{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T22:45:08Z","timestamp":1772750708718,"version":"3.50.1"},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,4,21]],"date-time":"2023-04-21T00:00:00Z","timestamp":1682035200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100020950","name":"National Science and Technology Council","doi-asserted-by":"publisher","award":["110-2811-E-001-502"],"award-info":[{"award-number":["110-2811-E-001-502"]}],"id":[{"id":"10.13039\/501100020950","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Academia Sinica Grand Challenge Program","award":["AS-GC-110-L15"],"award-info":[{"award-number":["AS-GC-110-L15"]}]},{"name":"Academia Sinica Grand Challenge Program","award":["AS-GC-110-L15"],"award-info":[{"award-number":["AS-GC-110-L15"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Ubiquitous presence of short extrachromosomal circular DNAs (eccDNAs) in eukaryotic cells has perplexed generations of biologists. Their widespread origins in the genome lacking apparent specificity led some studies to conclude their formation as random or near-random. Despite this, the search for specific formation of short eccDNA continues with a recent surge of interest in biomarker development.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To shed new light on the conflicting views on short eccDNAs\u2019 randomness, here we present DeepCircle, a bioinformatics framework incorporating convolution- and attention-based neural networks to assess their predictability. Short human eccDNAs from different datasets indeed have low similarity in genomic locations, but DeepCircle successfully learned shared DNA sequence features to make accurate cross-datasets predictions (accuracy: convolution-based models: 79.65\u2009\u00b1\u20094.7%, attention-based models: 83.31\u2009\u00b1\u20094.18%).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>The excellent performance of our models shows that the intrinsic predictability of eccDNAs is encoded in the sequences across tissue origins. Our work demonstrates how the perceived lack of specificity in genomics data can be re-assessed by deep learning models to uncover unexpected similarity.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bib\/bbad147","type":"journal-article","created":{"date-parts":[[2023,4,24]],"date-time":"2023-04-24T05:25:53Z","timestamp":1682313953000},"source":"Crossref","is-referenced-by-count":15,"title":["Short human eccDNAs are predictable from sequences"],"prefix":"10.1093","volume":"24","author":[{"given":"Kai-Li","family":"Chang","sequence":"first","affiliation":[{"name":"Institute of Information Science, Academia Sinica , Taipei, 115 , Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jia-Hong","family":"Chen","sequence":"additional","affiliation":[{"name":"Institute of Information Science, Academia Sinica , Taipei, 115 , Taiwan"},{"name":"Department of Electrical Engineering, National Taiwan University , Taipei, 106 , Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tzu-Chieh","family":"Lin","sequence":"additional","affiliation":[{"name":"Institute of Information Science, Academia Sinica , Taipei, 115 , Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun-Yi","family":"Leu","sequence":"additional","affiliation":[{"name":"Institute of Molecular Biology, Academia Sinica , Taipei 115 , Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheng-Fu","family":"Kao","sequence":"additional","affiliation":[{"name":"Institute of Cellular and Organismic Biology, Academia Sinica , Taipei 115 , Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jin Yung","family":"Wong","sequence":"additional","affiliation":[{"name":"Institute of Information Science, Academia Sinica , Taipei, 115 , 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