{"id":"https://openalex.org/W4408393259","doi":"https://doi.org/10.1021/acs.jcim.4c02139","title":"FDPSM: Feature-Driven Prediction Modeling of Pathogenic Synonymous Mutations","display_name":"FDPSM: Feature-Driven Prediction Modeling of Pathogenic Synonymous Mutations","publication_year":2025,"publication_date":"2025-03-13","ids":{"openalex":"https://openalex.org/W4408393259","doi":"https://doi.org/10.1021/acs.jcim.4c02139","pmid":"https://pubmed.ncbi.nlm.nih.gov/40082068"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c02139","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c02139","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5030684470","display_name":"Fangfang Jin","orcid":"https://orcid.org/0000-0002-2255-1423"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fangfang Jin","raw_affiliation_strings":["Anhui University","Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology","Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Anhui University","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology","institution_ids":[]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108059952","display_name":"Na Cheng","orcid":"https://orcid.org/0000-0002-5446-0489"},"institutions":[{"id":"https://openalex.org/I197869895","display_name":"Anhui Medical University","ror":"https://ror.org/03xb04968","country_code":"CN","type":"education","lineage":["https://openalex.org/I197869895"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Na Cheng","raw_affiliation_strings":["Anhui Medical University","School of Biomedical Engineering","School of Biomedical Engineering, Anhui Medical University, Hefei, Anhui 230032, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Anhui Medical University","institution_ids":["https://openalex.org/I197869895"]},{"raw_affiliation_string":"School of Biomedical Engineering","institution_ids":[]},{"raw_affiliation_string":"School of Biomedical Engineering, Anhui Medical University, Hefei, Anhui 230032, China","institution_ids":["https://openalex.org/I197869895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100382742","display_name":"Lihua Wang","orcid":"https://orcid.org/0000-0002-9204-9850"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]},{"id":"https://openalex.org/I3132008074","display_name":"Huangshan University","ror":"https://ror.org/05akhmy90","country_code":"CN","type":"education","lineage":["https://openalex.org/I3132008074"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lihua Wang","raw_affiliation_strings":["Anhui University","Huangshan University","Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology","School of Information Engineering","Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China","School of Information Engineering, Huangshan University, Huangshan, Anhui 245041, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Anhui University","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"Huangshan University","institution_ids":["https://openalex.org/I3132008074"]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology","institution_ids":[]},{"raw_affiliation_string":"School of Information Engineering","institution_ids":[]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"School of Information Engineering, Huangshan University, Huangshan, Anhui 245041, China","institution_ids":["https://openalex.org/I3132008074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100658814","display_name":"Bin Ye","orcid":"https://orcid.org/0000-0002-5359-4389"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]},{"id":"https://openalex.org/I4390039265","display_name":"PRG S&Tech (South Korea)","ror":"https://ror.org/02sr2ee22","country_code":null,"type":"company","lineage":["https://openalex.org/I4390039265"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bin Ye","raw_affiliation_strings":["Anhui University","Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology","School of Computer Science and Technology","Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China","School of Computer Science and Technology, Anhui University, Hefei, Anhui 230601, China"],"raw_orcid":"https://orcid.org/0000-0002-5359-4389","affiliations":[{"raw_affiliation_string":"Anhui University","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology","institution_ids":[]},{"raw_affiliation_string":"School of Computer Science and Technology","institution_ids":["https://openalex.org/I4390039265"]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"School of Computer Science and Technology, Anhui University, Hefei, Anhui 230601, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065943710","display_name":"Junfeng Xia","orcid":"https://orcid.org/0000-0003-3024-1705"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Junfeng Xia","raw_affiliation_strings":["Anhui University","Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology","Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China"],"raw_orcid":"https://orcid.org/0000-0003-3024-1705","affiliations":[{"raw_affiliation_string":"Anhui University","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology","institution_ids":[]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China","institution_ids":["https://openalex.org/I143868143"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5065943710","https://openalex.org/A5100658814"],"corresponding_institution_ids":["https://openalex.org/I143868143","https://openalex.org/I4390039265"],"apc_list":null,"apc_paid":null,"fwci":2.9019,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.89418055,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"65","issue":"6","first_page":"3064","last_page":"3076"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9958999752998352,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9958999752998352,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9793000221252441,"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":0.9502999782562256,"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/feature","display_name":"Feature (linguistics)","score":0.6219760179519653},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45765626430511475},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.43811318278312683},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.4132826626300812},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38513433933258057},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36781010031700134},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3383181095123291},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.27221155166625977}],"concepts":[{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.6219760179519653},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45765626430511475},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.43811318278312683},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.4132826626300812},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38513433933258057},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36781010031700134},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3383181095123291},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.27221155166625977},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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}],"mesh":[{"descriptor_ui":"D000069456","descriptor_name":"Silent Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069456","descriptor_name":"Silent Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069456","descriptor_name":"Silent Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.4c02139","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c02139","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40082068","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40082068","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2245046682","display_name":null,"funder_award_id":"U22A2038","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3925882961","display_name":"\u81f4\u75c5\u540c\u4e49\u7a81\u53d8\u7684\u751f\u7269\u4fe1\u606f\u5b66\u7814\u7a76","funder_award_id":"62072003","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5537947129","display_name":null,"funder_award_id":"62402006","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"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":61,"referenced_works":["https://openalex.org/W1900984040","https://openalex.org/W1925054293","https://openalex.org/W1984068087","https://openalex.org/W2002999243","https://openalex.org/W2011582941","https://openalex.org/W2018363492","https://openalex.org/W2027373346","https://openalex.org/W2087439897","https://openalex.org/W2101099267","https://openalex.org/W2103145565","https://openalex.org/W2132312350","https://openalex.org/W2145191876","https://openalex.org/W2148105023","https://openalex.org/W2179147211","https://openalex.org/W2288571328","https://openalex.org/W2403357649","https://openalex.org/W2417483443","https://openalex.org/W2493808054","https://openalex.org/W2605196967","https://openalex.org/W2742600815","https://openalex.org/W2765235107","https://openalex.org/W2904632775","https://openalex.org/W2905452503","https://openalex.org/W2909194804","https://openalex.org/W2915985519","https://openalex.org/W2918497364","https://openalex.org/W2948505931","https://openalex.org/W2970048450","https://openalex.org/W2974907528","https://openalex.org/W2990435446","https://openalex.org/W2993201046","https://openalex.org/W3029661147","https://openalex.org/W3037601773","https://openalex.org/W3095895133","https://openalex.org/W3126160703","https://openalex.org/W3134631034","https://openalex.org/W3156417804","https://openalex.org/W3175980491","https://openalex.org/W3199639770","https://openalex.org/W4220991811","https://openalex.org/W4224026474","https://openalex.org/W4225545948","https://openalex.org/W4289936559","https://openalex.org/W4303671988","https://openalex.org/W4313706580","https://openalex.org/W4322719781","https://openalex.org/W4322770791","https://openalex.org/W4366605966","https://openalex.org/W4367173606","https://openalex.org/W4378640002","https://openalex.org/W4379209153","https://openalex.org/W4385737488","https://openalex.org/W4385999365","https://openalex.org/W4386861232","https://openalex.org/W4387576685","https://openalex.org/W4388578439","https://openalex.org/W4390616142","https://openalex.org/W4390655913","https://openalex.org/W4392683328","https://openalex.org/W4392785459","https://openalex.org/W4392982815"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W3147584709","https://openalex.org/W2977677679","https://openalex.org/W1992327129","https://openalex.org/W2381986121","https://openalex.org/W2370918718","https://openalex.org/W2256933480","https://openalex.org/W2027854990","https://openalex.org/W2146849562","https://openalex.org/W2028961943"],"abstract_inverted_index":{"Synonymous":[0],"mutations,":[1,56,156,190],"once":[2],"considered":[3],"to":[4,11,30,46,88,108],"be":[5],"biologically":[6],"neutral,":[7],"are":[8],"now":[9],"recognized":[10],"affect":[12],"protein":[13],"expression":[14],"and":[15,51,72,104,128,153,169,195],"function":[16],"by":[17,162],"altering":[18],"the":[19,33,36,48,149,159,167,186],"RNA":[20],"splicing,":[21],"stability,":[22],"or":[23],"translation":[24],"efficiency.":[25],"These":[26],"effects":[27],"can":[28],"contribute":[29],"disease,":[31],"making":[32],"prediction":[34,70,84,133],"of":[35,54,64,75,101,118,171,188],"pathogenicity":[37,138,187],"a":[38,82,97,115,192],"crucial":[39],"task.":[40,201],"Computational":[41],"methods":[42,59,183],"have":[43],"been":[44],"developed":[45],"analyze":[47],"sequence":[49],"features":[50,143],"biological":[52],"functions":[53],"synonymous":[55,91,155,189],"but":[57],"existing":[58,182],"face":[60],"limitations,":[61],"including":[62,120],"scarcity":[63],"labeled":[65],"data,":[66],"reliance":[67],"on":[68,96,132],"other":[69,136],"tools,":[71],"insufficient":[73],"representation":[74],"feature":[76,160],"interrelationships.":[77],"Here,":[78],"we":[79,157],"present":[80],"FDPSM,":[81],"novel":[83],"method":[85,113],"specifically":[86],"designed":[87],"predict":[89],"pathogenic":[90,152],"mutations.":[92],"FDPSM":[93,179,202],"was":[94],"trained":[95],"robust":[98],"data":[99],"set":[100,117,161],"4251":[102],"positive":[103],"negative":[105],"training":[106],"samples":[107],"enhance":[109],"predictive":[110],"accuracy.":[111],"The":[112,174],"leveraged":[114],"comprehensive":[116],"features,":[119],"genomic":[121],"context,":[122],"conservation,":[123],"splicing":[124],"effects,":[125,127],"functional":[126],"epigenomics,":[129],"without":[130],"relying":[131],"scores":[134],"from":[135,166],"mutation":[137],"tools.":[139],"Recognizing":[140],"that":[141,178],"original":[142],"alone":[144],"may":[145],"not":[146],"fully":[147],"capture":[148],"distinctions":[150],"between":[151],"benign":[154],"enhanced":[158],"extracting":[163],"effective":[164],"information":[165],"interactions":[168],"distribution":[170],"these":[172],"features.":[173],"experimental":[175],"results":[176],"showed":[177],"significantly":[180],"outperformed":[181],"in":[184],"predicting":[185],"offering":[191],"more":[193],"accurate":[194],"reliable":[196],"tool":[197],"for":[198],"this":[199],"important":[200],"is":[203],"available":[204],"at":[205],"https://github.com/xialab-ahu/FDPSM.":[206]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-07-25T09:21:30.201066","created_date":"2025-10-10T00:00:00"}
