{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T06:47:16Z","timestamp":1780987636817,"version":"3.54.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2022,7,26]],"date-time":"2022-07-26T00:00:00Z","timestamp":1658793600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Research Foundation Singapore, Clinician Scientist","award":["NMRC\/CSA-INV\/0017\/2017"],"award-info":[{"award-number":["NMRC\/CSA-INV\/0017\/2017"]}]},{"name":"National Research Foundation Singapore, Clinician Scientist","award":["MOH-000654"],"award-info":[{"award-number":["MOH-000654"]}]},{"name":"Singapore Ministry of Health\u2019s National Medical Research Council"},{"name":"Ministry of Education, Singapore, Academic Research Fund Tier 1","award":["2019-T1-001-018"],"award-info":[{"award-number":["2019-T1-001-018"]}]},{"name":"National Cancer Centre Research Fund Terry Fox Grant","award":["NCCRF-YR2018-NOV-1"],"award-info":[{"award-number":["NCCRF-YR2018-NOV-1"]}]},{"name":"Nanyang Technological University Start-Up"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>DNA fibre assay has a potential application in genomic medicine, cancer and stem cell research at the single-molecule level. A major challenge for the clinical and research implementation of DNA fibre assays is the slow speed in which manual analysis takes place as it limits the clinical actionability. While automatic detection of DNA fibres speeds up this process considerably, current publicly available software have limited features in terms of their user interface for manual correction of results, which in turn limit their accuracy and ability to account for atypical structures that may be important in diagnosis or investigative studies. We recognize that core improvements can be made to the GUI to allow for direct interaction with automatic results to preserve accuracy as well as enhance the versatility of automatic DNA fibre detection for use in variety of situations.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>To address the unmet needs of diverse DNA fibre analysis investigations, we propose DNA Stranding, an open-source software that is able to perform accurate fibre length quantification (13.22% mean relative error) and fibre pattern recognition (R\u2009&amp;gt;\u20090.93) with up to six fibre patterns supported. With the graphical interface, we developed, user can conduct semi-automatic analyses which benefits from the advantages of both automatic and manual processes to improve workflow efficiency without compromising accuracy.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The software package is available at https:\/\/github.com\/lgole\/DNAStranding.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac533","type":"journal-article","created":{"date-parts":[[2022,7,26]],"date-time":"2022-07-26T18:00:26Z","timestamp":1658858426000},"page":"4395-4402","source":"Crossref","is-referenced-by-count":17,"title":["Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level"],"prefix":"10.1093","volume":"38","author":[{"given":"Longjie","family":"Li","sequence":"first","affiliation":[{"name":"Institute of Molecular and Cell Biology, A*STAR , Singapore 138673, Singapore"},{"name":"Bioinformatics Institute, A*STAR , Singapore 138671, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arun Mouli","family":"Kolinjivadi","sequence":"additional","affiliation":[{"name":"Lee Kong Chian School of Medicine, Nanyang Technological University , Singapore 308232, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kok Haur","family":"Ong","sequence":"additional","affiliation":[{"name":"Institute of Molecular and Cell Biology, A*STAR , Singapore 138673, Singapore"},{"name":"Bioinformatics Institute, A*STAR , Singapore 138671, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David M","family":"Young","sequence":"additional","affiliation":[{"name":"Institute of Molecular and Cell Biology, A*STAR , Singapore 138673, Singapore"},{"name":"Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California , San Francisco, CA 94158, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriel Pik Liang","family":"Marini","sequence":"additional","affiliation":[{"name":"Bioinformatics Institute, A*STAR , Singapore 138671, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sock Hoai","family":"Chan","sequence":"additional","affiliation":[{"name":"Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre , Singapore 169610, Singapore"},{"name":"Oncology Academic Clinical Program, Duke-NUS Medical School Singapore , Singapore 169857, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siao Ting","family":"Chong","sequence":"additional","affiliation":[{"name":"Lee Kong Chian School of Medicine, Nanyang Technological University , Singapore 308232, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ee Ling","family":"Chew","sequence":"additional","affiliation":[{"name":"Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre , Singapore 169610, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haoda","family":"Lu","sequence":"additional","affiliation":[{"name":"Bioinformatics Institute, A*STAR , Singapore 138671, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurent","family":"Gole","sequence":"additional","affiliation":[{"name":"Institute of Molecular and Cell Biology, A*STAR , Singapore 138673, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5092-1009","authenticated-orcid":false,"given":"Weimiao","family":"Yu","sequence":"additional","affiliation":[{"name":"Institute of Molecular and Cell Biology, A*STAR , Singapore 138673, Singapore"},{"name":"Bioinformatics Institute, A*STAR , Singapore 138671, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanne","family":"Ngeow","sequence":"additional","affiliation":[{"name":"Lee Kong Chian School of Medicine, Nanyang Technological University , Singapore 308232, Singapore"},{"name":"Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre , Singapore 169610, Singapore"},{"name":"Oncology Academic Clinical Program, Duke-NUS Medical School Singapore , Singapore 169857, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,7,26]]},"reference":[{"key":"2023041408371721400_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13046-020-01554-6","article-title":"Variants of uncertain significance in the era of high-throughput genome sequencing: a lesson from breast and ovary cancers","volume":"39","author":"Federici","year":"2020","journal-title":"J. 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