{"id":"https://openalex.org/W4414369244","doi":"https://doi.org/10.1093/bioinformatics/btaf515","title":"Graph neural network and diffusion model for modeling RNA interatomic interactions","display_name":"Graph neural network and diffusion model for modeling RNA interatomic interactions","publication_year":2025,"publication_date":"2025-09-01","ids":{"openalex":"https://openalex.org/W4414369244","doi":"https://doi.org/10.1093/bioinformatics/btaf515","pmid":"https://pubmed.ncbi.nlm.nih.gov/40971857"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf515","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf515","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf515/64274808/btaf515.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf515/64274808/btaf515.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102726864","display_name":"J. \u0141os Marek","orcid":"https://orcid.org/0000-0001-8564-4435"},"institutions":[{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Marek Justyna","raw_affiliation_strings":["Institute of Computing Science, Poznan University of Technology , Poznan 60-965,","Institute of Computing Science, Poznan University of Technology, Poznan, 60-965, Poland"],"affiliations":[{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology , Poznan 60-965,","institution_ids":["https://openalex.org/I46597724"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Poznan, 60-965, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069434073","display_name":"Craig L. Zirbel","orcid":"https://orcid.org/0000-0002-3281-918X"},"institutions":[{"id":"https://openalex.org/I157417397","display_name":"Bowling Green State University","ror":"https://ror.org/00ay7va13","country_code":"US","type":"education","lineage":["https://openalex.org/I157417397"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Craig Zirbel","raw_affiliation_strings":["Department of Mathematics and Statistics, Bowling Green State University , Bowling Green, OH 43403-0206,","Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403-0206, United States"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, Bowling Green State University , Bowling Green, OH 43403-0206,","institution_ids":["https://openalex.org/I157417397"]},{"raw_affiliation_string":"Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403-0206, United States","institution_ids":["https://openalex.org/I157417397"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045163807","display_name":"Maciej Antczak","orcid":"https://orcid.org/0000-0002-5320-2023"},"institutions":[{"id":"https://openalex.org/I4210152414","display_name":"Institute of Bioorganic Chemistry, Polish Academy of Sciences","ror":"https://ror.org/04ejdtr48","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210152414","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Maciej Antczak","raw_affiliation_strings":["Department of Structural Bioinformatics, Institute of Bioorganic Chemistry PAS , Poznan 61-704,","Institute of Computing Science, Poznan University of Technology , Poznan 60-965,","Department of Structural Bioinformatics, Institute of Bioorganic Chemistry PAS, Poznan, 61-704, Poland","Institute of Computing Science, Poznan University of Technology, Poznan, 60-965, Poland"],"affiliations":[{"raw_affiliation_string":"Department of Structural Bioinformatics, Institute of Bioorganic Chemistry PAS , Poznan 61-704,","institution_ids":["https://openalex.org/I4210152414"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology , Poznan 60-965,","institution_ids":["https://openalex.org/I46597724"]},{"raw_affiliation_string":"Department of Structural Bioinformatics, Institute of Bioorganic Chemistry PAS, Poznan, 61-704, Poland","institution_ids":["https://openalex.org/I4210152414"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Poznan, 60-965, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056736610","display_name":"Marta Szachniuk","orcid":"https://orcid.org/0000-0002-8724-7908"},"institutions":[{"id":"https://openalex.org/I4210152414","display_name":"Institute of Bioorganic Chemistry, Polish Academy of Sciences","ror":"https://ror.org/04ejdtr48","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210152414","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Marta Szachniuk","raw_affiliation_strings":["Department of Structural Bioinformatics, Institute of Bioorganic Chemistry PAS , Poznan 61-704,","Institute of Computing Science, Poznan University of Technology , Poznan 60-965,","Department of Structural Bioinformatics, Institute of Bioorganic Chemistry PAS, Poznan, 61-704, Poland","Institute of Computing Science, Poznan University of Technology, Poznan, 60-965, Poland"],"affiliations":[{"raw_affiliation_string":"Department of Structural Bioinformatics, Institute of Bioorganic Chemistry PAS , Poznan 61-704,","institution_ids":["https://openalex.org/I4210152414"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology , Poznan 60-965,","institution_ids":["https://openalex.org/I46597724"]},{"raw_affiliation_string":"Department of Structural Bioinformatics, Institute of Bioorganic Chemistry PAS, Poznan, 61-704, Poland","institution_ids":["https://openalex.org/I4210152414"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Poznan, 60-965, Poland","institution_ids":["https://openalex.org/I46597724"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5102726864"],"corresponding_institution_ids":["https://openalex.org/I46597724"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.835,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.93855587,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"41","issue":"9","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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":1.0,"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/T11482","display_name":"RNA modifications and cancer","score":0.9995999932289124,"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":0.9972000122070312,"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/source-code","display_name":"Source code","score":0.7103999853134155},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5670999884605408},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5575000047683716},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5551000237464905},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.5347999930381775},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5055000185966492}],"concepts":[{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.7103999853134155},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6809999942779541},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5670999884605408},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5575000047683716},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5551000237464905},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.5347999930381775},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5248000025749207},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5055000185966492},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.49970000982284546},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.46470001339912415},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.34790000319480896},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.3285999894142151},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32820001244544983},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.31369999051094055},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.2969000041484833},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2770000100135803},{"id":"https://openalex.org/C2992708514","wikidata":"https://www.wikidata.org/wiki/Q48968323","display_name":"Quantitative biology","level":2,"score":0.26969999074935913},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.26759999990463257},{"id":"https://openalex.org/C104122410","wikidata":"https://www.wikidata.org/wiki/Q1416406","display_name":"Network model","level":2,"score":0.26570001244544983},{"id":"https://openalex.org/C2984499602","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Computer software","level":2,"score":0.26420000195503235}],"mesh":[{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf515","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf515","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf515/64274808/btaf515.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40971857","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40971857","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},{"id":"pmh:oai:europepmc.org:11280889","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12472125","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12472125","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12472125/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf515","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf515","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf515/64274808/btaf515.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5147762766","display_name":null,"funder_award_id":"2024/53/B/ST6/02789","funder_id":"https://openalex.org/F4320322650","funder_display_name":"Narodowym Centrum Nauki"},{"id":"https://openalex.org/G5167034069","display_name":null,"funder_award_id":"2020/39/O/ST6/01488","funder_id":"https://openalex.org/F4320322650","funder_display_name":"Narodowym Centrum Nauki"}],"funders":[{"id":"https://openalex.org/F4320322650","display_name":"Narodowym Centrum Nauki","ror":"https://ror.org/03ha2q922"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414369244.pdf","grobid_xml":"https://content.openalex.org/works/W4414369244.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W2062183533","https://openalex.org/W2086561953","https://openalex.org/W2119896557","https://openalex.org/W2122774834","https://openalex.org/W2130479394","https://openalex.org/W2136567909","https://openalex.org/W2140673705","https://openalex.org/W2141411594","https://openalex.org/W2147853461","https://openalex.org/W2341963847","https://openalex.org/W2520967483","https://openalex.org/W2596417560","https://openalex.org/W2944959599","https://openalex.org/W2950772678","https://openalex.org/W2952457720","https://openalex.org/W2999044305","https://openalex.org/W3034567160","https://openalex.org/W3100348855","https://openalex.org/W3177828909","https://openalex.org/W3195820203","https://openalex.org/W3203459683","https://openalex.org/W4214725635","https://openalex.org/W4282929726","https://openalex.org/W4286721853","https://openalex.org/W4366990642","https://openalex.org/W4384831773","https://openalex.org/W4386704695","https://openalex.org/W4386804219","https://openalex.org/W4387931208","https://openalex.org/W4388412569","https://openalex.org/W4388520896","https://openalex.org/W4394718179","https://openalex.org/W4396721167","https://openalex.org/W4396908238","https://openalex.org/W4404595545","https://openalex.org/W4411886797"],"related_works":[],"abstract_inverted_index":{"The":[0],"GraphaRNA":[1],"source":[2],"code":[3],"is":[4],"available":[5],"on":[6,17],"GitHub":[7],"(github.com/mjustynaPhD/GraphaRNA);":[8],"training/test":[9],"datasets":[10],"and":[11],"pre-trained":[12],"model":[13],"weights":[14],"are":[15],"provided":[16],"Zenodo":[18],"(zenodo.org/records/13750967).":[19]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
