{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T11:35:15Z","timestamp":1778585715244,"version":"3.51.4"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2020,3,27]],"date-time":"2020-03-27T00:00:00Z","timestamp":1585267200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["11971039"],"award-info":[{"award-number":["11971039"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["11471022"],"award-info":[{"award-number":["11471022"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["71532001"],"award-info":[{"award-number":["71532001"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Recruitment Program of Global Youth Experts of China"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Whole-genome sequencing (WGS) is widely used for copy number variation (CNV) detection. However, for most bacteria, their circular genome structure and high replication rate make reads more enriched near the replication origin. CNV detection based on read depth could be seriously influenced by such replication bias.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We show that the replication bias is widespread using \u223c200 bacterial WGS data. We develop CNV-BAC (CNV-Bacteria) that can properly normalize the replication bias and other known biases in bacterial WGS data and can accurately detect CNVs. Simulation and real data analysis show that CNV-BAC achieves the best performance in CNV detection compared with available algorithms.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>CNV-BAC is available at https:\/\/github.com\/XiDsLab\/CNV-BAC.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa208","type":"journal-article","created":{"date-parts":[[2020,3,23]],"date-time":"2020-03-23T08:08:19Z","timestamp":1584950899000},"page":"3890-3891","source":"Crossref","is-referenced-by-count":6,"title":["CNV-BAC: Copy number Variation Detection in Bacterial Circular Genome"],"prefix":"10.1093","volume":"36","author":[{"given":"Linjie","family":"Wu","sequence":"first","affiliation":[{"name":"School of Mathematical Sciences"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Han","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Mathematical Sciences"},{"name":"Center for Statistical Science , Peking University, Beijing 100871, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuchao","family":"Xia","sequence":"additional","affiliation":[{"name":"School of Applied Science , Beijing Information Science and Technology University, Beijing 100101, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7545-7361","authenticated-orcid":false,"given":"Ruibin","family":"Xi","sequence":"additional","affiliation":[{"name":"School of Mathematical Sciences"},{"name":"Center for Statistical Science , Peking University, Beijing 100871, China"},{"name":"Department of Biostatistics , Peking University, Beijing 100871, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,3,27]]},"reference":[{"key":"2023063011294252300_btaa208-B1","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1101\/gr.114876.110","article-title":"CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing","volume":"21","author":"Abyzov","year":"2011","journal-title":"Genome Res"},{"key":"2023063011294252300_btaa208-B2","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1093\/bioinformatics\/btr670","article-title":"Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data","volume":"28","author":"Boeva","year":"2012","journal-title":"Bioinformatics"},{"key":"2023063011294252300_btaa208-B3","doi-asserted-by":"crossref","first-page":"1708","DOI":"10.1093\/bioinformatics\/btv070","article-title":"CNOGpro: detection and quantification of CNVs in prokaryotic whole-genome sequencing data","volume":"31","author":"Brynildsrud","year":"2015","journal-title":"Bioinformatics"},{"key":"2023063011294252300_btaa208-B4","doi-asserted-by":"crossref","first-page":"1745","DOI":"10.1073\/pnas.1814265116","article-title":"Sequential evolution of virulence and resistance during clonal spread of community-acquired methicillin-resistant Staphylococcus aureus","volume":"116","author":"Copin","year":"2019","journal-title":"Proc. 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