{"id":"https://openalex.org/W4406958312","doi":"https://doi.org/10.1093/bioinformatics/btaf034","title":"Enhanced O-glycosylation site prediction using explainable machine learning technique with spatial local environment","display_name":"Enhanced O-glycosylation site prediction using explainable machine learning technique with spatial local environment","publication_year":2025,"publication_date":"2025-01-29","ids":{"openalex":"https://openalex.org/W4406958312","doi":"https://doi.org/10.1093/bioinformatics/btaf034","pmid":"https://pubmed.ncbi.nlm.nih.gov/39878910"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf034","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf034","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf034/61683442/btaf034.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/btaf034/61683442/btaf034.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058530112","display_name":"Seokyoung Hong","orcid":"https://orcid.org/0000-0002-8729-1837"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Seokyoung Hong","raw_affiliation_strings":["Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, MA 02139,","Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, MA 02139,","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043508338","display_name":"Krishna Gopal Chattaraj","orcid":"https://orcid.org/0000-0003-2613-7251"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Krishna Gopal Chattaraj","raw_affiliation_strings":["Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, MA 02139,","Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, MA 02139,","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044228369","display_name":"Jing Guo","orcid":"https://orcid.org/0000-0001-6752-6064"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jing Guo","raw_affiliation_strings":["Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, MA 02139,","Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, MA 02139,","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000143645","display_name":"Bernhardt L. Trout","orcid":"https://orcid.org/0000-0003-1417-9470"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bernhardt L Trout","raw_affiliation_strings":["Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, MA 02139,","Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, MA 02139,","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083684552","display_name":"Richard D. Braatz","orcid":"https://orcid.org/0000-0003-4304-3484"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Richard D Braatz","raw_affiliation_strings":["Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, MA 02139,","Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States"],"raw_orcid":"https://orcid.org/0000-0003-4304-3484","affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, MA 02139,","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5083684552"],"corresponding_institution_ids":["https://openalex.org/I63966007"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.818,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.67465577,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"41","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.8664000034332275,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.8664000034332275,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.07270000129938126,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.015200000256299973,"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/computer-science","display_name":"Computer science","score":0.8044912815093994},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6495848894119263},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6420568823814392},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5877545475959778},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5762881636619568},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.5443404316902161},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5124995708465576},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.5001165866851807},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4956573247909546},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4823002815246582},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43864476680755615},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.42863577604293823},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.42220890522003174},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.41595935821533203}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8044912815093994},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6495848894119263},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6420568823814392},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5877545475959778},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5762881636619568},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.5443404316902161},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5124995708465576},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.5001165866851807},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4956573247909546},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4823002815246582},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43864476680755615},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.42863577604293823},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.42220890522003174},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.41595935821533203},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C62649853","wikidata":"https://www.wikidata.org/wiki/Q199687","display_name":"Remote sensing","level":1,"score":0.0},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.0},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaf034","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf034","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf034/61683442/btaf034.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:39878910","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39878910","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:publications.polymtl.ca:66494","is_oa":false,"landing_page_url":"https://publications.polymtl.ca/66494/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401013","display_name":"PolyPublie (\u00c9cole Polytechnique de Montr\u00e9al)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45683168","host_organization_name":"Polytechnique Montr\u00e9al","host_organization_lineage":["https://openalex.org/I45683168"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Article de revue"},{"id":"pmh:oai:pubmedcentral.nih.gov:11814488","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11814488","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11814488/pdf/btaf034.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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"},{"id":"pmh:oai:dspace.mit.edu:1721.1/164930","is_oa":true,"landing_page_url":"https://hdl.handle.net/1721.1/164930","pdf_url":null,"source":{"id":"https://openalex.org/S4306400425","display_name":"DSpace@MIT (Massachusetts Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63966007","host_organization_name":"Massachusetts Institute of Technology","host_organization_lineage":["https://openalex.org/I63966007"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Oxford University Press","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf034","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf034","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf034/61683442/btaf034.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/G119483429","display_name":null,"funder_award_id":"70NANB17H002","funder_id":"https://openalex.org/F4320337821","funder_display_name":"National Institute for Innovation in Manufacturing Biopharmaceuticals"},{"id":"https://openalex.org/G3567290435","display_name":null,"funder_award_id":"70NANB17H002","funder_id":"https://openalex.org/F4320306111","funder_display_name":"U.S. Department of Commerce"},{"id":"https://openalex.org/G4260295368","display_name":null,"funder_award_id":"P0017304","funder_id":"https://openalex.org/F4320322064","funder_display_name":"Korea Institute for Advancement of Technology"},{"id":"https://openalex.org/G6179227475","display_name":"THE NATIONAL INSTITUTE FOR INNOVATION IN MANUFACTURING BIOPHARMACEUTICALS (NIIMBL)","funder_award_id":"70NANB17H002","funder_id":"https://openalex.org/F4320332178","funder_display_name":"National Institute of Standards and Technology"},{"id":"https://openalex.org/G739298440","display_name":null,"funder_award_id":"70NANB21H086","funder_id":"https://openalex.org/F4320337821","funder_display_name":"National Institute for Innovation in Manufacturing Biopharmaceuticals"},{"id":"https://openalex.org/G7477002594","display_name":null,"funder_award_id":"P0017304","funder_id":"https://openalex.org/F4320321681","funder_display_name":"Ministry of Trade, Industry and Energy"},{"id":"https://openalex.org/G7603189620","display_name":"THE NATIONAL INSTITUTE FOR INNOVATION IN MANUFACTURING BIOPHARMACEUTICALS (NIIMBL)","funder_award_id":"70NANB21H086","funder_id":"https://openalex.org/F4320332178","funder_display_name":"National Institute of Standards and Technology"}],"funders":[{"id":"https://openalex.org/F4320306111","display_name":"U.S. Department of Commerce","ror":"https://ror.org/04chq2495"},{"id":"https://openalex.org/F4320321681","display_name":"Ministry of Trade, Industry and Energy","ror":"https://ror.org/008nkqk13"},{"id":"https://openalex.org/F4320322064","display_name":"Korea Institute for Advancement of Technology","ror":"https://ror.org/015w1qa96"},{"id":"https://openalex.org/F4320332178","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416"},{"id":"https://openalex.org/F4320337407","display_name":"Division of Human Resource Development","ror":"https://ror.org/03mamvh39"},{"id":"https://openalex.org/F4320337821","display_name":"National Institute for Innovation in Manufacturing Biopharmaceuticals","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4406958312.pdf","grobid_xml":"https://content.openalex.org/works/W4406958312.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1484551801","https://openalex.org/W2029667189","https://openalex.org/W2058183980","https://openalex.org/W2063768466","https://openalex.org/W2066414494","https://openalex.org/W2074328536","https://openalex.org/W2130479394","https://openalex.org/W2149376055","https://openalex.org/W2154677603","https://openalex.org/W2460144244","https://openalex.org/W2528774686","https://openalex.org/W2555870966","https://openalex.org/W2789316776","https://openalex.org/W2939599083","https://openalex.org/W2979040066","https://openalex.org/W2997604048","https://openalex.org/W2999309192","https://openalex.org/W3002225207","https://openalex.org/W3087067568","https://openalex.org/W3124481539","https://openalex.org/W3207838037","https://openalex.org/W4295765292","https://openalex.org/W4360942084","https://openalex.org/W4381620722","https://openalex.org/W4389385479","https://openalex.org/W4396721167","https://openalex.org/W4401009568","https://openalex.org/W4401405048","https://openalex.org/W4403717981","https://openalex.org/W6659581585","https://openalex.org/W6670280255","https://openalex.org/W6760602923","https://openalex.org/W6795720836"],"related_works":["https://openalex.org/W1603736412","https://openalex.org/W2754214645","https://openalex.org/W4304185162","https://openalex.org/W2061685118","https://openalex.org/W3006282800","https://openalex.org/W2462100143","https://openalex.org/W1770503332","https://openalex.org/W3125207769","https://openalex.org/W2577825108","https://openalex.org/W2949684406"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,184],"accurate":[2],"prediction":[3,166],"of":[4,41,85,106,117,133,140,151],"O-GlcNAcylation":[5,94],"sites":[6],"is":[7],"crucial":[8],"for":[9,173],"understanding":[10,177],"disease":[11],"mechanisms":[12],"and":[13,30,88,178],"developing":[14],"effective":[15],"treatments.":[16],"Previous":[17],"machine":[18],"learning":[19],"(ML)":[20],"models":[21],"primarily":[22],"relied":[23],"on":[24],"primary":[25],"or":[26],"secondary":[27],"protein":[28],"structural":[29],"related":[31],"properties,":[32],"which":[33],"have":[34],"limitations":[35],"in":[36,176,190,195],"capturing":[37],"the":[38,66,70,86,104,111,126,130,136,152,171,196],"spatial":[39,58,67],"interactions":[40],"neighboring":[42],"amino":[43],"acids.":[44],"This":[45,161],"study":[46,192],"introduces":[47],"local":[48],"environmental":[49],"features":[50,109,134,155,188],"as":[51,95,119,121],"a":[52,142],"novel":[53],"approach":[54],"that":[55],"incorporates":[56],"three-dimensional":[57],"information,":[59],"significantly":[60],"improving":[61],"model":[62,112,127],"performance":[63],"by":[64],"considering":[65],"context":[68],"around":[69],"target":[71],"site.":[72],"Additionally,":[73],"we":[74],"utilize":[75],"sparse":[76],"recurrent":[77],"neural":[78],"networks":[79],"to":[80,89],"effectively":[81],"capture":[82],"sequential":[83],"nature":[84],"proteins":[87],"identify":[90],"key":[91],"factors":[92],"influencing":[93],"an":[96,114],"explainable":[97],"ML":[98],"model.":[99],"RESULTS:":[100],"Our":[101],"findings":[102],"demonstrate":[103],"effectiveness":[105],"our":[107],"proposed":[108],"with":[110,125,159],"achieving":[113,135],"F1":[115,138],"score":[116,139],"28.3%,":[118],"well":[120],"feature":[122],"selection":[123],"capability":[124],"using":[128],"only":[129,164],"top":[131,153],"20%":[132],"highest":[137],"32.02%,":[141],"1.4-fold":[143],"improvement":[144],"over":[145],"existing":[146],"PTM":[147],"models.":[148],"Statistical":[149],"analysis":[150],"20":[154],"confirmed":[156],"their":[157],"consistency":[158],"literature.":[160],"method":[162],"not":[163],"boosts":[165],"accuracy":[167],"but":[168],"also":[169],"paves":[170],"way":[172],"further":[174],"research":[175],"targeting":[179],"O-GlcNAcylation.":[180],"AVAILABILITY":[181],"AND":[182],"IMPLEMENTATION:":[183],"entire":[185],"code,":[186],"data,":[187],"used":[189],"this":[191],"are":[193],"available":[194],"GitHub":[197],"repository:":[198],"https://github.com/pseokyoung/o-glcnac-prediction.":[199]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-07-31T08:31:51.225901","created_date":"2025-10-10T00:00:00"}
