{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T14:47:25Z","timestamp":1777560445487,"version":"3.51.4"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2021,6,24]],"date-time":"2021-06-24T00:00:00Z","timestamp":1624492800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Simon Fraser University President\u2019s Research"},{"DOI":"10.13039\/501100000038","name":"NSERC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CREATE scholarship"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>A sequencing-based genomic assay such as ChIP-seq outputs a real-valued signal for each position in the genome that measures the strength of activity at that position. Most genomic signals lack the property of variance stabilization. That is, a difference between 0 and 100 reads usually has a very different statistical importance from a difference between 1000 and 1100 reads. A statistical model such as a negative binomial distribution can account for this pattern, but learning these models is computationally challenging. Therefore, many applications\u2014including imputation and segmentation and genome annotation (SAGA)\u2014instead use Gaussian models and use a transformation such as log or inverse hyperbolic sine (asinh) to stabilize variance.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We show here that existing transformations do not fully stabilize variance in genomic datasets. To solve this issue, we propose VSS, a method that produces variance-stabilized signals for sequencing-based genomic signals. VSS learns the empirical relationship between the mean and variance of a given signal dataset and produces transformed signals that normalize for this dependence. We show that VSS successfully stabilizes variance and that doing so improves downstream applications such as SAGA. VSS will eliminate the need for downstream methods to implement complex mean\u2013variance relationship models, and will enable genomic signals to be easily understood by eye.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/faezeh-bayat\/VSS<\/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\/btab457","type":"journal-article","created":{"date-parts":[[2021,6,18]],"date-time":"2021-06-18T07:09:52Z","timestamp":1624000192000},"page":"4383-4391","source":"Crossref","is-referenced-by-count":6,"title":["VSS: variance-stabilized signals for sequencing-based genomic signals"],"prefix":"10.1093","volume":"37","author":[{"given":"Faezeh","family":"Bayat","sequence":"first","affiliation":[{"name":"Department of Computing Science, Simon Fraser University , Burnaby, BC V5A 1S6, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2502-0262","authenticated-orcid":false,"given":"Maxwell","family":"Libbrecht","sequence":"additional","affiliation":[{"name":"Department of Computing Science, Simon Fraser University , Burnaby, BC V5A 1S6, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,6,24]]},"reference":[{"key":"2023061310453782800_btab457-B1","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol"},{"key":"2023061310453782800_btab457-B2","doi-asserted-by":"crossref","first-page":"1765","DOI":"10.1038\/nprot.2013.099","article-title":"Count-based differential expression analysis of RNA sequencing data using R and Bioconductor","volume":"8","author":"Anders","year":"2013","journal-title":"Nat. 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