{"id":"https://openalex.org/W4362698482","doi":"https://doi.org/10.1186/s12859-023-05257-5","title":"Stack-VTP: prediction of vesicle transport proteins based on stacked ensemble classifier and evolutionary information","display_name":"Stack-VTP: prediction of vesicle transport proteins based on stacked ensemble classifier and evolutionary information","publication_year":2023,"publication_date":"2023-04-07","ids":{"openalex":"https://openalex.org/W4362698482","doi":"https://doi.org/10.1186/s12859-023-05257-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/37029385"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05257-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05257-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05257-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05257-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100401949","display_name":"Yu Chen","orcid":"https://orcid.org/0000-0001-6883-0922"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yu Chen","raw_affiliation_strings":["College of Information and Computer Engineering, Northeast Forestry University, Harbin, China"],"affiliations":[{"raw_affiliation_string":"College of Information and Computer Engineering, Northeast Forestry University, Harbin, China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019000951","display_name":"Lixin Gao","orcid":"https://orcid.org/0009-0000-8951-091X"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lixin Gao","raw_affiliation_strings":["College of Information and Computer Engineering, Northeast Forestry University, Harbin, China"],"affiliations":[{"raw_affiliation_string":"College of Information and Computer Engineering, Northeast Forestry University, Harbin, China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100671125","display_name":"Tianjiao Zhang","orcid":"https://orcid.org/0000-0001-9807-8620"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tianjiao Zhang","raw_affiliation_strings":["College of Information and Computer Engineering, Northeast Forestry University, Harbin, China. tianjiaozhang@nefu.edu.cn","College of Information and Computer Engineering, Northeast Forestry University, Harbin, China"],"affiliations":[{"raw_affiliation_string":"College of Information and Computer Engineering, Northeast Forestry University, Harbin, China. tianjiaozhang@nefu.edu.cn","institution_ids":[]},{"raw_affiliation_string":"College of Information and Computer Engineering, Northeast Forestry University, Harbin, China","institution_ids":["https://openalex.org/I47689461"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100401949"],"corresponding_institution_ids":["https://openalex.org/I47689461"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.6226,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.69471059,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"24","issue":"1","first_page":"137","last_page":"137"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","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/T12254","display_name":"Machine Learning in Bioinformatics","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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9948999881744385,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9923999905586243,"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/classifier","display_name":"Classifier (UML)","score":0.5714957118034363},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5486796498298645},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5322313904762268},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5210268497467041},{"id":"https://openalex.org/keywords/stack","display_name":"Stack (abstract data type)","score":0.45447736978530884},{"id":"https://openalex.org/keywords/ensemble-learning","display_name":"Ensemble learning","score":0.43098515272140503},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3529737591743469},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3444477915763855},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2488572597503662},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1958174705505371},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14788910746574402},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08655482530593872}],"concepts":[{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.5714957118034363},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5486796498298645},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5322313904762268},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5210268497467041},{"id":"https://openalex.org/C9395851","wikidata":"https://www.wikidata.org/wiki/Q177929","display_name":"Stack (abstract data type)","level":2,"score":0.45447736978530884},{"id":"https://openalex.org/C45942800","wikidata":"https://www.wikidata.org/wiki/Q245652","display_name":"Ensemble learning","level":2,"score":0.43098515272140503},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3529737591743469},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3444477915763855},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2488572597503662},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1958174705505371},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14788910746574402},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08655482530593872}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D033921","descriptor_name":"Vesicular Transport Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D033921","descriptor_name":"Vesicular Transport Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D033921","descriptor_name":"Vesicular Transport Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D033921","descriptor_name":"Vesicular Transport Proteins","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":true},{"descriptor_ui":"D033921","descriptor_name":"Vesicular Transport Proteins","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":true},{"descriptor_ui":"D033921","descriptor_name":"Vesicular Transport Proteins","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":true},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-023-05257-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05257-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05257-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37029385","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37029385","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10080812","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10080812","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10080812/pdf/12859_2023_Article_5257.pdf","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:e0a6b50edf9f451cb5c7bbaba1fd6757","is_oa":true,"landing_page_url":"https://doaj.org/article/e0a6b50edf9f451cb5c7bbaba1fd6757","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 24, Iss 1, Pp 1-18 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05257-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05257-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05257-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2376276132","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G3076383002","display_name":null,"funder_award_id":"2572021BH01","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6890957027","display_name":null,"funder_award_id":"62172087","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"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4362698482.pdf"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W28412257","https://openalex.org/W843551813","https://openalex.org/W1253096047","https://openalex.org/W1975670646","https://openalex.org/W1981174113","https://openalex.org/W2028598757","https://openalex.org/W2030793934","https://openalex.org/W2040953865","https://openalex.org/W2047987426","https://openalex.org/W2049313357","https://openalex.org/W2053186076","https://openalex.org/W2068361619","https://openalex.org/W2078691152","https://openalex.org/W2092170487","https://openalex.org/W2103291381","https://openalex.org/W2130924270","https://openalex.org/W2140679062","https://openalex.org/W2147614625","https://openalex.org/W2155653793","https://openalex.org/W2770191688","https://openalex.org/W2889337219","https://openalex.org/W2898454434","https://openalex.org/W2950445386","https://openalex.org/W2963959402","https://openalex.org/W2969086705","https://openalex.org/W2982010568","https://openalex.org/W3004732066","https://openalex.org/W3043901899","https://openalex.org/W3091812365","https://openalex.org/W3092453021","https://openalex.org/W3093610272","https://openalex.org/W3105609465","https://openalex.org/W4205205141","https://openalex.org/W4206950877","https://openalex.org/W4239510810","https://openalex.org/W4291383372"],"related_works":["https://openalex.org/W2380576232","https://openalex.org/W2937054111","https://openalex.org/W2066223521","https://openalex.org/W373327546","https://openalex.org/W2321534397","https://openalex.org/W2058958858","https://openalex.org/W1835805572","https://openalex.org/W2148243540","https://openalex.org/W2077601556","https://openalex.org/W2013178899"],"abstract_inverted_index":{"Vesicle":[0],"transport":[1,12,30,49,105],"proteins":[2,31,106],"not":[3],"only":[4],"play":[5],"an":[6],"important":[7],"role":[8],"in":[9,20],"the":[10,21,26,54,82,88,93,100,113,126,152],"transmembrane":[11],"of":[13,23,28,114,122,141],"molecules,":[14],"but":[15],"also":[16],"have":[17],"a":[18,37],"place":[19],"field":[22],"biomedicine,":[24],"so":[25],"identification":[27],"vesicle":[29,48,104],"is":[32,97],"particularly":[33],"important.":[34],"We":[35],"propose":[36],"method":[38,124,144],"based":[39],"on":[40,125],"ensemble":[41],"learning":[42],"and":[43,70,75,80,119,133,139,148],"evolutionary":[44],"information":[45],"to":[46,86],"identify":[47],"proteins.":[50],"Firstly,":[51],"we":[52,61],"preprocess":[53],"imbalanced":[55],"dataset":[56],"by":[57],"random":[58],"undersampling.":[59],"Secondly,":[60],"extract":[62,73],"position-specific":[63],"scoring":[64],"matrix":[65],"(PSSM)":[66],"from":[67,78],"protein":[68],"sequences,":[69],"then":[71],"further":[72],"AADP-PSSM":[74],"RPSSM":[76],"features":[77],"PSSM,":[79],"use":[81],"Max-Relevance-Max-Distance":[83],"(MRMD)":[84],"algorithm":[85],"select":[87],"optimal":[89,94],"feature":[90,95],"subset.":[91],"Finally,":[92],"subset":[96],"fed":[98],"into":[99],"stacked":[101],"classifier":[102],"for":[103],"identification.":[107],"The":[108,136],"experimental":[109],"results":[110],"show":[111],"that":[112],"accuracy":[115],"(ACC),":[116],"sensitivity":[117],"(SN)":[118],"specificity":[120],"(SP)":[121],"our":[123,142],"independent":[127],"testing":[128],"set":[129],"are":[130,145],"82.53%,":[131],"0.774":[132],"0.836,":[134],"respectively.":[135],"SN,":[137],"SP":[138],"ACC":[140],"proposed":[143],"0.013,":[146],"0.007":[147],"0.76%":[149],"higher":[150],"than":[151],"current":[153],"state-of-the-art":[154],"methods.":[155]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}