{"id":"https://openalex.org/W2569814361","doi":"https://doi.org/10.1093/bioinformatics/btw701","title":"ESA-UbiSite: accurate prediction of human ubiquitination sites by identifying a set of effective negatives","display_name":"ESA-UbiSite: accurate prediction of human ubiquitination sites by identifying a set of effective negatives","publication_year":2016,"publication_date":"2016-11-08","ids":{"openalex":"https://openalex.org/W2569814361","doi":"https://doi.org/10.1093/bioinformatics/btw701","mag":"2569814361","pmid":"https://pubmed.ncbi.nlm.nih.gov/28062441"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw701","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw701","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/5/661/25148329/btw701.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/5/661/25148329/btw701.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035255825","display_name":"Jyun-Rong Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Jyun-Rong Wang","raw_affiliation_strings":["Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I148366613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113678857","display_name":"Wen-Lin Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I143003336","display_name":"Minghsin University of Science and Technology","ror":"https://ror.org/054etzm63","country_code":"TW","type":"education","lineage":["https://openalex.org/I143003336"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Wen-Lin Huang","raw_affiliation_strings":["Department and Institute of Industrial Engineering and Management, Minghsin University of Science and Technology, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department and Institute of Industrial Engineering and Management, Minghsin University of Science and Technology, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I143003336"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081321440","display_name":"Ming\u2010Ju Tsai","orcid":"https://orcid.org/0000-0003-3621-3334"},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Ming-Ju Tsai","raw_affiliation_strings":["Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I148366613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113795095","display_name":"Kai-Ti Hsu","orcid":null},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Kai-Ti Hsu","raw_affiliation_strings":["Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I148366613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112007823","display_name":"Hui-Ling Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Hui-Ling Huang","raw_affiliation_strings":["Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan","Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I148366613"]},{"raw_affiliation_string":"Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I148366613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070924732","display_name":"Shinn\u2010Ying Ho","orcid":"https://orcid.org/0000-0002-1901-8353"},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Shinn-Ying Ho","raw_affiliation_strings":["Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan","Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I148366613"]},{"raw_affiliation_string":"Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I148366613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5070924732"],"corresponding_institution_ids":["https://openalex.org/I148366613"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.4823,"has_fulltext":false,"cited_by_count":59,"citation_normalized_percentile":{"value":0.92989774,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"33","issue":"5","first_page":"661","last_page":"668"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.6468999981880188,"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":0.6468999981880188,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.163100004196167,"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/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.05620000138878822,"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/set","display_name":"Set (abstract data type)","score":0.6312296390533447},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6286559104919434},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4139145612716675},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3649851083755493},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33420056104660034},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16942614316940308},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.06637457013130188}],"concepts":[{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6312296390533447},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6286559104919434},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4139145612716675},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3649851083755493},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33420056104660034},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16942614316940308},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.06637457013130188}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":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":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","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":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","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":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btw701","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw701","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/5/661/25148329/btw701.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28062441","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28062441","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw701","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw701","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/5/661/25148329/btw701.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5247883035","display_name":null,"funder_award_id":"MOST-105-2627-M-009-008","funder_id":"https://openalex.org/F4320321040","funder_display_name":"National Science Council"},{"id":"https://openalex.org/G7089230189","display_name":null,"funder_award_id":"MOST-105-2221-E-009-138-MY2","funder_id":"https://openalex.org/F4320321040","funder_display_name":"National Science Council"}],"funders":[{"id":"https://openalex.org/F4320321040","display_name":"National Science Council","ror":"https://ror.org/02kv4zf79"},{"id":"https://openalex.org/F4320323443","display_name":"National Chiao Tung University","ror":"https://ror.org/00se2k293"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W413431681","https://openalex.org/W1568400197","https://openalex.org/W1618846043","https://openalex.org/W1833977909","https://openalex.org/W1904882776","https://openalex.org/W1913193691","https://openalex.org/W1967391569","https://openalex.org/W1974515407","https://openalex.org/W1978650123","https://openalex.org/W1982411844","https://openalex.org/W1991036637","https://openalex.org/W1991244466","https://openalex.org/W1996164344","https://openalex.org/W2003204068","https://openalex.org/W2006505144","https://openalex.org/W2014525284","https://openalex.org/W2014731953","https://openalex.org/W2020738975","https://openalex.org/W2023919356","https://openalex.org/W2047750588","https://openalex.org/W2051166632","https://openalex.org/W2053967598","https://openalex.org/W2056499061","https://openalex.org/W2056775476","https://openalex.org/W2056804360","https://openalex.org/W2057197272","https://openalex.org/W2060287713","https://openalex.org/W2061184183","https://openalex.org/W2066622802","https://openalex.org/W2069313265","https://openalex.org/W2070106972","https://openalex.org/W2075319133","https://openalex.org/W2083522539","https://openalex.org/W2086831875","https://openalex.org/W2093693973","https://openalex.org/W2094355065","https://openalex.org/W2104244040","https://openalex.org/W2114441129","https://openalex.org/W2124351063","https://openalex.org/W2125983734","https://openalex.org/W2139577310","https://openalex.org/W2148145769","https://openalex.org/W2148853951","https://openalex.org/W2152084880","https://openalex.org/W2152339342","https://openalex.org/W2153635508","https://openalex.org/W2155239883","https://openalex.org/W2156524622","https://openalex.org/W2157658519","https://openalex.org/W2164260969","https://openalex.org/W2164632416","https://openalex.org/W2167485812","https://openalex.org/W4213345021","https://openalex.org/W4244191430"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"Motivation:":[0],"Numerous":[1],"ubiquitination":[2,27,55,66],"sites":[3,21,24,45,61,67],"remain":[4],"undiscovered":[5],"because":[6],"of":[7,10,79,109],"the":[8,72],"limitations":[9],"mass":[11],"spectrometry-based":[12],"methods.":[13,115,134],"Existing":[14],"prediction":[15,29,49,114,133],"methods":[16],"use":[17,76],"randomly":[18],"selected":[19],"non-validated":[20,44,60],"as":[22,68],"non-ubiquitination":[23],"to":[25,39,52,64,124],"train":[26],"site":[28,132],"models.":[30],"Results:":[31],"We":[32],"propose":[33],"an":[34,47],"evolutionary":[35],"screening":[36],"algorithm":[37],"(ESA)":[38],"select":[40],"effective":[41,98],"negatives":[42,99],"among":[43],"and":[46,74,104,126,136],"ESA-based":[48],"method,":[50],"ESA-UbiSite,":[51],"identify":[53],"human":[54],"sites.":[56],"The":[57,116],"ESA":[58,73,117],"selects":[59],"least":[62],"likely":[63],"be":[65],"training":[69],"negatives.":[70],"Moreover,":[71],"ESA-UbiSite":[75,96],"a":[77,85,105],"set":[78],"well-selected":[80],"physicochemical":[81],"properties":[82],"together":[83],"with":[84,97],"support":[86],"vector":[87],"machine":[88],"for":[89],"accurate":[90],"prediction.":[91],"Experimental":[92],"results":[93],"show":[94],"that":[95],"achieved":[100],"0.92":[101,125],"test":[102,120],"accuracy":[103,121],"Matthews's":[106],"correlation":[107],"coefficient":[108],"0.48,":[110],"better":[111],"than":[112],"existing":[113],"increased":[118],"ESA-UbiSite's":[119],"from":[122],"0.75":[123],"can":[127],"improve":[128],"other":[129],"post-translational":[130],"modification":[131],"Availability":[135],"Implementation:":[137],"An":[138],"ESA-UbiSite-based":[139],"web":[140],"server":[141],"has":[142],"been":[143],"established":[144],"at":[145,156],"http://iclab.life.nctu.edu.tw/iclab_webtools/ESAUbiSite/":[146],".":[147],"Contact:":[148],"syho@mail.nctu.edu.tw.":[149],"Supplementary":[150,152],"information:":[151],"data":[153],"are":[154],"available":[155],"Bioinformatics":[157],"online.":[158]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":1}],"updated_date":"2026-06-20T22:02:38.213706","created_date":"2025-10-10T00:00:00"}
