{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T15:15:39Z","timestamp":1777043739629,"version":"3.51.4"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T00:00:00Z","timestamp":1774483200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Prism\u2014National Precision Medicine Center in Oncology"},{"name":"France 2030 program and the French National Research Agency","award":["ANR-23-IAHU-0002"],"award-info":[{"award-number":["ANR-23-IAHU-0002"]}]},{"DOI":"10.13039\/100008884","name":"Edward P. Evans Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008884","id-type":"DOI","asserted-by":"publisher"}]},{"name":"INSERM ATIP-Avenir Program"},{"DOI":"10.13039\/501100016037","name":"Gustave Roussy Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100016037","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Qube Research & Technologies Foundation"},{"name":"ARC Foundation Fellowship program"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,4,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Liquid biopsy offers a non-invasive approach to study tumor-derived genetic material circulating in plasma. Beyond genetic alterations, the fragmentomic features of cell-free DNA\u2014such as fragment size, genomic position, and end-motifs\u2014provide valuable insights into the biological and clinical context of DNA release. fRagmentomics is a user-friendly R package designed to characterize cfDNA fragments overlapping one or multiple small mutations of any type, starting from an aligned sequencing file (BAM). It supports multiple mutation input formats, accommodates one-based and zero-based genomic conventions, resolves mutation representation ambiguities, and accepts any reference file in FASTA format. For each fragment overlapping a mutation of interest, fRagmentomics outputs fragment-level features including its fragment size, end-motifs, and mutational status, along with additional fragment-level or read-level information. The package implements an indel-aware and optionally soft-clip-preserving fragment size computation that improves accuracy over conventional size estimates based solely on aligned positions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>fRagmentomics is licensed under GNU General Public License v3.0 and available at https:\/\/github.com\/ElsaB-Lab\/fRagmentomics, https:\/\/anaconda.org\/elsab-lab\/r-fragmentomics and https:\/\/bioconductor.org\/packages\/fRagmentomics, with documentation and a tutorial.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Contact<\/jats:title>\n                    <jats:p>yoann.pradat@gustaveroussy.fr, elsa.bernard@gustaveroussy.fr<\/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\/btag152","type":"journal-article","created":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T12:40:46Z","timestamp":1774356046000},"source":"Crossref","is-referenced-by-count":0,"title":["<i>fRagmentomics<\/i>\n                    : an R package for integrating cell-free DNA fragment features with mutational status to support liquid biopsy interpretation"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-3237-092X","authenticated-orcid":false,"given":"Killian","family":"Maudet","sequence":"first","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, Gustave Roussy, Inserm UMR 1361 Cancer Data Science, IHU PRISM National PRecISion Medicine Center in Oncology , Villejuif, 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