{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,16]],"date-time":"2025-12-16T23:53:57Z","timestamp":1765929237086,"version":"3.48.0"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T00:00:00Z","timestamp":1762560000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["101001623-PALVIREVOL"],"award-info":[{"award-number":["101001623-PALVIREVOL"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Endogenous viral elements (EVEs) offer valuable insights into virus and host evolution, but their detection remains computationally and biologically challenging. We present HI-FEVER, a user-friendly Nextflow pipeline for the discovery of EVEs in eukaryotic host genomes. HI-FEVER is highly parallelizable and customizable, ensuring computational efficiency while allowing researchers to fine-tune parameters to their specific needs. Its output provides a comprehensive analysis of discovered EVEs, including detailed annotations which can provide evolutionary insights. HI-FEVER scales seamlessly to handle millions of viral protein queries across multiple host genomes on both laptops and high-performance computing nodes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The HI-FEVER source code is available on GitHub at https:\/\/github.com\/PaleovirologyLab\/hi-fever. Minimal reference databases, test datasets and benchmarking results are hosted on the Open Science Framework at https:\/\/osf.io\/y357r. A detailed wiki is available at https:\/\/github.com\/PaleovirologyLab\/hi-fever\/wiki, including usage instructions, parameter descriptions, and guidance on interpreting outputs. The pipeline includes a Pixi environment compatible with Conda and Apptainer containerization, and Docker images. HI-FEVER has been tested on Linux, Windows (via WSL2), and macOS (Intel and ARM64).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf610","type":"journal-article","created":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T13:10:04Z","timestamp":1762434604000},"source":"Crossref","is-referenced-by-count":0,"title":["HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6120-7211","authenticated-orcid":false,"given":"Laura","family":"Mu\u00f1oz-Baena","sequence":"first","affiliation":[{"name":"Department of Biology, University of Oxford , Oxford, OX1 3EL,","place":["United Kingdom"]}]},{"given":"Emma F","family":"Harding","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Oxford , Oxford, OX1 3EL,","place":["United Kingdom"]}]},{"given":"Jose Gabriel","family":"Nino Barreat","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Oxford , Oxford, OX1 3EL,","place":["United Kingdom"]},{"name":"Natural History Museum Life Sciences Department, , London, SW7 5BD,","place":["United Kingdom"]}]},{"given":"Cormac M","family":"Kinsella","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Oxford , Oxford, OX1 3EL,","place":["United Kingdom"]},{"name":"Swedish Museum of Natural History Department of Bioinformatics and Genetics, , Stockholm, SE-104 05,","place":["Sweden"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3328-6204","authenticated-orcid":false,"given":"Aris","family":"Katzourakis","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Oxford , Oxford, OX1 3EL,","place":["United 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