{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:03:10Z","timestamp":1792785790159,"version":"4.5.0"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,11,2]],"date-time":"2020-11-02T00:00:00Z","timestamp":1604275200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005416","name":"Norwegian Research Council","doi-asserted-by":"publisher","award":["187615"],"award-info":[{"award-number":["187615"]}],"id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Helse S\u00f8r-\u00d8st and the University of Oslo through the Centre for Molecular Medicine Norway"},{"DOI":"10.13039\/501100005416","name":"Norwegian Research Council","doi-asserted-by":"publisher","award":["288404"],"award-info":[{"award-number":["288404"]}],"id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008730","name":"Norwegian Cancer Society","doi-asserted-by":"publisher","award":["197884"],"award-info":[{"award-number":["197884"]}],"id":[{"id":"10.13039\/100008730","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Accurate motif enrichment analyses depend on the choice of background DNA sequences used, which should ideally match the sequence composition of the foreground sequences. It is important to avoid false positive enrichment due to sequence biases in the genome, such as GC-bias. Therefore, relying on an appropriate set of background sequences is crucial for enrichment analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed BiasAway, a command line tool and its dedicated easy-to-use web server to generate synthetic sequences matching any k-mer nucleotide composition or select genomic DNA sequences matching the mononucleotide composition of the foreground sequences through four different models. For genomic sequences, we provide precomputed partitions of genomes from nine species with five different bin sizes to generate appropriate genomic background sequences.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>BiasAway source code is freely available from Bitbucket (https:\/\/bitbucket.org\/CBGR\/biasaway) and can be easily installed using bioconda or pip. The web server is available at https:\/\/biasaway.uio.no and a detailed documentation is available at https:\/\/biasaway.readthedocs.io.<\/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\/btaa928","type":"journal-article","created":{"date-parts":[[2020,10,19]],"date-time":"2020-10-19T11:31:07Z","timestamp":1603107067000},"page":"1607-1609","source":"Crossref","is-referenced-by-count":31,"title":["BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6459-6224","authenticated-orcid":false,"given":"Aziz","family":"Khan","sequence":"first","affiliation":[{"name":"Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , 0349 Oslo, Norway"},{"name":"Stanford University School of Medicine, Stanford Cancer Institute , Stanford, CA 94304, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafael","family":"Riudavets Puig","sequence":"additional","affiliation":[{"name":"Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , 0349 Oslo, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Boddie","sequence":"additional","affiliation":[{"name":"Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , 0349 Oslo, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5127-5459","authenticated-orcid":false,"given":"Anthony","family":"Mathelier","sequence":"additional","affiliation":[{"name":"Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , 0349 Oslo, Norway"},{"name":"Department of Medical Genetics, Oslo University Hospital , 0424 Oslo, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,11,2]]},"reference":[{"key":"2023051709444339600_btaa928-B1","doi-asserted-by":"crossref","first-page":"1720","DOI":"10.1126\/science.1162327","article-title":"Diversity and complexity in DNA recognition by transcription factors","volume":"324","author":"Badis","year":"2009","journal-title":"Science"},{"key":"2023051709444339600_btaa928-B2","doi-asserted-by":"crossref","first-page":"24","DOI":"10.3389\/fgene.2016.00024","article-title":"Analysis of genomic sequence motifs for deciphering transcription factor binding and transcriptional regulation in eukaryotic cells","volume":"7","author":"Boeva","year":"2016","journal-title":"Front. 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