novel approach for accurately identifying target MGEs within the microbiome. DeepMobilome leverages a convolutional neural network trained on read alignment data derived from sequence alignment map (SAM) files, providing superior accuracy in detecting MGEs. Trained on 364 647 cases, DeepMobilome achieved a high validation accuracy of 0.99. DeepMobilome consistently outperformed existing methods in discerning the presence of target MGE sequences across diverse test sets. In single-genome test scenarios, DeepMobilome showed an F1-score of 0.935, compared to 0.755 and 0.670 for MGEfinder and ISMapper, respectively, demonstrating its substantial improvements in prediction accuracy. Extensive evaluations across simulated microbiomes further validated the robustness and reliability of DeepMobilome in practical applications. In real microbiome data, DeepMobilome successfully identified six ARG-carrying MGEs across diverse populations. By addressing the limitations of current methods, DeepMobilome offers a powerful tool for advancing our understanding of ARG dissemination and supports targeted interventions in combating antibiotic resistance.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bib\/bbaf450","type":"journal-article","created":{"date-parts":[[2025,9,7]],"date-time":"2025-09-07T17:19:49Z","timestamp":1757265589000},"source":"Crossref","is-referenced-by-count":1,"title":["DeepMobilome: predicting mobile genetic elements using sequencing reads of microbiomes"],"prefix":"10.1093","volume":"26","author":[{"given":"Youna","family":"Cho","sequence":"first","affiliation":[{"name":"Department of Computer Science, Hanyang University , 222 Wangsimni-ro, Seoul 04763 ,","place":["Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erin","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Hanyang University , 222 Wangsimni-ro, Seoul 04763 ,","place":["Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Minyoung","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Artificial Intelligence, Hanyang University , 222 Wangsimni-ro, Seoul 04763 ,","place":["Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2724-9477","authenticated-orcid":false,"given":"Mina","family":"Rho","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Hanyang University , 222 Wangsimni-ro, Seoul 04763 ,","place":["Republic of Korea"]},{"name":"Department of Artificial Intelligence, Hanyang University , 222 Wangsimni-ro, Seoul 04763 ,","place":["Republic of Korea"]},{"name":"Department of Biomedical Informatics, Hanyang University , 222 Wangsimni-ro, Seoul 04763 ,","place":["Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,9,7]]},"reference":[{"key":"2025090713194181400_ref1","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1038\/nrmicro1235","article-title":"Mobile genetic elements: The agents of open source evolution","volume":"3","author":"Frost","year":"2005","journal-title":"Nat Rev Microbiol"},{"key":"2025090713194181400_ref2","doi-asserted-by":"publisher","first-page":"849667","DOI":"10.3389\/fmicb.2022.849667","article-title":"Editorial: The role of mobile genetic elements in bacterial evolution and their adaptability","volume":"13","author":"Vale","year":"2022","journal-title":"Front Microbiol"},{"key":"2025090713194181400_ref3","first-page":"255","article-title":"Mobile genetic elements as natural tools for genome evolution","volume":"260","journal-title":"Methods Mol Biol"},{"key":"2025090713194181400_ref4","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.00173","article-title":"Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer","volume":"7","author":"Wintersdorff","year":"2016","journal-title":"Front Microbiol"},{"key":"2025090713194181400_ref5","doi-asserted-by":"publisher","first-page":"167","DOI":"10.2147\/IDR.S48820","article-title":"Horizontal gene transfer in the human gastrointestinal tract: Potential spread of antibiotic resistance genes","volume":"7","author":"Huddleston","year":"2014","journal-title":"Infect Drug Resist"},{"key":"2025090713194181400_ref6","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1139\/cjm-2018-0275","article-title":"Horizontal transfer of antibiotic resistance genes in clinical environments","volume":"65","author":"Lerminiaux","year":"2019","journal-title":"Can J Microbiol"},{"key":"2025090713194181400_ref7","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1016\/j.tim.2020.05.003","article-title":"Probing the mobilome: Discoveries in the dynamic microbiome","volume":"29","author":"Carr","year":"2021","journal-title":"Trends Microbiol"},{"key":"2025090713194181400_ref8","volume-title":"Global vaccine safety blueprint","author":"World Health Organization","year":"2012","edition":"3rd"},{"key":"2025090713194181400_ref9","doi-asserted-by":"publisher","first-page":"629139","DOI":"10.3389\/fmicb.2021.629139","article-title":"ESBL and AmpC beta-lactamase encoding genes in E. 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