{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:17Z","timestamp":1772138057869,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,3,17]],"date-time":"2023-03-17T00:00:00Z","timestamp":1679011200000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Research Council Horizon 2020","award":["802567"],"award-info":[{"award-number":["802567"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Efficient tapping into genomic information from a single microscopic image of an intact DNA molecule is an outstanding challenge and its solution will open new frontiers in molecular diagnostics. Here, a new computational method for optical genome mapping utilizing deep learning is presented, termed DeepOM. Utilization of a convolutional neural network, trained on simulated images of labeled DNA molecules, improves the success rate in the alignment of DNA images to genomic references.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The method is evaluated on acquired images of human DNA molecules stretched in nano-channels. The accuracy of the method is benchmarked against state-of-the-art commercial software Bionano Solve. The results show a significant advantage in alignment success rate for molecules shorter than 50\u2009kb. DeepOM improves the yield, sensitivity, and throughput of optical genome mapping experiments in applications of human genomics and microbiology.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The source code for the presented method is publicly available at https:\/\/github.com\/yevgenin\/DeepOM.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad137","type":"journal-article","created":{"date-parts":[[2023,3,16]],"date-time":"2023-03-16T19:23:18Z","timestamp":1678994598000},"source":"Crossref","is-referenced-by-count":10,"title":["DeepOM: single-molecule optical genome mapping via deep learning"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7484-727X","authenticated-orcid":false,"given":"Yevgeni","family":"Nogin","sequence":"first","affiliation":[{"name":"Russel Berrie Nanotechnology Institute, Technion , Haifa 320003, Israel"}]},{"given":"Tahir","family":"Detinis Zur","sequence":"additional","affiliation":[{"name":"Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Tel Aviv University , Tel Aviv 6997801, Israel"}]},{"given":"Sapir","family":"Margalit","sequence":"additional","affiliation":[{"name":"Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Tel Aviv University , Tel Aviv 6997801, Israel"}]},{"given":"Ilana","family":"Barzilai","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Technion , Haifa 320003, Israel"}]},{"given":"Onit","family":"Alalouf","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Technion , Haifa 320003, Israel"},{"name":"Lorry I. Lokey Center for Life Sciences and Engineering, Technion , Haifa 320003, Israel"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7107-7529","authenticated-orcid":false,"given":"Yuval","family":"Ebenstein","sequence":"additional","affiliation":[{"name":"Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Tel Aviv University , Tel Aviv 6997801, Israel"},{"name":"Department of Biomedical Engineering, Tel Aviv University , Tel Aviv 6997801, Israel"}]},{"given":"Yoav","family":"Shechtman","sequence":"additional","affiliation":[{"name":"Russel Berrie Nanotechnology Institute, Technion , Haifa 320003, Israel"},{"name":"Department of Biomedical Engineering, Technion , Haifa 320003, Israel"},{"name":"Lorry I. Lokey Center for Life Sciences and Engineering, Technion , Haifa 320003, Israel"}]}],"member":"286","published-online":{"date-parts":[[2023,3,17]]},"reference":[{"key":"2023050514432335500_btad137-B1","volume-title":"Algorithms in Bioinformatics: First International Workshop, WABI 2001 \u00c5rhus Denmark, August 28\u201331, 2001 Proceedings","author":"Anantharaman"},{"key":"2023050514432335500_btad137-B2","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1093\/bioinformatics\/btx437","article-title":"Irys extract","volume":"34","author":"Arielly","year":"2018","journal-title":"Bioinformatics"},{"key":"2023050514432335500_btad137-B3","doi-asserted-by":"crossref","first-page":"lqz007","DOI":"10.1093\/nargab\/lqz007","article-title":"Identifying microbial species by single-molecule DNA optical mapping and resampling statistics","volume":"2","author":"Bouwens","year":"2020","journal-title":"NAR Genom 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