{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T14:04:04Z","timestamp":1769522644492,"version":"3.49.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2023,10,31]],"date-time":"2023-10-31T00:00:00Z","timestamp":1698710400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Korea government","award":["2020R1A2C2005612"],"award-info":[{"award-number":["2020R1A2C2005612"]}]},{"name":"Korea government","award":["2022R1G1A1004613"],"award-info":[{"award-number":["2022R1G1A1004613"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The origins of replication sites (ORIs) are precise regions inside the DNA sequence where the replication process begins. These locations are critical for preserving the genome\u2019s integrity during cell division and guaranteeing the faithful transfer of genetic data from generation to generation. The advent of experimental techniques has aided in the discovery of ORIs in many species. Experimentation, on the other hand, is often more time-consuming and pricey than computational approaches, and it necessitates specific equipment and knowledge. Recently, ORI sites have been predicted using computational techniques like motif-based searches and artificial intelligence algorithms based on sequence characteristics and chromatin states.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this article, we developed ORI-Explorer, a unique artificial intelligence-based technique that combines multiple feature engineering techniques to train CatBoost Classifier for recognizing ORIs from four distinct eukaryotic species. ORI-Explorer was created by utilizing a unique combination of three traditional feature-encoding techniques and a feature set obtained from a deep-learning neural network model. The ORI-Explorer has significantly outperformed current predictors on the testing dataset. Furthermore, by employing the sophisticated SHapley Additive exPlanation method, we give crucial insights that aid in comprehending model success, highlighting the most relevant features vital for forecasting cell-specific ORIs. ORI-Explorer is also intended to aid community-wide attempts in discovering potential ORIs and developing innovative verifiable biological hypotheses.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The used datasets along with the source code are made available through https:\/\/github.com\/Z-Abbas\/ORI-Explorer and https:\/\/zenodo.org\/record\/8358679.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad664","type":"journal-article","created":{"date-parts":[[2023,11,6]],"date-time":"2023-11-06T13:01:11Z","timestamp":1699275671000},"source":"Crossref","is-referenced-by-count":18,"title":["ORI-Explorer: a unified cell-specific tool for origin of replication sites prediction by feature fusion"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1472-183X","authenticated-orcid":false,"given":"Zeeshan","family":"Abbas","sequence":"first","affiliation":[{"name":"Department of Electronics and Information Engineering, Jeonbuk National University , Jeonju 54896, South Korea"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0914-7132","authenticated-orcid":false,"given":"Mobeen Ur","family":"Rehman","sequence":"additional","affiliation":[{"name":"Khalifa University Center for Autonomous Robotic Systems (KUCARS), Khalifa University , Abu Dhabi, United Arab Emirates"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5678-3479","authenticated-orcid":false,"given":"Hilal","family":"Tayara","sequence":"additional","affiliation":[{"name":"School of International Engineering and Science, Jeonbuk National University , Jeonju 54896, South Korea"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1952-0001","authenticated-orcid":false,"given":"Kil To","family":"Chong","sequence":"additional","affiliation":[{"name":"Department of Electronics and Information Engineering, Jeonbuk National University , Jeonju 54896, South Korea"},{"name":"Advances Electronics and Information Research Center, Jeonbuk National University , Jeonju 54896, South Korea"}]}],"member":"286","published-online":{"date-parts":[[2023,10,31]]},"reference":[{"key":"2023111117021901200_btad664-B1","doi-asserted-by":"publisher","first-page":"2533","DOI":"10.1109\/TCBB.2021.3083789","article-title":"ZayyuNet- A unified deep learning model for the identification of epigenetic modifications using raw genomic sequences","volume":"19","author":"Abbas","year":"2022","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"2023111117021901200_btad664-B2","author":"Agarap","year":"2018"},{"key":"2023111117021901200_btad664-B3","first-page":"2623","author":"Akiba","year":"2019"},{"key":"2023111117021901200_btad664-B4","first-page":"6","article-title":"Comparison between XGBoost, lightGBM and CatBoost using a home credit dataset","volume":"13","author":"Al Daoud","year":"2019","journal-title":"Int J Comput Inf Eng"},{"key":"2023111117021901200_btad664-B5","doi-asserted-by":"crossref","first-page":"1703","DOI":"10.1126\/science.1085544","article-title":"The deep roots of eukaryotes","volume":"300","author":"Baldauf","year":"2003","journal-title":"Science"},{"key":"2023111117021901200_btad664-B6","doi-asserted-by":"crossref","first-page":"876","DOI":"10.1128\/MMBR.00029-06","article-title":"DNA replication in the archaea","volume":"70","author":"Barry","year":"2006","journal-title":"Microbiol Mol Biol Rev"},{"key":"2023111117021901200_btad664-B7","doi-asserted-by":"crossref","first-page":"eaah6317","DOI":"10.1126\/science.aah6317","article-title":"Mechanisms for initiating cellular DNA replication","volume":"355","author":"Bleichert","year":"2017","journal-title":"Science"},{"key":"2023111117021901200_btad664-B8","first-page":"785","author":"Chen","year":"2016"},{"key":"2023111117021901200_btad664-B9","first-page":"1","article-title":"Xgboost: extreme gradient boosting. R Package Version 0.4-2","author":"Chen","year":"2015"},{"key":"2023111117021901200_btad664-B10","author":"Chung","year":"2014"},{"key":"2023111117021901200_btad664-B11","doi-asserted-by":"crossref","first-page":"e2003243","DOI":"10.1371\/journal.pbio.2003243","article-title":"60 years ago, Francis Crick changed the logic of biology","volume":"15","author":"Cobb","year":"2017","journal-title":"PLoS Biol"},{"key":"2023111117021901200_btad664-B12","doi-asserted-by":"crossref","first-page":"9780293","DOI":"10.34133\/2022\/9780293","article-title":"Accurate identification of DNA replication origin by fusing epigenomics and chromatin interaction information","volume":"2022","author":"Dao","year":"2022","journal-title":"Research"},{"key":"2023111117021901200_btad664-B13","doi-asserted-by":"crossref","first-page":"1940","DOI":"10.1093\/bib\/bbaa017","article-title":"A computational platform to identify origins of replication sites in eukaryotes","volume":"22","author":"Dao","year":"2021","journal-title":"Brief Bioinform"},{"key":"2023111117021901200_btad664-B14","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/nature25787","article-title":"The mechanism of eukaryotic CMG helicase activation","volume":"555","author":"Douglas","year":"2018","journal-title":"Nature"},{"key":"2023111117021901200_btad664-B15","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1038\/s41467-019-08302-1","article-title":"Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer","volume":"10","author":"Du","year":"2019","journal-title":"Nat Commun"},{"key":"2023111117021901200_btad664-B16","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.1093\/bioinformatics\/bts151","article-title":"DeOri: a database of eukaryotic DNA replication origins","volume":"28","author":"Gao","year":"2012","journal-title":"Bioinformatics"},{"key":"2023111117021901200_btad664-B17","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/1471-2105-9-79","article-title":"Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes","volume":"9","author":"Gao","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023111117021901200_btad664-B18","first-page":"2021","author":"He","year":"2021"},{"key":"2023111117021901200_btad664-B19","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1162\/neco.1997.9.8.1735","article-title":"Long short-term memory","volume":"9","author":"Hochreiter","year":"1997","journal-title":"Neural Comput"},{"key":"2023111117021901200_btad664-B20","doi-asserted-by":"crossref","first-page":"4425","DOI":"10.1016\/j.egyr.2021.07.008","article-title":"A novel feature engineered-CatBoost-based supervised machine learning framework for electricity theft detection","volume":"7","author":"Hussain","year":"2021","journal-title":"Energy Rep"},{"key":"2023111117021901200_btad664-B21","doi-asserted-by":"crossref","first-page":"15655","DOI":"10.3390\/ijms232415655","article-title":"XML-CIMT: explainable machine learning (XML) model for predicting chemical-induced mitochondrial toxicity","volume":"23","author":"Jaganathan","year":"2022","journal-title":"Int J Mol Sci"},{"key":"2023111117021901200_btad664-B22","author":"Ke","year":"2017"},{"key":"2023111117021901200_btad664-B23","doi-asserted-by":"crossref","first-page":"bbaa159","DOI":"10.1093\/bib\/bbaa159","article-title":"DeepATT: a hybrid category attention neural network for identifying functional effects of DNA sequences","volume":"22","author":"Li","year":"2021","journal-title":"Brief Bioinform"},{"key":"2023111117021901200_btad664-B24","doi-asserted-by":"crossref","first-page":"3086","DOI":"10.1093\/bioinformatics\/bty312","article-title":"iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC","volume":"34","author":"Liu","year":"2018","journal-title":"Bioinformatics"},{"key":"2023111117021901200_btad664-B25","author":"Lundberg","year":"2017"},{"key":"2023111117021901200_btad664-B26","doi-asserted-by":"crossref","first-page":"482","DOI":"10.3389\/fmicb.2014.00482","article-title":"Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes","volume":"5","author":"Luo","year":"2014","journal-title":"Front Microbiol"},{"key":"2023111117021901200_btad664-B27","doi-asserted-by":"crossref","first-page":"a010207","DOI":"10.1101\/cshperspect.a010207","article-title":"Chromatin and DNA replication","volume":"5","author":"MacAlpine","year":"2013","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"2023111117021901200_btad664-B28","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.dnarep.2018.09.003","article-title":"Regulation of the initiation of DNA replication in human cells","volume":"72","author":"Moiseeva","year":"2018","journal-title":"DNA Repair (Amst)"},{"key":"2023111117021901200_btad664-B29","doi-asserted-by":"crossref","first-page":"e00119","DOI":"10.1128\/JB.00119-19","article-title":"Does the semiconservative nature of DNA replication facilitate coherent phenotypic diversity?","volume":"201","author":"Norris","year":"2019","journal-title":"J Bacteriol"},{"key":"2023111117021901200_btad664-B30","author":"Prokhorenkova","year":"2018"},{"key":"2023111117021901200_btad664-B31","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.biosystems.2017.12.005","article-title":"Prediction of replication sites in Saccharomyces cerevisiae genome using DNA segment properties: multi-view ensemble learning (MEL) approach","volume":"163","author":"Singh","year":"2018","journal-title":"Biosystems"},{"key":"2023111117021901200_btad664-B32","author":"Vaswani","year":"2017"},{"key":"2023111117021901200_btad664-B33","doi-asserted-by":"crossref","first-page":"bbaa275","DOI":"10.1093\/bib\/bbaa275","article-title":"Computational prediction and interpretation of cell-specific replication origin sites from multiple eukaryotes by exploiting stacking framework","volume":"22","author":"Wei","year":"2021","journal-title":"Brief Bioinform"},{"key":"2023111117021901200_btad664-B34","doi-asserted-by":"crossref","first-page":"bbad095","DOI":"10.1093\/bib\/bbad095","article-title":"DeepFormer: a hybrid network based on convolutional neural network and flow-attention mechanism for identifying the function of DNA sequences","volume":"24","author":"Yao","year":"2023","journal-title":"Brief Bioinform"},{"key":"2023111117021901200_btad664-B35","doi-asserted-by":"crossref","first-page":"69783","DOI":"10.18632\/oncotarget.11975","article-title":"iOri-Human: identify human origin of replication by incorporating dinucleotide physicochemical properties into pseudo nucleotide composition","volume":"7","author":"Zhang","year":"2016","journal-title":"Oncotarget"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad664\/52713673\/btad664.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/11\/btad664\/53217249\/btad664.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/11\/btad664\/53217249\/btad664.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,11]],"date-time":"2023-11-11T17:03:03Z","timestamp":1699722183000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad664\/7334464"}},"subtitle":[],"editor":[{"given":"Anthony","family":"Mathelier","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2023,10,31]]},"references-count":35,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2023,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad664","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,11,1]]},"published":{"date-parts":[[2023,10,31]]},"article-number":"btad664"}}