{"id":"https://openalex.org/W2888425535","doi":"https://doi.org/10.1145/3233547.3233599","title":"The PepSeq Pipeline","display_name":"The PepSeq Pipeline","publication_year":2018,"publication_date":"2018-08-15","ids":{"openalex":"https://openalex.org/W2888425535","doi":"https://doi.org/10.1145/3233547.3233599","mag":"2888425535"},"language":"en","primary_location":{"id":"doi:10.1145/3233547.3233599","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3233547.3233599","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-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/A5091061027","display_name":"Tanner Jensen","orcid":"https://orcid.org/0000-0002-1873-8607"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tanner D. Jensen","raw_affiliation_strings":["Brigham Young University, Provo, UT, USA"],"affiliations":[{"raw_affiliation_string":"Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032035402","display_name":"Kristi A. Bresciano","orcid":null},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kristi A. Bresciano","raw_affiliation_strings":["Brigham Young University, Provo, UT, USA"],"affiliations":[{"raw_affiliation_string":"Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057413879","display_name":"Emma Kay Dallon","orcid":null},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emma Dallon","raw_affiliation_strings":["Brigham Young University, Provo, UT, USA"],"affiliations":[{"raw_affiliation_string":"Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063608648","display_name":"Mao Fujimoto","orcid":"https://orcid.org/0000-0002-2020-935X"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Stanley Fujimoto","raw_affiliation_strings":["Brigham Young University, Provo, UT, USA"],"affiliations":[{"raw_affiliation_string":"Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052915205","display_name":"Cole A. Lyman","orcid":"https://orcid.org/0000-0001-7921-165X"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cole A. Lyman","raw_affiliation_strings":["Brigham Young University, Provo, UT, USA"],"affiliations":[{"raw_affiliation_string":"Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040488523","display_name":"Enoch Stewart","orcid":null},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Enoch Stewart","raw_affiliation_strings":["Brigham Young University, Provo, UT, USA"],"affiliations":[{"raw_affiliation_string":"Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067036422","display_name":"Joel S. Griffitts","orcid":"https://orcid.org/0000-0003-1177-272X"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joel Griffitts","raw_affiliation_strings":["Brigham Young University, Provo, UT, USA"],"affiliations":[{"raw_affiliation_string":"Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058435710","display_name":"Mark Clement","orcid":"https://orcid.org/0000-0003-4902-3521"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark J. Clement","raw_affiliation_strings":["Brigham Young University, Provo, UT, USA"],"affiliations":[{"raw_affiliation_string":"Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5091061027"],"corresponding_institution_ids":["https://openalex.org/I100005738"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.07727628,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"2","issue":null,"first_page":"139","last_page":"144"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13326","display_name":"Biochemical and Structural Characterization","score":0.9988999962806702,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.9988999962806702,"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/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.996399998664856,"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/pipeline","display_name":"Pipeline (software)","score":0.7470382452011108},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.6412545442581177},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6203674077987671},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.567936360836029},{"id":"https://openalex.org/keywords/antimicrobial-peptides","display_name":"Antimicrobial peptides","score":0.5434842109680176},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.4894470274448395},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.428882896900177},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.41425585746765137},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3792046308517456},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3212541341781616},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2798506021499634},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.23589855432510376},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.21754315495491028},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12477758526802063}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7470382452011108},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.6412545442581177},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6203674077987671},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.567936360836029},{"id":"https://openalex.org/C540938839","wikidata":"https://www.wikidata.org/wiki/Q1201508","display_name":"Antimicrobial peptides","level":3,"score":0.5434842109680176},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.4894470274448395},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.428882896900177},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.41425585746765137},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3792046308517456},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3212541341781616},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2798506021499634},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.23589855432510376},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.21754315495491028},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12477758526802063}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3233547.3233599","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3233547.3233599","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.7599999904632568,"display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1576731213","https://openalex.org/W2057198053","https://openalex.org/W2130387209","https://openalex.org/W2133990480","https://openalex.org/W2148143831","https://openalex.org/W2213443318","https://openalex.org/W2525356667","https://openalex.org/W2558941103","https://openalex.org/W2586832190","https://openalex.org/W2606253804","https://openalex.org/W2731161895","https://openalex.org/W2769836604","https://openalex.org/W2887488356"],"related_works":["https://openalex.org/W2883687614","https://openalex.org/W2314450753","https://openalex.org/W4385723643","https://openalex.org/W2396126703","https://openalex.org/W2390495284","https://openalex.org/W3136610278","https://openalex.org/W3037187668","https://openalex.org/W2999569426","https://openalex.org/W1614895742","https://openalex.org/W2158714878"],"abstract_inverted_index":{"Bacteria":[0],"with":[1,116],"resistance":[2],"genes":[3],"are":[4,15,174],"becoming":[5],"ever":[6],"more":[7],"common,":[8],"and":[9,28,176,183],"new":[10,21,74],"methods":[11,22],"of":[12,19,54,98,125,153],"discovering":[13],"antibiotics":[14,34],"being":[16],"developed.":[17],"One":[18],"these":[20,36,160],"involves":[23],"researchers":[24],"creating":[25],"random":[26],"peptides":[27,37,53,101,148,173],"testing":[29],"their":[30],"antimicrobial":[31],"activity.":[32],"Developing":[33],"from":[35,85,109],"requires":[38],"understanding":[39],"which":[40],"sequence":[41,66],"motifs":[42,84,107,134,154,161],"will":[43],"be":[44,60,163,190],"toxic":[45,52,100,127,133,147,175],"to":[46,82,123,144,166,177],"bacteria.":[47],"To":[48],"determine":[49],"if":[50],"the":[51,70,99,103,110,126,151,156,168],"a":[55,73,78,86],"randomly-generated":[56],"peptide":[57,87,104],"library":[58,105,137],"can":[59,94,162,189],"uniquely":[61],"classified":[62],"based":[63],"solely":[64],"on":[65,113,150],"motifs,":[67],"we":[68,119],"created":[69],"PepSeq":[71],"Pipeline:":[72],"software":[75],"that":[76,91,138],"utilizes":[77],"Random":[79],"Forest":[80],"algorithm":[81],"extract":[83],"library.":[88,157],"We":[89],"found":[90,191],"this":[92,187],"pipeline":[93,130],"accurately":[95],"classify":[96,121,145],"56%":[97],"in":[102,135,155,186],"using":[106],"extracted":[108,131],"model.":[111],"Testing":[112],"simulated":[114],"data":[115,184],"less":[117],"noise,":[118],"could":[120],"up":[122],"94%":[124],"peptides.":[128],"The":[129,181],"significant":[132],"every":[136],"was":[139],"tested,":[140],"but":[141],"its":[142],"ability":[143],"all":[146],"depended":[149],"number":[152],"Once":[158],"extracted,":[159],"used":[164,185],"both":[165],"understand":[167],"biology":[169],"behind":[170],"why":[171],"certain":[172],"create":[178],"novel":[179],"antibiotics.":[180],"code":[182],"analysis":[188],"at":[192],"https://github.com/tjense25/pep-seq-pipeline.":[193]},"counts_by_year":[{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}