{"id":"https://openalex.org/W4253088151","doi":"https://doi.org/10.1109/csb.2004.1332486","title":"Deriving a novel codon index by combining period-3 and fractal features of DNA sequences","display_name":"Deriving a novel codon index by combining period-3 and fractal features of DNA sequences","publication_year":2004,"publication_date":"2004-11-08","ids":{"openalex":"https://openalex.org/W4253088151","doi":"https://doi.org/10.1109/csb.2004.1332486"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2004.1332486","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332486","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","issn_l":"1752-7791","issn":["1752-7791"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","raw_type":"proceedings-article"},"type":"conference-paper","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/A5100683128","display_name":"Qi Yan","orcid":"https://orcid.org/0000-0002-5236-9673"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yan Qi","raw_affiliation_strings":["Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103038001","display_name":"Jianbo Gao","orcid":null},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianbo Gao","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050881210","display_name":"Yinping Cao","orcid":"https://orcid.org/0000-0003-3433-5397"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yinhe Cao","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084857367","display_name":"Wen\u2010wen Tung","orcid":"https://orcid.org/0000-0001-8627-1503"},"institutions":[{"id":"https://openalex.org/I107766831","display_name":"NSF National Center for Atmospheric Research","ror":"https://ror.org/05cvfcr44","country_code":"US","type":"facility","lineage":["https://openalex.org/I107766831","https://openalex.org/I1311060795","https://openalex.org/I2799356940","https://openalex.org/I4210141337","https://openalex.org/I4210150888"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wen-wen Tung","raw_affiliation_strings":["National Center for Atmospheric Research, Boulder, CO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Atmospheric Research, Boulder, CO, USA","institution_ids":["https://openalex.org/I107766831"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.40674349,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"509","last_page":"510"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12946","display_name":"Fractal and DNA sequence analysis","score":0.9984999895095825,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.9984999895095825,"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":0.996999979019165,"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":0.9961000084877014,"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/fractal","display_name":"Fractal","score":0.7152895927429199},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.45180147886276245},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45157474279403687},{"id":"https://openalex.org/keywords/coding-region","display_name":"Coding region","score":0.4498533010482788},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4482576251029968},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4328622817993164},{"id":"https://openalex.org/keywords/codon-usage-bias","display_name":"Codon usage bias","score":0.42834991216659546},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38528114557266235},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.37248292565345764},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.3578420877456665},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.2932263910770416},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2870039939880371},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25131112337112427},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22471603751182556}],"concepts":[{"id":"https://openalex.org/C40636538","wikidata":"https://www.wikidata.org/wiki/Q81392","display_name":"Fractal","level":2,"score":0.7152895927429199},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.45180147886276245},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45157474279403687},{"id":"https://openalex.org/C91779695","wikidata":"https://www.wikidata.org/wiki/Q3780824","display_name":"Coding region","level":3,"score":0.4498533010482788},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4482576251029968},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4328622817993164},{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.42834991216659546},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38528114557266235},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.37248292565345764},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3578420877456665},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2932263910770416},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2870039939880371},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25131112337112427},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22471603751182556},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/csb.2004.1332486","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332486","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","issn_l":"1752-7791","issn":["1752-7791"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","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":0,"referenced_works":[],"related_works":["https://openalex.org/W2013332237","https://openalex.org/W1522259561","https://openalex.org/W2355920812","https://openalex.org/W2295517574","https://openalex.org/W2380221404","https://openalex.org/W2373248682","https://openalex.org/W2225738837","https://openalex.org/W2377607201","https://openalex.org/W2350213167","https://openalex.org/W4379347121"],"abstract_inverted_index":{"Summary":[0],"form":[1],"only":[2,184],"given.":[3],"When":[4],"a":[5,39,87],"gene":[6,265],"finding":[7,266],"algorithm":[8],"incorporates":[9],"multiple":[10],"useful":[11,185],"and":[12,32,69,76,110,113,141,163,283],"non-redundant":[13],"sources":[14],"of":[15,60,90,118,126,144,189,202,217,231,248,271],"information":[16],"about":[17],"coding":[18,67,75,109,250],"regions,":[19],"it":[20,221,276],"becomes":[21],"more":[22],"successful.":[23],"It":[24,131,149],"is":[25,52,105,114,121,132,138,150,157,174,182,208,274,277],"thus":[26],"highly":[27,177],"desirable":[28],"to":[29,210,223],"find":[30],"new":[31],"efficient":[33],"codon":[34,41,212],"indices.":[35],"Here":[36],"we":[37,44],"propose":[38],"novel":[40],"index,":[42],"which":[43],"call":[45],"the":[46,63,70,119,127,135,145,171,180,187,200,232,239,246,255,272],"period-3":[47,64,85,162],"fractal":[48,71,95,164],"deviation":[49],"(PFD).":[50],"This":[51,176,219,253],"obtained":[53],"by":[54,123],"simultaneously":[55],"considering":[56],"two":[57,80],"incompatible":[58,83],"features":[59,81,165,270],"DNA":[61,204],"sequences,":[62,112,192],"feature":[65,72],"in":[66,73],"regions":[68],"both":[74],"non-coding":[77,111],"regions.":[78],"These":[79],"are":[82,98,166],"because":[84],"defines":[86],"specific":[88,101],"scale":[89],"three":[91],"nucleotide":[92],"bases":[93],"while":[94],"means":[96],"there":[97],"not":[99,183,280],"any":[100],"scales.":[102],"The":[103,116,206],"PFD":[104,120,207,225,233],"very":[106,139,197],"different":[107],"for":[108,186,199],"reading-frame-dependent.":[115],"accuracy":[117,137,156,247],"evaluated":[122],"studying":[124],"all":[125],"16":[128],"yeast":[129],"chromosomes.":[130],"found":[133,152],"that":[134,153,179,275],"percentage":[136,155],"high":[140],"quite":[142],"independent":[143],"sliding":[146],"window":[147,172],"size.":[148],"also":[151,195],"this":[154],"much":[158],"higher":[159],"than":[160],"when":[161,170],"characterized":[167],"alone,":[168],"especially":[169],"size":[173],"small.":[175],"suggests":[178],"method":[181,273],"study":[188,201],"long":[190],"genome":[191],"but":[193],"may":[194,259],"be":[196,260,285],"powerful":[198],"short":[203],"segments.":[205],"complementary":[209],"other":[211,227],"indices,":[213],"including":[214],"Fourier":[215],"measures":[216],"period-3.":[218],"makes":[220],"possible":[222],"integrate":[224],"with":[226,235],"measures.":[228],"Indeed,":[229],"integration":[230],"measure":[234,256],"those":[236],"indices":[237],"using":[238],"Fisher":[240],"linear":[241],"discriminant":[242],"analysis":[243],"significantly":[244],"improves":[245],"protein":[249],"sequence":[251],"identification;":[252],"implies":[254],"proposed":[257],"here":[258],"readily":[261],"incorporated":[262],"into":[263],"existing":[264],"algorithms.":[267],"Other":[268],"salient":[269],"non-parametric,":[278],"does":[279],"require":[281],"training,":[282],"can":[284],"fully":[286],"automated.":[287]},"counts_by_year":[],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
