{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T10:54:19Z","timestamp":1782471259010,"version":"3.54.5"},"reference-count":66,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,11,18]],"date-time":"2021-11-18T00:00:00Z","timestamp":1637193600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["PKU2021LCXQ015"],"award-info":[{"award-number":["PKU2021LCXQ015"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009399","name":"Peking University Third Hospital","doi-asserted-by":"publisher","award":["BYSYYZD2021001"],"award-info":[{"award-number":["BYSYYZD2021001"]}],"id":[{"id":"10.13039\/501100009399","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170493"],"award-info":[{"award-number":["32170493"]}],"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":["32170656"],"award-info":[{"award-number":["32170656"]}],"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":["H16-82003137"],"award-info":[{"award-number":["H16-82003137"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Rapid advances in high-throughput sequencing technologies have led to the discovery of thousands of extrachromosomal circular DNAs (eccDNAs) in the human genome. Loss-of-function experiments are difficult to conduct on circular and linear chromosomes, as they usually overlap. Hence, it is challenging to interpret the molecular functions of eccDNAs. Here, we present CircleBase (http:\/\/circlebase.maolab.org), an integrated resource and analysis platform used to curate and interpret eccDNAs in multiple cell types. CircleBase identifies putative functional eccDNAs by incorporating sequencing datasets, computational predictions, and manual annotations. It classifies them into six sections including targeting genes, epigenetic regulations, regulatory elements, chromatin accessibility, chromatin interactions, and genetic variants. The eccDNA targeting and regulatory networks are displayed by informative visualization tools and then prioritized. Functional enrichment analyses revealed that the top-ranked cancer cell eccDNAs were enriched in oncogenic pathways such as the Ras and PI3K-Akt signaling pathways. In contrast, eccDNAs from healthy individuals were not significantly enriched. CircleBase provides a user-friendly interface for searching, browsing, and analyzing eccDNAs in various cell\/tissue types. Thus, it is useful to screen for potential functional eccDNAs and interpret their molecular mechanisms in human cancers and other diseases.<\/jats:p>","DOI":"10.1093\/nar\/gkab1104","type":"journal-article","created":{"date-parts":[[2021,10,25]],"date-time":"2021-10-25T11:09:38Z","timestamp":1635160178000},"page":"D72-D82","source":"Crossref","is-referenced-by-count":44,"title":["CircleBase: an integrated resource and analysis platform for human eccDNAs"],"prefix":"10.1093","volume":"50","author":[{"given":"Xiaolu","family":"Zhao","sequence":"first","affiliation":[{"name":"Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China"},{"name":"National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China"},{"name":"Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China"},{"name":"Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology (Peking University Third Hospital), Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leisheng","family":"Shi","sequence":"additional","affiliation":[{"name":"Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China"},{"name":"University of Chinese Academy of Sciences, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shasha","family":"Ruan","sequence":"additional","affiliation":[{"name":"Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China"},{"name":"The First Clinical College of Wuhan University, Wuhan, Hubei, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjian","family":"Bi","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yifan","family":"Chen","sequence":"additional","affiliation":[{"name":"Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China"},{"name":"Biobank, Peking University Third Hospital, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lin","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3896-0002","authenticated-orcid":false,"given":"Yifan","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Biochemistry & Molecular Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingkun","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China"},{"name":"University of Chinese Academy of Sciences, Beijing, China"},{"name":"Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2126-1376","authenticated-orcid":false,"given":"Jie","family":"Qiao","sequence":"additional","affiliation":[{"name":"Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China"},{"name":"National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China"},{"name":"Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China"},{"name":"Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology (Peking University Third Hospital), Beijing, China"},{"name":"Beijing Advanced Innovation Center for Genomics, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0852-4266","authenticated-orcid":false,"given":"Fengbiao","family":"Mao","sequence":"additional","affiliation":[{"name":"Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,11,18]]},"reference":[{"key":"2022010507322526900_B1","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1101\/gr.907603","article-title":"Extrachromosomal circular DNA of tandemly repeated genomic sequences in Drosophila","volume":"13","author":"Cohen","year":"2003","journal-title":"Genome Res."},{"key":"2022010507322526900_B2","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1073\/pnas.53.2.356","article-title":"Molecular size and circularity of DNA in cells of mammals and higher plants","volume":"53","author":"Hotta","year":"1965","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2022010507322526900_B3","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/S0140-6736(65)90131-5","article-title":"Minute chromatin bodies in malignant tumours of childhood","volume":"1","author":"Cox","year":"1965","journal-title":"Lancet"},{"key":"2022010507322526900_B4","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.gde.2021.01.001","article-title":"Extrachromosomal DNA (ecDNA) in cancer pathogenesis","volume":"66","author":"Wu","year":"2021","journal-title":"Curr. Opin. Genet. Dev."},{"key":"2022010507322526900_B5","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1016\/j.ccell.2021.03.006","article-title":"Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription","volume":"39","author":"Zhu","year":"2021","journal-title":"Cancer Cell"},{"key":"2022010507322526900_B6","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1038\/nature21356","article-title":"Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity","volume":"543","author":"Turner","year":"2017","journal-title":"Nature"},{"key":"2022010507322526900_B7","doi-asserted-by":"crossref","first-page":"1330","DOI":"10.1016\/j.cell.2019.10.039","article-title":"Functional enhancers shape extrachromosomal oncogene amplifications","volume":"179","author":"Morton","year":"2019","journal-title":"Cell"},{"key":"2022010507322526900_B8","first-page":"5563","article-title":"Isolation and structural analysis of a 1.2-megabase N-myc amplicon from a human neuroblastoma","volume":"12","author":"Schneider","year":"1992","journal-title":"Mol. Cell Biol."},{"key":"2022010507322526900_B9","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1038\/s41586-019-1763-5","article-title":"Circular ecDNA promotes accessible chromatin and high oncogene expression","volume":"575","author":"Wu","year":"2019","journal-title":"Nature"},{"key":"2022010507322526900_B10","first-page":"1179","article-title":"Amplicon structure in multidrug-resistant murine cells: a nonrearranged region of genomic DNA corresponding to large circular DNA","volume":"12","author":"St\u00e5hl","year":"1992","journal-title":"Mole. Cell Biol."},{"key":"2022010507322526900_B11","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1126\/science.1241328","article-title":"Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA","volume":"343","author":"Nathanson","year":"2014","journal-title":"Science"},{"key":"2022010507322526900_B12","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/s41568-019-0128-6","article-title":"Extrachromosomal oncogene amplification in tumour pathogenesis and evolution","volume":"19","author":"Verhaak","year":"2019","journal-title":"Nat. Rev. Can."},{"key":"2022010507322526900_B13","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/S1476-5586(03)80002-7","article-title":"c-Myc-induced extrachromosomal elements carry active chromatin","volume":"5","author":"Smith","year":"2003","journal-title":"Neoplasia"},{"key":"2022010507322526900_B14","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1038\/s41588-019-0547-z","article-title":"Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma","volume":"52","author":"Koche","year":"2020","journal-title":"Nat. Genet."},{"key":"2022010507322526900_B15","first-page":"1","article-title":"Molecular characterization of cell-free eccDNAs in human plasma","volume":"7","author":"Zhu","year":"2017","journal-title":"Scient. Rep."},{"key":"2022010507322526900_B16","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene Expression Omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"Edgar","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B17","doi-asserted-by":"crossref","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"NCBI GEO: archive for functional genomics data sets-update","volume":"41","author":"Barrett","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B18","doi-asserted-by":"crossref","DOI":"10.1016\/j.gpb.2021.08.001","article-title":"The genome sequence archive family: toward explosive data growth and diverse data types","author":"Chen","year":"2021","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2022010507322526900_B19","doi-asserted-by":"crossref","first-page":"1836","DOI":"10.1101\/gr.253492.119","article-title":"Identification and dynamic quantification of regulatory elements using total RNA","volume":"29","author":"Duttke","year":"2019","journal-title":"Genome Res."},{"key":"2022010507322526900_B20","doi-asserted-by":"crossref","first-page":"D1431","DOI":"10.1093\/nar\/gkaa922","article-title":"VARAdb: a comprehensive variation annotation database for human","volume":"49","author":"Pan","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B21","doi-asserted-by":"crossref","first-page":"1428","DOI":"10.1038\/ng.3950","article-title":"Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines","volume":"49","author":"Cao","year":"2017","journal-title":"Nat. Genet."},{"key":"2022010507322526900_B22","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/database\/bax028","article-title":"GeneHancer: genome-wide integration of enhancers and target genes in GeneCards","volume":"2017","author":"Fishilevich","year":"2017","journal-title":"Database (Oxford)"},{"key":"2022010507322526900_B23","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1016\/j.ccell.2018.08.018","article-title":"HOXA9 reprograms the enhancer landscape to promote leukemogenesis","volume":"34","author":"Sun","year":"2018","journal-title":"Cancer Cell"},{"key":"2022010507322526900_B24","doi-asserted-by":"crossref","first-page":"D164","DOI":"10.1093\/nar\/gkv1002","article-title":"dbSUPER: a database of super-enhancers in mouse and human genome","volume":"44","author":"Khan","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B25","first-page":"D58","article-title":"EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue\/cell types across nine species","volume":"48","author":"Gao","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B26","first-page":"D198","article-title":"SEA version 3.0: a comprehensive extension and update of the Super-Enhancer archive","volume":"48","author":"Chen","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B27","doi-asserted-by":"crossref","first-page":"D235","DOI":"10.1093\/nar\/gky1025","article-title":"SEdb: a comprehensive human super-enhancer database","volume":"47","author":"Jiang","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B28","doi-asserted-by":"crossref","first-page":"2478","DOI":"10.1038\/nprot.2017.124","article-title":"Chromatin-state discovery and genome annotation with ChromHMM","volume":"12","author":"Ernst","year":"2017","journal-title":"Nat. Protoc."},{"key":"2022010507322526900_B29","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"Dunham","year":"2012","journal-title":"Nature"},{"key":"2022010507322526900_B30","doi-asserted-by":"crossref","first-page":"D1044","DOI":"10.1093\/nar\/gky1139","article-title":"OncoBase: a platform for decoding regulatory somatic mutations in human cancers","volume":"47","author":"Li","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B31","doi-asserted-by":"crossref","first-page":"2727","DOI":"10.1093\/bioinformatics\/btw375","article-title":"4DGenome: a comprehensive database of chromatin interactions","volume":"32","author":"Teng","year":"2016","journal-title":"Bioinformatics"},{"key":"2022010507322526900_B32","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1038\/ncomms1396","article-title":"Ranking stability and super-stable nodes in complex networks","volume":"2","author":"Ghoshal","year":"2011","journal-title":"Nat. Commun."},{"key":"2022010507322526900_B33","doi-asserted-by":"crossref","first-page":"100141","DOI":"10.1016\/j.xinn.2021.100141","article-title":"clusterProfiler 4.0: a universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"The Innovation"},{"key":"2022010507322526900_B34","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"2022010507322526900_B35","doi-asserted-by":"crossref","first-page":"D355","DOI":"10.1093\/nar\/gkp896","article-title":"KEGG for representation and analysis of molecular networks involving diseases and drugs","volume":"38","author":"Kanehisa","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B36","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate - a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J R Stat Soc B"},{"key":"2022010507322526900_B37","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/s41576-018-0089-8","article-title":"Chromatin accessibility and the regulatory epigenome","volume":"20","author":"Klemm","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"2022010507322526900_B38","doi-asserted-by":"crossref","first-page":"D55","DOI":"10.1093\/nar\/gkaa943","article-title":"ATACdb: a comprehensive human chromatin accessibility database","volume":"49","author":"Wang","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B39","doi-asserted-by":"crossref","first-page":"D729","DOI":"10.1093\/nar\/gky1094","article-title":"Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis","volume":"47","author":"Zheng","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B40","doi-asserted-by":"crossref","first-page":"eaav1898","DOI":"10.1126\/science.aav1898","article-title":"The chromatin accessibility landscape of primary human cancers","volume":"362","author":"Corces","year":"2018","journal-title":"Science"},{"key":"2022010507322526900_B41","doi-asserted-by":"crossref","first-page":"e46255","DOI":"10.15252\/embr.201846255","article-title":"ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data","volume":"19","author":"Oki","year":"2018","journal-title":"EMBO Rep."},{"key":"2022010507322526900_B42","doi-asserted-by":"crossref","first-page":"D104","DOI":"10.1093\/nar\/gkaa1057","article-title":"GTRD: an integrated view of transcription regulation","volume":"49","author":"Kolmykov","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B43","first-page":"D180","article-title":"ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments","volume":"48","author":"Cheneby","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B44","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1038\/nbt1010-1045","article-title":"The NIH roadmap epigenomics mapping consortium","volume":"28","author":"Bernstein","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"2022010507322526900_B45","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"dbSNP: the NCBI database of genetic variation","volume":"29","author":"Sherry","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B46","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1038\/s41586-020-2308-7","article-title":"The mutational constraint spectrum quantified from variation in 141,456 humans","volume":"581","author":"Karczewski","year":"2020","journal-title":"Nature"},{"key":"2022010507322526900_B47","doi-asserted-by":"crossref","first-page":"D1005","DOI":"10.1093\/nar\/gky1120","article-title":"The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019","volume":"47","author":"Buniello","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B48","doi-asserted-by":"crossref","first-page":"D869","DOI":"10.1093\/nar\/gkv1317","article-title":"GWASdb v2: an update database for human genetic variants identified by genome-wide association studies","volume":"44","author":"Li","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B49","first-page":"D913","article-title":"Gene4Denovo: an integrated database and analytic platform for de novo mutations in humans","volume":"48","author":"Zhao","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B50","doi-asserted-by":"crossref","first-page":"D154","DOI":"10.1093\/nar\/gkv1308","article-title":"RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins","volume":"44","author":"Mao","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B51","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1126\/science.1262110","article-title":"Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans","volume":"348","author":"GTEx Consortium","year":"2015","journal-title":"Science"},{"key":"2022010507322526900_B52","doi-asserted-by":"crossref","first-page":"D971","DOI":"10.1093\/nar\/gkx861","article-title":"PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types","volume":"46","author":"Gong","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B53","doi-asserted-by":"crossref","first-page":"1740","DOI":"10.1093\/bioinformatics\/btw041","article-title":"BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications","volume":"32","author":"Cui","year":"2016","journal-title":"Bioinformatics"},{"key":"2022010507322526900_B54","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","article-title":"SciPy 1.0: fundamental algorithms for scientific computing in Python","volume":"17","author":"Virtanen","year":"2020","journal-title":"Nat. Methods"},{"key":"2022010507322526900_B55","doi-asserted-by":"crossref","first-page":"D92","DOI":"10.1093\/nar\/gkx918","article-title":"EpiDenovo: a platform for linking regulatory de novo mutations to developmental epigenetics and diseases","volume":"46","author":"Mao","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B56","doi-asserted-by":"crossref","first-page":"D1289","DOI":"10.1093\/nar\/gkaa1033","article-title":"OncoVar: an integrated database and analysis platform for oncogenic driver variants in cancers","volume":"49","author":"Wang","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B57","doi-asserted-by":"crossref","first-page":"D1046","DOI":"10.1093\/nar\/gkaa1070","article-title":"The UCSC Genome Browser database: 2021 update","volume":"49","author":"Navarro\u00a0Gonzalez","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507322526900_B58","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1038\/s41586-020-1969-6","article-title":"Pan-cancer analysis of whole genomes","volume":"578","author":"ICGC\/TCGA Pan-Cancer Analysis of Whole Genomes Consortium","year":"2020","journal-title":"Nature"},{"key":"2022010507322526900_B59","doi-asserted-by":"crossref","first-page":"W199","DOI":"10.1093\/nar\/gkz401","article-title":"WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs","volume":"47","author":"Liao","year":"2019","journal-title":"Nucleic Acids Rese."},{"key":"2022010507322526900_B60","doi-asserted-by":"crossref","first-page":"891-+","DOI":"10.1038\/s41588-020-0678-2","article-title":"Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers","volume":"52","author":"Kim","year":"2020","journal-title":"Nat. Genet."},{"key":"2022010507322526900_B61","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1016\/j.annonc.2020.03.303","article-title":"Extrachromosomal DNA\u2014relieving heredity constraints, accelerating tumour evolution","volume":"31","author":"Bailey","year":"2020","journal-title":"Ann. Oncol."},{"key":"2022010507322526900_B62","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1007\/978-1-0716-0323-9_15","article-title":"Circle-Seq: isolation and sequencing of chromosome-derived circular DNA elements in cells","volume":"2119","author":"Moller","year":"2020","journal-title":"Methods Mol. Biol."},{"key":"2022010507322526900_B63","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1186\/s13059-021-02406-y","article-title":"SMOOTH-seq: single-cell genome sequencing of human cells on a third-generation sequencing platform","volume":"22","author":"Fan","year":"2021","journal-title":"Genome Biol."},{"key":"2022010507322526900_B64","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1038\/s41467-018-08200-y","article-title":"Exploring the landscape of focal amplifications in cancer using AmpliconArchitect","volume":"10","author":"Deshpande","year":"2019","journal-title":"Nat. Commun."},{"key":"2022010507322526900_B65","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1186\/s12859-019-3160-3","article-title":"Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads","volume":"20","author":"Prada-Luengo","year":"2019","journal-title":"BMC Bioinformatics"},{"key":"2022010507322526900_B66","doi-asserted-by":"crossref","first-page":"eaba2489","DOI":"10.1126\/sciadv.aba2489","article-title":"ATAC-seq identifies thousands of extrachromosomal circular DNA in cancer and cell lines","volume":"6","author":"Kumar","year":"2020","journal-title":"Sci. Adv."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D72\/42057738\/gkab1104.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D72\/42057738\/gkab1104.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,10]],"date-time":"2024-09-10T18:51:19Z","timestamp":1725994279000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/D1\/D72\/6430829"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11,18]]},"references-count":66,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2021,11,18]]},"published-print":{"date-parts":[[2022,1,7]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkab1104","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,7]]},"published":{"date-parts":[[2021,11,18]]}}}