{"id":"https://openalex.org/W4406238264","doi":"https://doi.org/10.1109/bibm62325.2024.10821861","title":"Iterative Glycan Structure Generation by Component Localization and Classification from Mass Spectra","display_name":"Iterative Glycan Structure Generation by Component Localization and Classification from Mass Spectra","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406238264","doi":"https://doi.org/10.1109/bibm62325.2024.10821861"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10821861","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10821861","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5100733931","display_name":"Defeng Li","orcid":"https://orcid.org/0000-0002-9316-3313"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Defeng Li","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China"],"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045475851","display_name":"Z. D. Nie","orcid":"https://orcid.org/0000-0002-0234-4208"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zizheng Nie","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China"],"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084905540","display_name":"Yanmin Liu","orcid":"https://orcid.org/0000-0002-1571-5370"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanmin Liu","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China"],"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077227556","display_name":"Xiaojun Cai","orcid":null},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaojun Cai","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China"],"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100419841","display_name":"Yong Zhang","orcid":"https://orcid.org/0000-0003-0513-8941"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yong Zhang","raw_affiliation_strings":["Sichuan University,West China Hospital,Department of Nephrology and Institutes for Systems Genetics,Chengdu,China,610041"],"affiliations":[{"raw_affiliation_string":"Sichuan University,West China Hospital,Department of Nephrology and Institutes for Systems Genetics,Chengdu,China,610041","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074194686","display_name":"Xuefeng Cui","orcid":"https://orcid.org/0000-0003-0350-1495"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuefeng Cui","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China"],"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100733931"],"corresponding_institution_ids":["https://openalex.org/I80143920"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.22055565,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"314","last_page":"319"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.972000002861023,"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":0.972000002861023,"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/component","display_name":"Component (thermodynamics)","score":0.6586690545082092},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6117969751358032},{"id":"https://openalex.org/keywords/glycan","display_name":"Glycan","score":0.5781151056289673},{"id":"https://openalex.org/keywords/mass-spectrum","display_name":"Mass spectrum","score":0.5355745553970337},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3755798935890198},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3445664048194885},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32043036818504333},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.29827994108200073},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.2718502879142761},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.16359645128250122},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.0869596004486084}],"concepts":[{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.6586690545082092},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6117969751358032},{"id":"https://openalex.org/C206212055","wikidata":"https://www.wikidata.org/wiki/Q2553138","display_name":"Glycan","level":3,"score":0.5781151056289673},{"id":"https://openalex.org/C40325409","wikidata":"https://www.wikidata.org/wiki/Q2360668","display_name":"Mass spectrum","level":3,"score":0.5355745553970337},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3755798935890198},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3445664048194885},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32043036818504333},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.29827994108200073},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.2718502879142761},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.16359645128250122},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0869596004486084},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0},{"id":"https://openalex.org/C108625454","wikidata":"https://www.wikidata.org/wiki/Q187126","display_name":"Glycoprotein","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10821861","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10821861","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W2097831308","https://openalex.org/W2101771116","https://openalex.org/W2110438218","https://openalex.org/W2130871863","https://openalex.org/W2409069109","https://openalex.org/W2752557010","https://openalex.org/W2766585573","https://openalex.org/W2907049841","https://openalex.org/W2921437380","https://openalex.org/W3082670149","https://openalex.org/W3136924813","https://openalex.org/W3152110994","https://openalex.org/W3188243150","https://openalex.org/W3208691473","https://openalex.org/W3214881753","https://openalex.org/W4298002166","https://openalex.org/W4313527263","https://openalex.org/W4380854021","https://openalex.org/W4383619439","https://openalex.org/W4390970098","https://openalex.org/W4390992168","https://openalex.org/W6607393083","https://openalex.org/W6804049574"],"related_works":["https://openalex.org/W183875936","https://openalex.org/W2051487156","https://openalex.org/W2089644524","https://openalex.org/W4379977790","https://openalex.org/W4380090585","https://openalex.org/W1531549338","https://openalex.org/W102498190","https://openalex.org/W2008437729","https://openalex.org/W1585007664","https://openalex.org/W2073681303"],"abstract_inverted_index":{"Analyzing":[0],"intact":[1,133],"glycopeptides":[2,135],"via":[3,193],"mass":[4,82,184],"spectrometry":[5,83,185],"data":[6],"elucidates":[7],"the":[8,29,34,37,45,52,103,171,194],"glycan":[9,30,79,104,174],"composition":[10],"and":[11,22,39,98,101,177],"attachment":[12],"sites,":[13],"which":[14,155],"are":[15],"pivotal":[16],"for":[17,60,75],"investigating":[18],"protein":[19],"folding,":[20],"stability,":[21],"function.":[23],"GlycanFinder,":[24],"an":[25,91],"advanced":[26],"technique,":[27],"builds":[28],"structure":[31,105,175],"starting":[32],"from":[33,81,137,157],"peptide":[35],"(i.e.,":[36,44],"root)":[38],"sequentially":[40],"adds":[41],"monosaccharide":[42],"components":[43],"leaves).":[46],"However,":[47],"its":[48],"major":[49],"limitation":[50],"is":[51],"dependence":[53],"on":[54,128],"predefined":[55,129],"rules":[56],"with":[57],"strong":[58],"assumptions":[59],"leaf":[61],"addition":[62],"locations.":[63],"To":[64],"address":[65],"this":[66],"issue,":[67],"we":[68,142],"introduce":[69],"MS2Glycan,":[70],"a":[71,111,118,149],"deep":[72],"learning":[73],"method":[74],"iteratively":[76],"generating":[77],"novel":[78],"structures":[80],"data.":[84,186],"It":[85],"models":[86],"component":[87,106,123],"generation":[88],"similarly":[89],"to":[90,121,159],"object":[92],"detection":[93],"task,":[94],"incorporating":[95],"both":[96],"localization":[97],"classification":[99],"sub-tasks,":[100],"constructs":[102],"by":[107,116],"component.":[108],"MS2Glycan":[109,144],"offers":[110,178],"key":[112],"improvement":[113],"over":[114],"GlycanFinder":[115],"using":[117],"data-driven":[119],"approach":[120],"predict":[122],"locations,":[124],"rather":[125],"than":[126],"relying":[127],"rules.":[130],"By":[131],"analyzing":[132],"N-linked":[134],"collected":[136],"five":[138],"different":[139],"mouse":[140],"tissues,":[141],"assessed":[143],"through":[145],"five-fold":[146],"cross-validation,":[147],"observing":[148],"notable":[150],"enhancement":[151],"in":[152],"structural":[153],"accuracy,":[154],"rose":[156],"32%":[158],"74%.":[160],"Additionally,":[161],"our":[162,166],"findings":[163],"indicate":[164],"that":[165],"model":[167],"more":[168],"effectively":[169],"mimics":[170],"principles":[172],"of":[173],"construction":[176],"valuable":[179],"insights":[180],"into":[181],"fully":[182],"leveraging":[183],"The":[187],"Python":[188],"implementation":[189],"can":[190],"be":[191],"accessed":[192],"following":[195],"link:":[196],"https://github.com/xfcui/MS2Glycan.":[197]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
