{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T14:15:15Z","timestamp":1771337715318,"version":"3.50.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,24]],"date-time":"2023-05-24T00:00:00Z","timestamp":1684886400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"University of Texas Dell Medical School Research Funds"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Alternate (non-B) DNA-forming structures, such as Z-DNA, G-quadruplex, triplex have demonstrated a potential role in cancer etiology. It has been found that non-B DNA-forming sequences can stimulate genetic instability in human cancer genomes, implicating them in the development of cancer and other genetic diseases. While there exist several non-B prediction tools and databases, they lack the ability to both analyze and visualize non-B data within a cancer context. Herein, we introduce NBBC, a non-B DNA burden explorer in cancer, that offers analyses and visualizations for non-B DNA forming motifs. To do so, we introduce \u2018non-B burden\u2019 as a metric to summarize the prevalence of non-B DNA motifs at the gene-, signature- and genomic site-levels. Using our non-B burden metric, we developed two analyses modules within a cancer context to assist in exploring both gene- and motif-level non-B type heterogeneity among gene signatures. NBBC is designed to serve as a new analysis and visualization platform for the exploration of non-B DNA, guided by non-B burden as a novel marker.<\/jats:p>","DOI":"10.1093\/nar\/gkad379","type":"journal-article","created":{"date-parts":[[2023,5,24]],"date-time":"2023-05-24T22:49:52Z","timestamp":1684968592000},"page":"W357-W364","source":"Crossref","is-referenced-by-count":11,"title":["NBBC: a non-B DNA burden explorer in cancer"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4646-6936","authenticated-orcid":false,"given":"Qi","family":"Xu","sequence":"first","affiliation":[{"name":"Department of Oncology, Dell Medical School, The University of Texas at Austin , Austin , TX \u00a078712, USA"},{"name":"Department of Molecular Biosciences, The University of Texas at Austin , Austin, TX 78712, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3458-3024","authenticated-orcid":false,"given":"Jeanne","family":"Kowalski","sequence":"additional","affiliation":[{"name":"Department of Oncology, Dell Medical School, The University of Texas at Austin , Austin , TX \u00a078712, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,5,24]]},"reference":[{"key":"2023070504570888200_B1","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1007\/s00018-009-0131-2","article-title":"Non-B DNA structure-induced genetic instability and evolution","volume":"67","author":"Zhao","year":"2010","journal-title":"Cell. Mol. Life Sci."},{"key":"2023070504570888200_B2","doi-asserted-by":"crossref","first-page":"959258","DOI":"10.3389\/fgene.2022.959258","article-title":"Non-canonical DNA structures: diversity and disease association","volume":"13","author":"Bansal","year":"2022","journal-title":"Front. Genet."},{"key":"2023070504570888200_B3","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.tig.2022.11.005","article-title":"Noncanonical DNA structures are drivers of genome evolution","volume":"39","author":"Makova","year":"2023","journal-title":"Trends Genet."},{"key":"2023070504570888200_B4","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.pbiomolbio.2019.03.004","article-title":"Cancer mutational burden is shaped by G4 DNA, replication stress and mitochondrial dysfunction","volume":"147","author":"Bacolla","year":"2019","journal-title":"Prog. Biophys. Mol. 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Commun."},{"key":"2023070504570888200_B18","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1093\/nar\/gkaa1269","article-title":"Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome","volume":"49","author":"Guiblet","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023070504570888200_B19","doi-asserted-by":"crossref","first-page":"12599","DOI":"10.3390\/ijms222212599","article-title":"The relevance of G-quadruplexes for DNA repair","volume":"22","author":"Linke","year":"2021","journal-title":"Int. J. Mol. 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