Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level

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 actionabili...

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Main Authors: Li, Longjie, Kolinjivadi, Arun Mouli, Ong, Kok Haur, Young, David M., Marini, Gabriel Pik Liang, Chan, Sock Hoai, Chong, Siao Ting, Chew, Ee Ling, Lu, Haoda, Gole, Laurent, Yu, Weimiao, Ngeow, Joanne
Other Authors: Lee Kong Chian School of Medicine (LKCMedicine)
Format: Article
Language:English
Published: 2023
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Online Access:https://hdl.handle.net/10356/164980
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Institution: Nanyang Technological University
Language: English
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spelling sg-ntu-dr.10356-1649802023-03-12T15:42:26Z Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level Li, Longjie Kolinjivadi, Arun Mouli Ong, Kok Haur Young, David M. Marini, Gabriel Pik Liang Chan, Sock Hoai Chong, Siao Ting Chew, Ee Ling Lu, Haoda Gole, Laurent Yu, Weimiao Ngeow, Joanne Lee Kong Chian School of Medicine (LKCMedicine) Science::Medicine Sofware Replication 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. Ministry of Education (MOE) Ministry of Health (MOH) National Research Foundation (NRF) Published version This work was supported by National Research Foundation Singapore, Clinician Scientist Award [NMRC/CSA-INV/0017/2017, MOH-000654] and administered by the Singapore Ministry of Health’s National Medical Research Council; and the Ministry of Education, Singapore, Academic Research Fund Tier 1 [2019-T1-001-018]; the National Cancer Centre Research Fund Terry Fox Grant [NCCRF-YR2018-NOV-1]; and the Nanyang Technological University Start-Up Grant (to J.N.). This work was jointly supported by BII and IMCB, BMRC, A*STAR research funding, and A*STAR BMRC ATR Grant. 2023-03-07T08:41:01Z 2023-03-07T08:41:01Z 2022 Journal Article Li, L., Kolinjivadi, A. M., Ong, K. H., Young, D. M., Marini, G. P. L., Chan, S. H., Chong, S. T., Chew, E. L., Lu, H., Gole, L., Yu, W. & Ngeow, J. (2022). Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level. Bioinformatics, 38(18), 4395-4402. https://dx.doi.org/10.1093/bioinformatics/btac533 1367-4811 https://hdl.handle.net/10356/164980 10.1093/bioinformatics/btac533 35881697 2-s2.0-85141891108 18 38 4395 4402 en NMRC/CSA-INV/0017/2017 MOH-000654 2019-T1-001-018 Bioinformatics © The Author(s) 2022. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic Science::Medicine
Sofware
Replication
spellingShingle Science::Medicine
Sofware
Replication
Li, Longjie
Kolinjivadi, Arun Mouli
Ong, Kok Haur
Young, David M.
Marini, Gabriel Pik Liang
Chan, Sock Hoai
Chong, Siao Ting
Chew, Ee Ling
Lu, Haoda
Gole, Laurent
Yu, Weimiao
Ngeow, Joanne
Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level
description 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.
author2 Lee Kong Chian School of Medicine (LKCMedicine)
author_facet Lee Kong Chian School of Medicine (LKCMedicine)
Li, Longjie
Kolinjivadi, Arun Mouli
Ong, Kok Haur
Young, David M.
Marini, Gabriel Pik Liang
Chan, Sock Hoai
Chong, Siao Ting
Chew, Ee Ling
Lu, Haoda
Gole, Laurent
Yu, Weimiao
Ngeow, Joanne
format Article
author Li, Longjie
Kolinjivadi, Arun Mouli
Ong, Kok Haur
Young, David M.
Marini, Gabriel Pik Liang
Chan, Sock Hoai
Chong, Siao Ting
Chew, Ee Ling
Lu, Haoda
Gole, Laurent
Yu, Weimiao
Ngeow, Joanne
author_sort Li, Longjie
title Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level
title_short Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level
title_full Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level
title_fullStr Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level
title_full_unstemmed Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level
title_sort automatic dna replication tract measurement to assess replication and repair dynamics at the single-molecule level
publishDate 2023
url https://hdl.handle.net/10356/164980
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