{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T15:09:19Z","timestamp":1789744159367,"version":"4.0.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T00:00:00Z","timestamp":1788739200000},"content-version":"vor","delay-in-days":7,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Translating genomic peak data into biologically meaningful knowledge typically requires bioinformatics expertise, creating a barrier for non-technical users. We developed peakScout to bridge the gap between peaks, genes, and gene annotations, enabling users to quickly focus on biological context rather than bioinformatics skills, in a reproducible and robust fashion.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>peakScout is a command line and web-based program that performs bidirectional mapping between genomic peaks and genes. The peak-to-gene mode identifies which genes are potentially regulated by specific genomic regions, while the gene-to-peak mode reveals which regulatory elements might influence particular genes of interest. An algorithm for nearest-feature detection handles the complex spatial relationships between genomic elements, considering factors like distance constraints and feature overlaps.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The web version of peakScout is available at https:\/\/vandydata.github.io\/peakScout\/. The command line version is available at https:\/\/github.com\/vandydata\/peakScout and archived on Zenodo (https:\/\/doi.org\/10.5281\/zenodo.21211605) under the GNU Affero General Public License v3.0. Installation instructions, example datasets, and usage examples are provided in the GitHub repository README file.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag653","type":"journal-article","created":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T11:22:52Z","timestamp":1788780172000},"source":"Crossref","is-referenced-by-count":0,"title":["peakScout\u2014a biologist-friendly tool for bidirectional peak-gene mapping"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4444-4979","authenticated-orcid":false,"given":"Alexander L","family":"Lin","sequence":"first","affiliation":[{"name":"Creative Data Solutions, Center for Stem Cell Biology, School of Medicine Basic Sciences, Vanderbilt University , Nashville, TN 37027,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-9154-2548","authenticated-orcid":false,"given":"Lana 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