{"id":"https://openalex.org/W3037436972","doi":"https://doi.org/10.1109/tcbb.2020.3004364","title":"Significance-Based Essential Protein Discovery","display_name":"Significance-Based Essential Protein Discovery","publication_year":2020,"publication_date":"2020-06-23","ids":{"openalex":"https://openalex.org/W3037436972","doi":"https://doi.org/10.1109/tcbb.2020.3004364","mag":"3037436972","pmid":"https://pubmed.ncbi.nlm.nih.gov/32750873"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2020.3004364","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.3004364","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","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":null,"display_name":"Yan Liu","orcid":"https://orcid.org/0000-0002-1386-812X"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Liu","raw_affiliation_strings":["School of Software, Dalian University of Technology, Dalian, China"],"raw_orcid":"https://orcid.org/0000-0002-1386-812X","affiliations":[{"raw_affiliation_string":"School of Software, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hao Liang","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Liang","raw_affiliation_strings":["School of Software, Dalian University of Technology, Dalian, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Quan Zou","orcid":"https://orcid.org/0000-0001-6406-1142"},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Quan Zou","raw_affiliation_strings":["Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China"],"raw_orcid":"https://orcid.org/0000-0001-6406-1142","affiliations":[{"raw_affiliation_string":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China","institution_ids":["https://openalex.org/I150229711"]}]},{"author_position":"last","author":{"id":null,"display_name":"Zengyou He","orcid":"https://orcid.org/0000-0001-9526-8816"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zengyou He","raw_affiliation_strings":["Key Laboratory for Ubiquitous Network and Service Software of Liaoning Province, Dalian, China","School of Software, Dalian University of Technology, Dalian, China"],"raw_orcid":"https://orcid.org/0000-0001-9526-8816","affiliations":[{"raw_affiliation_string":"Key Laboratory for Ubiquitous Network and Service Software of Liaoning Province, Dalian, China","institution_ids":[]},{"raw_affiliation_string":"School of Software, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.6509,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.66539427,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"19","issue":"1","first_page":"633","last_page":"642"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9830999970436096,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9830999970436096,"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":0.0052999998442828655,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.0019000000320374966,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/false-discovery-rate","display_name":"False discovery rate","score":0.8061000108718872},{"id":"https://openalex.org/keywords/centrality","display_name":"Centrality","score":0.7452999949455261},{"id":"https://openalex.org/keywords/multiple-comparisons-problem","display_name":"Multiple comparisons problem","score":0.5771999955177307},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5130000114440918},{"id":"https://openalex.org/keywords/statistical-hypothesis-testing","display_name":"Statistical hypothesis testing","score":0.5016000270843506},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4799000024795532},{"id":"https://openalex.org/keywords/statistic","display_name":"Statistic","score":0.43130001425743103},{"id":"https://openalex.org/keywords/null-hypothesis","display_name":"Null hypothesis","score":0.39750000834465027}],"concepts":[{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.8061000108718872},{"id":"https://openalex.org/C53811970","wikidata":"https://www.wikidata.org/wiki/Q5062194","display_name":"Centrality","level":2,"score":0.7452999949455261},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5960999727249146},{"id":"https://openalex.org/C183905921","wikidata":"https://www.wikidata.org/wiki/Q1038757","display_name":"Multiple comparisons problem","level":2,"score":0.5771999955177307},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5170000195503235},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5130000114440918},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.5016000270843506},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4799000024795532},{"id":"https://openalex.org/C89128539","wikidata":"https://www.wikidata.org/wiki/Q1949963","display_name":"Statistic","level":2,"score":0.43130001425743103},{"id":"https://openalex.org/C191988596","wikidata":"https://www.wikidata.org/wiki/Q628374","display_name":"Null hypothesis","level":2,"score":0.39750000834465027},{"id":"https://openalex.org/C169857963","wikidata":"https://www.wikidata.org/wiki/Q1461038","display_name":"Test statistic","level":3,"score":0.3873000144958496},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3785000145435333},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.3693999946117401},{"id":"https://openalex.org/C203763787","wikidata":"https://www.wikidata.org/wiki/Q371029","display_name":"Null (SQL)","level":2,"score":0.36739999055862427},{"id":"https://openalex.org/C22047676","wikidata":"https://www.wikidata.org/wiki/Q898680","display_name":"Clustering coefficient","level":3,"score":0.3506999909877777},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3386000096797943},{"id":"https://openalex.org/C36382193","wikidata":"https://www.wikidata.org/wiki/Q7068966","display_name":"Null model","level":2,"score":0.31299999356269836},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.304500013589859},{"id":"https://openalex.org/C93453677","wikidata":"https://www.wikidata.org/wiki/Q1017580","display_name":"Business process discovery","level":5,"score":0.2921000123023987},{"id":"https://openalex.org/C188598960","wikidata":"https://www.wikidata.org/wiki/Q7705805","display_name":"Test strategy","level":3,"score":0.2799000144004822},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.27090001106262207},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2612000107765198},{"id":"https://openalex.org/C40969351","wikidata":"https://www.wikidata.org/wiki/Q3516228","display_name":"Word error rate","level":2,"score":0.25200000405311584},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.2506999969482422}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2020.3004364","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.3004364","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32750873","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32750873","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1240581458","display_name":null,"funder_award_id":"61972066","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G306606422","display_name":"\u9762\u5411AP-MS\u6570\u636e\u7684\u86cb\u767d\u8d28\u76f8\u4e92\u4f5c\u7528\u7f51\u7edc\u63a8\u65ad\u7b97\u6cd5\u7814\u7a76","funder_award_id":"61572094","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G360331958","display_name":null,"funder_award_id":"DUT20YG106","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"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":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W1503938960","https://openalex.org/W1714524773","https://openalex.org/W1777916189","https://openalex.org/W1853409988","https://openalex.org/W1956379070","https://openalex.org/W1973758399","https://openalex.org/W1986310535","https://openalex.org/W1988496202","https://openalex.org/W1997751445","https://openalex.org/W1998152384","https://openalex.org/W1999808266","https://openalex.org/W2007245700","https://openalex.org/W2017975254","https://openalex.org/W2038492783","https://openalex.org/W2047998870","https://openalex.org/W2050721857","https://openalex.org/W2080187616","https://openalex.org/W2087194317","https://openalex.org/W2089125183","https://openalex.org/W2098979213","https://openalex.org/W2105089945","https://openalex.org/W2110065044","https://openalex.org/W2115550821","https://openalex.org/W2116117181","https://openalex.org/W2119114096","https://openalex.org/W2130790725","https://openalex.org/W2132582966","https://openalex.org/W2142437744","https://openalex.org/W2150934340","https://openalex.org/W2154897810","https://openalex.org/W2156345326","https://openalex.org/W2162891889","https://openalex.org/W2326727950","https://openalex.org/W2616561032","https://openalex.org/W2765203444","https://openalex.org/W2792330169","https://openalex.org/W2912802963","https://openalex.org/W2914622179","https://openalex.org/W2915554882","https://openalex.org/W2949475756"],"related_works":[],"abstract_inverted_index":{"The":[0,209],"identification":[1],"of":[2,38,45,52,64,68,81,129],"essential":[3,70,87,99,122,190],"proteins":[4,71],"is":[5,103,115,119,158,176,194,199,216],"an":[6,121],"important":[7],"problem":[8,90,102],"in":[9,72,138,182],"bioinformatics.":[10],"During":[11],"the":[12,32,36,50,62,66,79,86,98,112,126,141,144,151,155,161,167,172,179,183],"past":[13],"decades,":[14],"many":[15],"centrality":[16,47,59],"measures":[17],"and":[18,41,143,154,205],"algorithms":[19],"have":[20],"been":[21],"proposed":[22],"to":[23,218],"address":[24],"this":[25],"issue.":[26],"However,":[27],"existing":[28,82],"methods":[29],"still":[30],"deserve":[31],"following":[33],"drawbacks:":[34],"(1)":[35],"lack":[37],"a":[39,54,73,92,106,134],"context-free":[40],"readily":[42],"interpretable":[43],"quantification":[44],"their":[46,58],"values;":[48,60],"(2)":[49],"difficulty":[51],"specifying":[53],"proper":[55],"threshold":[56],"for":[57,169],"(3)":[61],"incapability":[63],"controlling":[65],"quality":[67],"reported":[69],"statistically":[74],"sound":[75],"manner.":[76],"To":[77,124],"overcome":[78],"limitations":[80],"solutions,":[83],"we":[84,132],"tackle":[85],"protein":[88,100,118,191],"discovery":[89,101,174,192],"from":[91],"significance":[93,128],"testing":[94,109,185],"perspective.":[95],"More":[96],"precisely,":[97],"formulated":[104],"as":[105,150,160,178,196],"multiple":[107,184],"hypothesis":[108,114],"problem,":[110],"where":[111],"null":[113],"that":[116,213],"each":[117,130,170],"not":[120],"protein.":[123],"quantify":[125],"statistical":[127],"protein,":[131,171],"present":[133],"p-value":[135,168],"calculation":[136],"method":[137,193,215],"which":[139,198],"both":[140,202],"degree":[142],"local":[145],"clustering":[146],"coefficient":[147],"are":[148],"used":[149,177],"test":[152],"statistic":[153],"Erd\u00f6s-R\u00e9nyi":[156],"model":[157],"employed":[159],"random":[162],"graph":[163],"model.":[164],"After":[165],"calculating":[166],"false":[173],"rate":[175,181],"error":[180],"correction":[186],"procedure.":[187],"Our":[188],"significance-based":[189],"named":[195],"SigEP,":[197],"tested":[200],"on":[201],"simulated":[203],"networks":[204],"real":[206],"PPI":[207],"networks.":[208],"experimental":[210],"results":[211],"show":[212],"our":[214],"able":[217],"achieve":[219],"better":[220],"performance":[221],"than":[222],"those":[223],"competing":[224],"algorithms.":[225]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2020-07-02T00:00:00"}