{"id":"https://openalex.org/W2020879581","doi":"https://doi.org/10.1109/cibcb.2010.5510703","title":"Classifying Cytochrome c Oxidase subunit 1 by translation initiation mechanism using side effect machines","display_name":"Classifying Cytochrome c Oxidase subunit 1 by translation initiation mechanism using side effect machines","publication_year":2010,"publication_date":"2010-05-01","ids":{"openalex":"https://openalex.org/W2020879581","doi":"https://doi.org/10.1109/cibcb.2010.5510703","mag":"2020879581"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb.2010.5510703","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2010.5510703","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology","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/A5020300392","display_name":"Justin Schonfeld","orcid":"https://orcid.org/0000-0001-8564-5964"},"institutions":[{"id":"https://openalex.org/I79817857","display_name":"University of Guelph","ror":"https://ror.org/01r7awg59","country_code":"CA","type":"education","lineage":["https://openalex.org/I79817857"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Justin Schonfeld","raw_affiliation_strings":["Biodiversity Institute of Ontario, University of Guelph, ONT, Canada","Biodiversity Institute of Ontario at the University of Guelph"],"affiliations":[{"raw_affiliation_string":"Biodiversity Institute of Ontario, University of Guelph, ONT, Canada","institution_ids":["https://openalex.org/I79817857"]},{"raw_affiliation_string":"Biodiversity Institute of Ontario at the University of Guelph","institution_ids":["https://openalex.org/I79817857"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108360962","display_name":"Dan Ashlock","orcid":null},"institutions":[{"id":"https://openalex.org/I79817857","display_name":"University of Guelph","ror":"https://ror.org/01r7awg59","country_code":"CA","type":"education","lineage":["https://openalex.org/I79817857"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Dan Ashlock","raw_affiliation_strings":["Department of Math, University of Guelph, ONT, Canada","Department of Math at the University of Guelph, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Math, University of Guelph, ONT, Canada","institution_ids":["https://openalex.org/I79817857"]},{"raw_affiliation_string":"Department of Math at the University of Guelph, Ontario, Canada","institution_ids":["https://openalex.org/I79817857"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5020300392"],"corresponding_institution_ids":["https://openalex.org/I79817857"],"apc_list":null,"apc_paid":null,"fwci":0.6609,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.67807011,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"19","issue":null,"first_page":"1","last_page":"7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9977999925613403,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9977999925613403,"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":0.996399998664856,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9914000034332275,"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/mechanism","display_name":"Mechanism (biology)","score":0.6961207389831543},{"id":"https://openalex.org/keywords/cytochrome-c-oxidase","display_name":"Cytochrome c oxidase","score":0.6286091208457947},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.5424085855484009},{"id":"https://openalex.org/keywords/side-effect","display_name":"Side effect (computer science)","score":0.5393270254135132},{"id":"https://openalex.org/keywords/protein-subunit","display_name":"Protein subunit","score":0.5110353231430054},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4839168190956116},{"id":"https://openalex.org/keywords/machine-translation","display_name":"Machine translation","score":0.4514632523059845},{"id":"https://openalex.org/keywords/signal","display_name":"SIGNAL (programming language)","score":0.44336459040641785},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43897002935409546},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4379495680332184},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4310768246650696},{"id":"https://openalex.org/keywords/oxidase-test","display_name":"Oxidase test","score":0.42422887682914734},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35996705293655396},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.32517415285110474},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3085305094718933},{"id":"https://openalex.org/keywords/mitochondrion","display_name":"Mitochondrion","score":0.29756760597229004},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.23378393054008484},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.19706344604492188},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1918245255947113}],"concepts":[{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.6961207389831543},{"id":"https://openalex.org/C123249941","wikidata":"https://www.wikidata.org/wiki/Q306116","display_name":"Cytochrome c oxidase","level":3,"score":0.6286091208457947},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.5424085855484009},{"id":"https://openalex.org/C3454156","wikidata":"https://www.wikidata.org/wiki/Q1144241","display_name":"Side effect (computer science)","level":2,"score":0.5393270254135132},{"id":"https://openalex.org/C104292427","wikidata":"https://www.wikidata.org/wiki/Q899781","display_name":"Protein subunit","level":3,"score":0.5110353231430054},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4839168190956116},{"id":"https://openalex.org/C203005215","wikidata":"https://www.wikidata.org/wiki/Q79798","display_name":"Machine translation","level":2,"score":0.4514632523059845},{"id":"https://openalex.org/C2779843651","wikidata":"https://www.wikidata.org/wiki/Q7390335","display_name":"SIGNAL (programming language)","level":2,"score":0.44336459040641785},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43897002935409546},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4379495680332184},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4310768246650696},{"id":"https://openalex.org/C38485361","wikidata":"https://www.wikidata.org/wiki/Q576379","display_name":"Oxidase test","level":3,"score":0.42422887682914734},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35996705293655396},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.32517415285110474},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3085305094718933},{"id":"https://openalex.org/C28859421","wikidata":"https://www.wikidata.org/wiki/Q39572","display_name":"Mitochondrion","level":2,"score":0.29756760597229004},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.23378393054008484},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.19706344604492188},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1918245255947113},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cibcb.2010.5510703","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2010.5510703","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310787","display_name":"Genome Canada","ror":"https://ror.org/029s29983"},{"id":"https://openalex.org/F4320319905","display_name":"Ontario Genomics Institute","ror":"https://ror.org/00c68jz96"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W66669671","https://openalex.org/W139956475","https://openalex.org/W1987424728","https://openalex.org/W2010201702","https://openalex.org/W2026487666","https://openalex.org/W2035435939","https://openalex.org/W2038248653","https://openalex.org/W2074131636","https://openalex.org/W2075849239","https://openalex.org/W2085525886","https://openalex.org/W2107903949","https://openalex.org/W2132339567","https://openalex.org/W2138121372","https://openalex.org/W2147646624","https://openalex.org/W2160877678","https://openalex.org/W2161714242","https://openalex.org/W2170885088","https://openalex.org/W2176788572","https://openalex.org/W2317136200","https://openalex.org/W2339378878","https://openalex.org/W2930291257","https://openalex.org/W4235169531","https://openalex.org/W6669478690","https://openalex.org/W6681678916","https://openalex.org/W6699591128","https://openalex.org/W6703787047"],"related_works":["https://openalex.org/W3107474891","https://openalex.org/W3069495034","https://openalex.org/W2988683168","https://openalex.org/W2509777158","https://openalex.org/W2079708906","https://openalex.org/W2008600114","https://openalex.org/W1995360843","https://openalex.org/W97426361","https://openalex.org/W1983384423","https://openalex.org/W2040395881"],"abstract_inverted_index":{"Cytochrome":[0],"c":[1],"oxidase":[2],"subunit":[3],"1":[4],"(cox1)":[5],"is":[6,119,123],"unusual":[7,41],"among":[8],"mitochondrial":[9],"genes":[10,77],"in":[11,64],"that":[12,93],"instead":[13],"of":[14,19,39,83,113,131],"using":[15],"AUG":[16],"or":[17],"one":[18],"the":[20,37,46,65,84,111,115],"recognized":[21],"alternative":[22],"start":[23,80],"codons":[24,81],"it":[25],"often":[26],"appears":[27],"to":[28,60,73,125],"use":[29,56],"an":[30],"unknown":[31],"means":[32],"for":[33,62,110],"initiating":[34],"translation.":[35],"However,":[36],"frequency":[38],"this":[40,53,102],"behavior":[42],"as":[43,45],"well":[44],"underlying":[47],"molecular":[48],"mechanism":[49],"are":[50,89],"unknown.":[51],"In":[52,101],"paper":[54],"we":[55],"side":[57,68,95,106],"effect":[58,69,87],"machines":[59,70,88,92],"probe":[61],"signal":[63],"sequence.":[66],"Evolved":[67],"were":[71,144],"able":[72],"correctly":[74],"classify":[75],"cox1":[76],"with":[78,98,139],"ambiguous":[79],"80.1%":[82],"time.":[85],"Side":[86],"finite":[90],"state":[91,116],"have":[94],"effects":[96],"associated":[97],"their":[99],"states.":[100],"study":[103],"a":[104,108,128],"simple":[105],"effect,":[107],"counter":[109],"number":[112],"times":[114],"was":[117],"entered,":[118],"used.":[120],"The":[121],"problem":[122],"found":[124,133],"be":[126],"challenging,":[127],"substantial":[129],"majority":[130],"replicates":[132],"no":[134],"signal,":[135],"but":[136],"some":[137],"classifiers":[138],"statistically":[140],"significant":[141],"classification":[142],"ability":[143],"located.":[145]},"counts_by_year":[{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
