{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,23]],"date-time":"2025-07-23T12:56:34Z","timestamp":1753275394812,"version":"3.37.3"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"22-23","license":[{"start":{"date-parts":[[2020,12,1]],"date-time":"2020-12-01T00:00:00Z","timestamp":1606780800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["DP190103407"],"award-info":[{"award-number":["DP190103407"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"publisher","award":["APP1162921","APP1184637"],"award-info":[{"award-number":["APP1162921","APP1184637"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Unbiased detection of protein\u2013protein and protein\u2013RNA interactions within ribonucleoprotein complexes are enabled through crosslinking followed by mass spectrometry. Yet, different methods detect different types of molecular interactions and therefore require the usage of different software packages with limited compatibility. We present crisscrosslinkeR, an R package that maps both protein\u2013protein and protein\u2013RNA interactions detected by different types of approaches for crosslinking with mass spectrometry. crisscrosslinkeR produces output files that are compatible with visualization using popular software packages for the generation of publication-quality figures.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>crisscrosslinkeR is a free and open-source package, available through GitHub: github.com\/egmg726\/crisscrosslinker.<\/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\/btaa1043","type":"journal-article","created":{"date-parts":[[2020,12,9]],"date-time":"2020-12-09T05:04:36Z","timestamp":1607490276000},"page":"5530-5532","source":"Crossref","is-referenced-by-count":3,"title":["crisscrosslinkeR: identification and visualization of protein\u2013RNA and protein\u2013protein interactions from crosslinking mass spectrometry"],"prefix":"10.1093","volume":"36","author":[{"given":"Emma H","family":"Gail","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Victoria 3800, Australia"},{"name":"Faculty of Medicine, Nursing and Health Sciences, Monash University , Clayton, Victoria 3800, Australia"}]},{"given":"Anup D","family":"Shah","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Victoria 3800, Australia"},{"name":"Faculty of Medicine, Nursing and Health Sciences, Monash University , Clayton, Victoria 3800, Australia"},{"name":"Monash Proteomics & Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University , Clayton, Victoria 3800, Australia"},{"name":"Monash Bioinformatics Platform, Monash Biomedicine Discovery Institute, Monash University , Clayton, Victoria 3800, Australia"}]},{"given":"Ralf B","family":"Schittenhelm","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Victoria 3800, Australia"},{"name":"Faculty of Medicine, Nursing and Health Sciences, Monash University , Clayton, Victoria 3800, Australia"},{"name":"Monash Proteomics & Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University , Clayton, Victoria 3800, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1085-6094","authenticated-orcid":false,"given":"Chen","family":"Davidovich","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Victoria 3800, Australia"},{"name":"Faculty of Medicine, Nursing and Health Sciences, Monash University , Clayton, Victoria 3800, Australia"},{"name":"EMBL-Australia and the ARC Centre of Excellence in Advanced Molecular Imaging , Clayton, Victoria 3800, Australia"}]}],"member":"286","published-online":{"date-parts":[[2020,12,21]]},"reference":[{"key":"2023062708411416500_btaa1043-B1","doi-asserted-by":"crossref","first-page":"3584","DOI":"10.1093\/bioinformatics\/bty366","article-title":"Jwalk and MNXL web server: model validation using restraints from crosslinking mass spectrometry","volume":"34","author":"Bullock","year":"2018","journal-title":"Bioinformatics"},{"key":"2023062708411416500_btaa1043-B2","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1016\/j.molcel.2016.06.029","article-title":"Comprehensive identification of RNA-binding domains in human","volume":"63","author":"Castello","year":"2016","journal-title":"Mol. 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