{"id":"https://openalex.org/W2055099963","doi":"https://doi.org/10.1142/s021972001450005x","title":"PhD7FASTER: PREDICTING CLONES PROPAGATING FASTER FROM THE Ph.D.-7 PHAGE DISPLAY PEPTIDE LIBRARY","display_name":"PhD7FASTER: PREDICTING CLONES PROPAGATING FASTER FROM THE Ph.D.-7 PHAGE DISPLAY PEPTIDE LIBRARY","publication_year":2013,"publication_date":"2013-11-20","ids":{"openalex":"https://openalex.org/W2055099963","doi":"https://doi.org/10.1142/s021972001450005x","mag":"2055099963"},"language":"en","primary_location":{"id":"doi:10.1142/s021972001450005x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972001450005x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-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/A5070268010","display_name":"Beibei Ru","orcid":"https://orcid.org/0000-0003-3897-7733"},"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":true,"raw_author_name":"BEIBEI RU","raw_affiliation_strings":["Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, P. R. China"],"affiliations":[{"raw_affiliation_string":"Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, P. R. China","institution_ids":["https://openalex.org/I150229711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021033668","display_name":"Peter A.C. \u2019t Hoen","orcid":"https://orcid.org/0000-0003-4450-3112"},"institutions":[{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"PETER A. C. 'T HOEN","raw_affiliation_strings":["Center for Human and Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Center for Human and Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands","institution_ids":["https://openalex.org/I2800006345"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069460960","display_name":"Fulei Nie","orcid":null},"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":"FULEI NIE","raw_affiliation_strings":["Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, P. R. China"],"affiliations":[{"raw_affiliation_string":"Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, P. R. China","institution_ids":["https://openalex.org/I150229711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041539298","display_name":"Hao Lin","orcid":"https://orcid.org/0000-0001-6265-2862"},"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":"HAO LIN","raw_affiliation_strings":["Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, P. R. China"],"affiliations":[{"raw_affiliation_string":"Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, P. R. China","institution_ids":["https://openalex.org/I150229711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079147107","display_name":"Feng\u2010Biao Guo","orcid":"https://orcid.org/0000-0002-1129-5233"},"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":"FENG-BIAO GUO","raw_affiliation_strings":["Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, P. R. China"],"affiliations":[{"raw_affiliation_string":"Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, P. R. China","institution_ids":["https://openalex.org/I150229711"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010405974","display_name":"Jian Huang","orcid":"https://orcid.org/0000-0003-3282-8892"},"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":"JIAN HUANG","raw_affiliation_strings":["Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, P. R. China"],"affiliations":[{"raw_affiliation_string":"Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, P. R. China","institution_ids":["https://openalex.org/I150229711"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5070268010"],"corresponding_institution_ids":["https://openalex.org/I150229711"],"apc_list":null,"apc_paid":null,"fwci":2.9072,"has_fulltext":false,"cited_by_count":44,"citation_normalized_percentile":{"value":0.89997877,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"12","issue":"01","first_page":"1450005","last_page":"1450005"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9993000030517578,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9991000294685364,"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/panning","display_name":"Panning (audio)","score":0.9494236707687378},{"id":"https://openalex.org/keywords/phage-display","display_name":"Phage display","score":0.8580068349838257},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.6467944383621216},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.564017117023468},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5314663052558899},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49433445930480957},{"id":"https://openalex.org/keywords/matthews-correlation-coefficient","display_name":"Matthews correlation coefficient","score":0.49045464396476746},{"id":"https://openalex.org/keywords/peptide-library","display_name":"Peptide library","score":0.48833200335502625},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.4876476526260376},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.458311527967453},{"id":"https://openalex.org/keywords/dipeptide","display_name":"Dipeptide","score":0.43042391538619995},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.37775516510009766},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3718133270740509},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1894453465938568},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.14076995849609375}],"concepts":[{"id":"https://openalex.org/C108944566","wikidata":"https://www.wikidata.org/wiki/Q1524510","display_name":"Panning (audio)","level":4,"score":0.9494236707687378},{"id":"https://openalex.org/C186268636","wikidata":"https://www.wikidata.org/wiki/Q896217","display_name":"Phage display","level":3,"score":0.8580068349838257},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.6467944383621216},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.564017117023468},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5314663052558899},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49433445930480957},{"id":"https://openalex.org/C164085508","wikidata":"https://www.wikidata.org/wiki/Q4811327","display_name":"Matthews correlation coefficient","level":3,"score":0.49045464396476746},{"id":"https://openalex.org/C2776471321","wikidata":"https://www.wikidata.org/wiki/Q7166526","display_name":"Peptide library","level":4,"score":0.48833200335502625},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.4876476526260376},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.458311527967453},{"id":"https://openalex.org/C2779138802","wikidata":"https://www.wikidata.org/wiki/Q418602","display_name":"Dipeptide","level":3,"score":0.43042391538619995},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.37775516510009766},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3718133270740509},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1894453465938568},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.14076995849609375},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C15336307","wikidata":"https://www.wikidata.org/wiki/Q1766051","display_name":"Lens (geology)","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C124913957","wikidata":"https://www.wikidata.org/wiki/Q1232548","display_name":"Zoom","level":3,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1142/s021972001450005x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972001450005x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmh:lumc:oai:scholarlypublications.universiteitleiden.nl:item_2993016","is_oa":false,"landing_page_url":"http://hdl.handle.net/1887/104743","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Bioinformatics and Computational Biology, 12(1)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:scholarlypublications.universiteitleiden.nl:item_2993016","is_oa":false,"landing_page_url":"https://hdl.handle.net/1887/104743","pdf_url":null,"source":{"id":"https://openalex.org/S4306400850","display_name":"Leiden Repository (Leiden University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I121797337","host_organization_name":"Leiden University","host_organization_lineage":["https://openalex.org/I121797337"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"Article / Letter to editor"}],"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"},{"id":"https://openalex.org/F4320334924","display_name":"Program for New Century Excellent Talents in University","ror":"https://ror.org/01mv9t934"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1589512874","https://openalex.org/W1964490586","https://openalex.org/W1966656460","https://openalex.org/W1973565539","https://openalex.org/W1975166819","https://openalex.org/W1992079221","https://openalex.org/W1997207214","https://openalex.org/W1999779721","https://openalex.org/W2006508505","https://openalex.org/W2010649076","https://openalex.org/W2026649873","https://openalex.org/W2029186733","https://openalex.org/W2033167476","https://openalex.org/W2048356293","https://openalex.org/W2058860357","https://openalex.org/W2062395662","https://openalex.org/W2070360032","https://openalex.org/W2080450255","https://openalex.org/W2082153947","https://openalex.org/W2084071030","https://openalex.org/W2091395656","https://openalex.org/W2099982459","https://openalex.org/W2101271566","https://openalex.org/W2102152570","https://openalex.org/W2114406337","https://openalex.org/W2124551984","https://openalex.org/W2133990480","https://openalex.org/W2147087392","https://openalex.org/W2153635508","https://openalex.org/W2160020195","https://openalex.org/W2166811939","https://openalex.org/W2417210895","https://openalex.org/W4211045835"],"related_works":["https://openalex.org/W2066892610","https://openalex.org/W2152440849","https://openalex.org/W3136489676","https://openalex.org/W2389347183","https://openalex.org/W2090059339","https://openalex.org/W2959190208","https://openalex.org/W2043061837","https://openalex.org/W3190042041","https://openalex.org/W2056665457","https://openalex.org/W2610098014"],"abstract_inverted_index":{"Phage":[0],"display":[1,49,125],"can":[2,174,198],"rapidly":[3],"discover":[4],"peptides":[5,78,88],"binding":[6],"to":[7,52,70,161,177],"any":[8],"given":[9],"target;":[10],"thus,":[11],"it":[12],"has":[13],"been":[14],"widely":[15],"used":[16],"in":[17,72,151],"basic":[18,29],"and":[19,32,95,141,181],"applied":[20],"research.":[21],"Each":[22],"round":[23],"of":[24,27,47,56,139,147,185,196],"panning":[25],"consists":[26],"two":[28],"processes:":[30],"Selection":[31],"amplification.":[33],"However,":[34],"recent":[35],"studies":[36],"have":[37],"showed":[38],"that":[39,172],"the":[40,45,73,122,156,183,189],"amplification":[41],"step":[42],"would":[43,91],"decrease":[44],"diversity":[46],"phage":[48,57,124],"libraries":[50],"due":[51],"different":[53],"propagation":[54],"capacity":[55],"clones.":[58],"This":[59],"may":[60],"induce":[61],"phages":[62,82],"with":[63,118],"growth":[64,119],"advantage":[65,120],"rather":[66],"than":[67,164],"specific":[68,186],"affinity":[69],"appear":[71],"final":[74],"experimental":[75],"results.":[76],"The":[77,193],"displayed":[79],"by":[80],"such":[81],"are":[83],"termed":[84],"as":[85,134],"propagation-related":[86],"target-unrelated":[87],"(PrTUPs).":[89],"They":[90],"mislead":[92],"further":[93],"analysis":[94],"research":[96],"if":[97],"not":[98],"removed.":[99],"In":[100,154],"this":[101],"paper,":[102],"we":[103],"describe":[104],"PhD7Faster,":[105],"an":[106,136],"ensemble":[107],"predictor":[108],"based":[109],"on":[110],"support":[111],"vector":[112],"machine":[113,167],"(SVM)":[114],"for":[115],"predicting":[116],"clones":[117],"from":[121,188],"Ph.D.-7":[123,191],"peptide":[126],"library.":[127,192],"By":[128],"using":[129],"reduced":[130],"dipeptide":[131],"composition":[132],"(ReDPC)":[133],"features,":[135],"accuracy":[137],"(Acc)":[138],"79.67%":[140],"a":[142],"Matthews":[143],"correlation":[144],"coefficient":[145],"(MCC)":[146],"0.595":[148],"were":[149],"achieved":[150],"5-fold":[152],"cross-validation.":[153],"addition,":[155],"SVM-based":[157],"model":[158],"was":[159],"demonstrated":[160],"perform":[162],"better":[163],"several":[165],"representative":[166],"learning":[168],"algorithms.":[169],"We":[170],"anticipate":[171],"PhD7Faster":[173,197],"assist":[175],"biologists":[176],"exclude":[178],"potential":[179],"PrTUPs":[180],"accelerate":[182],"finding":[184],"binders":[187],"popular":[190],"web":[194],"server":[195],"be":[199],"freely":[200],"accessed":[201],"at":[202],"http://immunet.cn/sarotup/cgi-bin/PhD7Faster.pl":[203],".":[204]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":3}],"updated_date":"2026-03-08T08:50:53.379069","created_date":"2016-06-24T00:00:00"}
