{"id":"https://openalex.org/W3115235257","doi":"https://doi.org/10.1093/bioinformatics/btaa1043","title":"crisscrosslinkeR: identification and visualization of protein\u2013RNA and protein\u2013protein interactions from crosslinking mass spectrometry","display_name":"crisscrosslinkeR: identification and visualization of protein\u2013RNA and protein\u2013protein interactions from crosslinking mass spectrometry","publication_year":2020,"publication_date":"2020-12-01","ids":{"openalex":"https://openalex.org/W3115235257","doi":"https://doi.org/10.1093/bioinformatics/btaa1043","mag":"3115235257","pmid":"https://pubmed.ncbi.nlm.nih.gov/33346827"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa1043","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1043","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062885003","display_name":"Emma H. Gail","orcid":null},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Emma H Gail","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Victoria 3800, Australia","Faculty of Medicine, Nursing and Health Sciences, Monash University , Clayton, Victoria 3800, Australia"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Victoria 3800, Australia","institution_ids":[]},{"raw_affiliation_string":"Faculty of Medicine, Nursing and Health Sciences, Monash University , Clayton, Victoria 3800, Australia","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007459116","display_name":"Anup D. Shah","orcid":"https://orcid.org/0000-0002-3793-1998"},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Anup D Shah","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Victoria 3800, Australia","Faculty of Medicine, Nursing and Health Sciences, Monash University , Clayton, Victoria 3800, Australia","Monash Bioinformatics Platform, Monash Biomedicine Discovery Institute, Monash University , Clayton, Victoria 3800, Australia","Monash Proteomics & Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University , Clayton, Victoria 3800, Australia"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Victoria 3800, Australia","institution_ids":[]},{"raw_affiliation_string":"Faculty of Medicine, Nursing and Health Sciences, Monash University , Clayton, Victoria 3800, Australia","institution_ids":["https://openalex.org/I56590836"]},{"raw_affiliation_string":"Monash Bioinformatics Platform, Monash Biomedicine Discovery Institute, Monash University , Clayton, Victoria 3800, Australia","institution_ids":["https://openalex.org/I56590836"]},{"raw_affiliation_string":"Monash Proteomics & Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University , Clayton, Victoria 3800, Australia","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087390081","display_name":"Ralf B. Schittenhelm","orcid":"https://orcid.org/0000-0001-8738-1878"},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Ralf B Schittenhelm","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Victoria 3800, Australia","Faculty of Medicine, Nursing and Health Sciences, Monash University , Clayton, Victoria 3800, Australia","Monash Proteomics & Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University , Clayton, Victoria 3800, Australia"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Victoria 3800, Australia","institution_ids":[]},{"raw_affiliation_string":"Faculty of Medicine, Nursing and Health Sciences, Monash University , Clayton, Victoria 3800, Australia","institution_ids":["https://openalex.org/I56590836"]},{"raw_affiliation_string":"Monash Proteomics & Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University , Clayton, Victoria 3800, Australia","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020232884","display_name":"Chen Davidovich","orcid":"https://orcid.org/0000-0002-1085-6094"},"institutions":[{"id":"https://openalex.org/I4210098306","display_name":"EMBL Australia","ror":"https://ror.org/00yx5cw48","country_code":"AU","type":"government","lineage":["https://openalex.org/I4210098306"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]},{"id":"https://openalex.org/I4210146297","display_name":"ARC Centre of Excellence in Advanced Molecular Imaging","ror":"https://ror.org/051e7s436","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1337719021","https://openalex.org/I2801453606","https://openalex.org/I4210132349","https://openalex.org/I4210146297","https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Chen Davidovich","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Victoria 3800, Australia","EMBL-Australia and the ARC Centre of Excellence in Advanced Molecular Imaging , Clayton, Victoria 3800, Australia","Faculty of Medicine, Nursing and Health Sciences, Monash University , Clayton, Victoria 3800, Australia"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Victoria 3800, Australia","institution_ids":[]},{"raw_affiliation_string":"EMBL-Australia and the ARC Centre of Excellence in Advanced Molecular Imaging , Clayton, Victoria 3800, Australia","institution_ids":["https://openalex.org/I4210146297","https://openalex.org/I4210098306"]},{"raw_affiliation_string":"Faculty of Medicine, Nursing and Health Sciences, Monash University , Clayton, Victoria 3800, Australia","institution_ids":["https://openalex.org/I56590836"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5020232884"],"corresponding_institution_ids":["https://openalex.org/I4210098306","https://openalex.org/I4210146297","https://openalex.org/I56590836"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0829,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.46059974,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"36","issue":"22-23","first_page":"5530","last_page":"5532"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.996399998664856,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6853293180465698},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6298975944519043},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.6044151186943054},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5812134742736816},{"id":"https://openalex.org/keywords/ribonucleoprotein","display_name":"Ribonucleoprotein","score":0.5643686056137085},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5381932854652405},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.45250168442726135},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4394710659980774},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3758348822593689},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35317501425743103},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2274475395679474},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1791936755180359},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.15161263942718506},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11849424242973328}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6853293180465698},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6298975944519043},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.6044151186943054},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5812134742736816},{"id":"https://openalex.org/C75934600","wikidata":"https://www.wikidata.org/wiki/Q419245","display_name":"Ribonucleoprotein","level":4,"score":0.5643686056137085},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5381932854652405},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.45250168442726135},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4394710659980774},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3758348822593689},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35317501425743103},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2274475395679474},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1791936755180359},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.15161263942718506},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11849424242973328},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaa1043","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1043","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33346827","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33346827","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1133333969","display_name":null,"funder_award_id":"APP1162921","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"},{"id":"https://openalex.org/G3063818017","display_name":null,"funder_award_id":"APP1184637","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"},{"id":"https://openalex.org/G8722975916","display_name":null,"funder_award_id":"DP190103407","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"}],"funders":[{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1986139734","https://openalex.org/W2036321220","https://openalex.org/W2045395320","https://openalex.org/W2052928602","https://openalex.org/W2061519290","https://openalex.org/W2120508443","https://openalex.org/W2183276865","https://openalex.org/W2422039703","https://openalex.org/W2480300184","https://openalex.org/W2544360569","https://openalex.org/W2618922802","https://openalex.org/W2760627581","https://openalex.org/W2766052208","https://openalex.org/W2800450994","https://openalex.org/W2917774877","https://openalex.org/W2918168812"],"related_works":["https://openalex.org/W2037531772","https://openalex.org/W1528262319","https://openalex.org/W2068608913","https://openalex.org/W1222908588","https://openalex.org/W3124914020","https://openalex.org/W1972739143","https://openalex.org/W2089905153","https://openalex.org/W2094449181","https://openalex.org/W2141033859","https://openalex.org/W2077542787"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
