{"id":"https://openalex.org/W2155570949","doi":"https://doi.org/10.1093/bioinformatics/bti424","title":"EGene: a configurable pipeline generation system for automated sequence analysis","display_name":"EGene: a configurable pipeline generation system for automated sequence analysis","publication_year":2005,"publication_date":"2005-04-06","ids":{"openalex":"https://openalex.org/W2155570949","doi":"https://doi.org/10.1093/bioinformatics/bti424","mag":"2155570949"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti424","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti424","pdf_url":null,"source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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"],"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/A5032097589","display_name":"Alan Mitchell Durham","orcid":"https://orcid.org/0000-0002-9846-6911"},"institutions":[{"id":"https://openalex.org/I4210131883","display_name":"Brazilian Society of Computational and Applied Mathematics","ror":"https://ror.org/03kcw4w74","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210131883"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"A. M. Durham","raw_affiliation_strings":["Depto. de Ci\u00eancias da Computa\u00e7\u00e3o, Instituto de Matem\u00e1tica e Estat\u00edstica S\u00e3o Paulo, SP, 05508-900, Brazil. alan@ime.usp.br"],"affiliations":[{"raw_affiliation_string":"Depto. de Ci\u00eancias da Computa\u00e7\u00e3o, Instituto de Matem\u00e1tica e Estat\u00edstica S\u00e3o Paulo, SP, 05508-900, Brazil. alan@ime.usp.br","institution_ids":["https://openalex.org/I4210131883"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031831286","display_name":"Andr\u00e9 Yoshiaki Kashiwabara","orcid":"https://orcid.org/0000-0003-3280-2035"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Y. Kashiwabara","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003179947","display_name":"Fernando T G Matsunaga","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"F. T. G. Matsunaga","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069379382","display_name":"Paulo H Ahagon","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"P. H. Ahagon","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013527657","display_name":"Fl\u00e1via Rainone","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"F. Rainone","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061018272","display_name":"Leonardo Varuzza","orcid":"https://orcid.org/0000-0002-0827-858X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"L. Varuzza","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5090385107","display_name":"Arthur Gruber","orcid":"https://orcid.org/0000-0001-8093-2278"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Gruber","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5032097589"],"corresponding_institution_ids":["https://openalex.org/I4210131883"],"apc_list":null,"apc_paid":null,"fwci":2.0252,"has_fulltext":false,"cited_by_count":68,"citation_normalized_percentile":{"value":0.86160714,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"21","issue":"12","first_page":"2812","last_page":"2813"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9976999759674072,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9976999759674072,"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":0.9933000206947327,"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":0.9854000210762024,"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":0.805654764175415},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.702522873878479},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6379266977310181},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.48192429542541504},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.397671103477478},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09335413575172424},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09108516573905945},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08106327056884766}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.805654764175415},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.702522873878479},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6379266977310181},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.48192429542541504},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.397671103477478},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09335413575172424},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09108516573905945},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08106327056884766}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti424","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti424","pdf_url":null,"source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":"pmh:oai:CiteSeerX.psu:10.1.1.884.5449","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.884.5449","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/21/12/2812.full.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.49000000953674316}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W1985726486","https://openalex.org/W1988431525","https://openalex.org/W2018240282","https://openalex.org/W2125973903","https://openalex.org/W2128374023","https://openalex.org/W2150313163"],"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/W4391913857","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"Summary:":[0],"EGene":[1,18,46],"is":[2,69],"a":[3,15,50],"generic,":[4],"flexible":[5],"and":[6,26,35,57],"modular":[7,16],"pipeline":[8,13,55],"generation":[9],"system":[10],"that":[11],"makes":[12],"construction":[14,56],"job.":[17],"allows":[19],"for":[20,66],"third-party":[21],"programs":[22],"to":[23,29,53,63],"be":[24],"used":[25],"integrated":[27],"according":[28],"the":[30],"needs":[31],"of":[32,61],"distinct":[33],"projects":[34],"without":[36],"any":[37],"previous":[38],"programming":[39],"or":[40],"formal":[41],"language":[42],"experience":[43],"being":[44],"required.":[45],"comes":[47],"with":[48],"CoEd,":[49],"visual":[51],"tool":[52],"facilitate":[54],"documentation.":[58],"A":[59],"series":[60],"components":[62],"build":[64],"pipelines":[65],"sequence":[67],"processing":[68],"provided.":[70],"Availability:":[71],"http://www.lbm.fmvz.usp.br/egene/":[72,78],"Contact:":[73],"alan@ime.usp.br;":[74],"argruber@usp.br":[75],"Supplementary":[76],"information:":[77]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":11},{"year":2012,"cited_by_count":6}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
