{"id":"https://openalex.org/W2028879784","doi":"https://doi.org/10.1109/bibe.2014.43","title":"Optimization and Analysis of Seriation Algorithm for Ordering Protein Networks","display_name":"Optimization and Analysis of Seriation Algorithm for Ordering Protein Networks","publication_year":2014,"publication_date":"2014-11-01","ids":{"openalex":"https://openalex.org/W2028879784","doi":"https://doi.org/10.1109/bibe.2014.43","mag":"2028879784"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2014.43","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2014.43","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE International Conference on Bioinformatics and Bioengineering","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/A5007948704","display_name":"Felipe A. Kuentzer","orcid":"https://orcid.org/0000-0003-3177-372X"},"institutions":[{"id":"https://openalex.org/I45643870","display_name":"Pontif\u00edcia Universidade Cat\u00f3lica do Rio Grande do Sul","ror":"https://ror.org/025vmq686","country_code":"BR","type":"education","lineage":["https://openalex.org/I45643870"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Felipe A. Kuentzer","raw_affiliation_strings":["Faculdade de Informatica, PUCRS University, Porto Alegre, Brazil","Fac. de Inf., PUCRS Univ., Porto Alegre, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculdade de Informatica, PUCRS University, Porto Alegre, Brazil","institution_ids":["https://openalex.org/I45643870"]},{"raw_affiliation_string":"Fac. de Inf., PUCRS Univ., Porto Alegre, Brazil","institution_ids":["https://openalex.org/I45643870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044409290","display_name":"Alexandre S. Pereira","orcid":null},"institutions":[{"id":"https://openalex.org/I45643870","display_name":"Pontif\u00edcia Universidade Cat\u00f3lica do Rio Grande do Sul","ror":"https://ror.org/025vmq686","country_code":"BR","type":"education","lineage":["https://openalex.org/I45643870"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Alexandre S. Pereira","raw_affiliation_strings":["Faculdade de Informatica, PUCRS University, Porto Alegre, Brazil","Fac. de Inf., PUCRS Univ., Porto Alegre, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculdade de Informatica, PUCRS University, Porto Alegre, Brazil","institution_ids":["https://openalex.org/I45643870"]},{"raw_affiliation_string":"Fac. de Inf., PUCRS Univ., Porto Alegre, Brazil","institution_ids":["https://openalex.org/I45643870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012146188","display_name":"Alexandre M. Amory","orcid":"https://orcid.org/0000-0001-8432-3162"},"institutions":[{"id":"https://openalex.org/I45643870","display_name":"Pontif\u00edcia Universidade Cat\u00f3lica do Rio Grande do Sul","ror":"https://ror.org/025vmq686","country_code":"BR","type":"education","lineage":["https://openalex.org/I45643870"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Alexandre M. Amory","raw_affiliation_strings":["Faculdade de Informatica, PUCRS University, Porto Alegre, Brazil","Fac. de Inf., PUCRS Univ., Porto Alegre, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculdade de Informatica, PUCRS University, Porto Alegre, Brazil","institution_ids":["https://openalex.org/I45643870"]},{"raw_affiliation_string":"Fac. de Inf., PUCRS Univ., Porto Alegre, Brazil","institution_ids":["https://openalex.org/I45643870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033108995","display_name":"Gabriel C. Perrone","orcid":null},"institutions":[{"id":"https://openalex.org/I130442723","display_name":"Universidade Federal do Rio Grande do Sul","ror":"https://ror.org/041yk2d64","country_code":"BR","type":"education","lineage":["https://openalex.org/I130442723"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Gabriel Perrone","raw_affiliation_strings":["Instituto de Fisica, UFRGS University, Porto Alegre, Brazil","Inst. de Fis., UFRGS Univ., Porto Alegre, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Instituto de Fisica, UFRGS University, Porto Alegre, Brazil","institution_ids":["https://openalex.org/I130442723"]},{"raw_affiliation_string":"Inst. de Fis., UFRGS Univ., Porto Alegre, Brazil","institution_ids":["https://openalex.org/I130442723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055915947","display_name":"Samoel R.M. Da Silva","orcid":null},"institutions":[{"id":"https://openalex.org/I130442723","display_name":"Universidade Federal do Rio Grande do Sul","ror":"https://ror.org/041yk2d64","country_code":"BR","type":"education","lineage":["https://openalex.org/I130442723"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Samoel R. M. da Silva","raw_affiliation_strings":["Inst. de Fis., UFRGS Univ., Brazil","Inst. de Fis., UFRGS Univ., Porto Alegre, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inst. de Fis., UFRGS Univ., Brazil","institution_ids":["https://openalex.org/I130442723"]},{"raw_affiliation_string":"Inst. de Fis., UFRGS Univ., Porto Alegre, Brazil","institution_ids":["https://openalex.org/I130442723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073175693","display_name":"J. Dinis","orcid":"https://orcid.org/0000-0001-5075-1601"},"institutions":[{"id":"https://openalex.org/I130442723","display_name":"Universidade Federal do Rio Grande do Sul","ror":"https://ror.org/041yk2d64","country_code":"BR","type":"education","lineage":["https://openalex.org/I130442723"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Joao M. Dinis","raw_affiliation_strings":["Instituto de Fisica, UFRGS University, Porto Alegre, Brazil","Inst. de Fis., UFRGS Univ., Porto Alegre, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Instituto de Fisica, UFRGS University, Porto Alegre, Brazil","institution_ids":["https://openalex.org/I130442723"]},{"raw_affiliation_string":"Inst. de Fis., UFRGS Univ., Porto Alegre, Brazil","institution_ids":["https://openalex.org/I130442723"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022969760","display_name":"Rita M. C. de Almeida","orcid":"https://orcid.org/0000-0003-3897-1841"},"institutions":[{"id":"https://openalex.org/I130442723","display_name":"Universidade Federal do Rio Grande do Sul","ror":"https://ror.org/041yk2d64","country_code":"BR","type":"education","lineage":["https://openalex.org/I130442723"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Rita M. C. de Almeida","raw_affiliation_strings":["Inst. de Fis., UFRGS Univ., Brazil","Inst. de Fis., UFRGS Univ., Porto Alegre, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inst. de Fis., UFRGS Univ., Brazil","institution_ids":["https://openalex.org/I130442723"]},{"raw_affiliation_string":"Inst. de Fis., UFRGS Univ., Porto Alegre, Brazil","institution_ids":["https://openalex.org/I130442723"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5007948704"],"corresponding_institution_ids":["https://openalex.org/I45643870"],"apc_list":null,"apc_paid":null,"fwci":0.4268,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.63329122,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"220","issue":null,"first_page":"231","last_page":"237"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9997000098228455,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9997000098228455,"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":0.9994999766349792,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9980000257492065,"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/seriation","display_name":"Seriation (archaeology)","score":0.7772930860519409},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6682219505310059},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4948346018791199},{"id":"https://openalex.org/keywords/reduction","display_name":"Reduction (mathematics)","score":0.4873374402523041},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.44020533561706543},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.4384390711784363},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.4355514645576477},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29207760095596313},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2857665419578552},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19368818402290344},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11299484968185425}],"concepts":[{"id":"https://openalex.org/C103303479","wikidata":"https://www.wikidata.org/wiki/Q358095","display_name":"Seriation (archaeology)","level":2,"score":0.7772930860519409},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6682219505310059},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4948346018791199},{"id":"https://openalex.org/C111335779","wikidata":"https://www.wikidata.org/wiki/Q3454686","display_name":"Reduction (mathematics)","level":2,"score":0.4873374402523041},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.44020533561706543},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.4384390711784363},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.4355514645576477},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29207760095596313},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2857665419578552},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19368818402290344},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11299484968185425},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"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/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibe.2014.43","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2014.43","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE International Conference on Bioinformatics and Bioengineering","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W143174683","https://openalex.org/W214150930","https://openalex.org/W566939682","https://openalex.org/W1727290854","https://openalex.org/W1970156673","https://openalex.org/W1998473728","https://openalex.org/W2024060531","https://openalex.org/W2027251412","https://openalex.org/W2036328877","https://openalex.org/W2061856021","https://openalex.org/W2103017472","https://openalex.org/W2105924489","https://openalex.org/W2109970232","https://openalex.org/W2122683221","https://openalex.org/W2123500593","https://openalex.org/W2132040456","https://openalex.org/W2133120537","https://openalex.org/W2137818934","https://openalex.org/W2185306546","https://openalex.org/W2233236690","https://openalex.org/W2503585183","https://openalex.org/W2795873946","https://openalex.org/W2801915865","https://openalex.org/W4229688926","https://openalex.org/W4236128208","https://openalex.org/W4242399520","https://openalex.org/W6642914199"],"related_works":["https://openalex.org/W2003388069","https://openalex.org/W4243787855","https://openalex.org/W2094625922","https://openalex.org/W4236259782","https://openalex.org/W2021272781","https://openalex.org/W2182482947","https://openalex.org/W3021724783","https://openalex.org/W2008037071","https://openalex.org/W1983988096","https://openalex.org/W2321529479"],"abstract_inverted_index":{"Analysis":[0],"by":[1,42,91],"Transcriptogram":[2],"was":[3,89],"developed":[4],"as":[5,28],"a":[6,29,47,53,68,73,123],"solution":[7],"to":[8,25,116,122],"reduce":[9],"the":[10,13,19,38,44,83,86,92,96,100,117,130,137],"noise":[11,35],"in":[12,37,52,60,142,153],"micro":[14],"array":[15],"measuring":[16],"technique":[17],"of":[18,31,46,85,95,126,150],"Transcriptome,":[20],"and":[21,129],"has":[22],"demonstrated":[23],"potential":[24],"be":[26],"applied":[27,115],"method":[30,88],"disease":[32],"diagnostics.":[33],"The":[34,64],"reduction":[36,125],"measurement":[39],"is":[40,158],"achieved":[41],"ordering":[43,65,97],"proteins":[45],"given":[48],"protein":[49],"interaction":[50],"network":[51,76,103,149],"linear":[54],"way,":[55],"allowing":[56],"gene":[57],"expression":[58],"analysis":[59],"whole":[61],"genome":[62],"scale.":[63],"process":[66],"uses":[67],"seriation":[69,118,164],"technique,":[70],"which":[71,120,157],"models":[72],"protein-protein":[74],"association":[75],"into":[77],"an":[78,147],"undirected":[79,148],"graph.":[80],"So":[81],"far,":[82],"viability":[84],"diagnosis":[87],"hindered":[90],"high":[93],"runtime":[94],"algorithm,":[98],"since":[99],"Homo":[101],"sapiens":[102],"can":[104],"have":[105],"around":[106],"30":[107],"thousand":[108],"proteins.":[109],"This":[110],"paper":[111],"presents":[112],"some":[113],"optimizations":[114],"problem,":[119],"lead":[121],"significant":[124],"execution":[127],"time":[128],"problem":[131],"complexity":[132],"analysed.":[133],"Results":[134],"show":[135],"that":[136],"algorithm":[138],"produces":[139],"good":[140],"results":[141],"reasonable":[143],"time,":[144],"e.g.":[145],"Order":[146],"9684":[151],"nodes":[152],"about":[154],"35":[155],"minutes,":[156],"faster":[159],"if":[160],"compared":[161],"with":[162],"other":[163],"techniques":[165],"evaluated.":[166]},"counts_by_year":[{"year":2016,"cited_by_count":3}],"updated_date":"2026-04-30T09:15:22.047038","created_date":"2025-10-10T00:00:00"}