{"id":"https://openalex.org/W2166915134","doi":"https://doi.org/10.1109/grc.2006.1635749","title":"Understanding microbial genomic structures and applications to biological pathway inference","display_name":"Understanding microbial genomic structures and applications to biological pathway inference","publication_year":2006,"publication_date":"2006-06-08","ids":{"openalex":"https://openalex.org/W2166915134","doi":"https://doi.org/10.1109/grc.2006.1635749","mag":"2166915134"},"language":"en","primary_location":{"id":"doi:10.1109/grc.2006.1635749","is_oa":false,"landing_page_url":"https://doi.org/10.1109/grc.2006.1635749","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2006 IEEE International Conference on Granular Computing","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/A5062568388","display_name":"Zhengchang Su","orcid":"https://orcid.org/0000-0003-4636-3440"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Z. Su","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Georgia, Athens, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Georgia, Athens, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080230841","display_name":"Feng Mao","orcid":"https://orcid.org/0000-0002-1582-4542"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"F. Mao","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Georgia, Athens, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Georgia, Athens, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031137221","display_name":"Hongsheng Wu","orcid":"https://orcid.org/0009-0002-0677-1992"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"H. Wu","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Georgia, Athens, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Georgia, Athens, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053687986","display_name":"Phuongan Dam","orcid":null},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"P. Dam","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Georgia, Athens, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Georgia, Athens, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046366431","display_name":"X. Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"X. Chen","raw_affiliation_strings":["Computer Science Department, University of California, Riverside, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of California, Riverside, USA","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101911266","display_name":"Tao Jiang","orcid":"https://orcid.org/0000-0003-3833-4498"},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"T. Jiang","raw_affiliation_strings":["Computer Science Department, University of California, Riverside, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, University of California, Riverside, USA","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026918414","display_name":"Victor Olman","orcid":null},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"V. Olman","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Georgia, Athens, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Georgia, Athens, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013071861","display_name":"Brian Palenik","orcid":"https://orcid.org/0000-0002-3717-9046"},"institutions":[{"id":"https://openalex.org/I150209017","display_name":"Scripps Institution of Oceanography","ror":"https://ror.org/04v7hvq31","country_code":"US","type":"facility","lineage":["https://openalex.org/I150209017","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"B. Palenik","raw_affiliation_strings":["Scripps Institute of Oceanography, University of California, San Diego, USA"],"affiliations":[{"raw_affiliation_string":"Scripps Institute of Oceanography, University of California, San Diego, USA","institution_ids":["https://openalex.org/I150209017","https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020171946","display_name":"Ying Xu","orcid":"https://orcid.org/0000-0002-7856-3343"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Y. Xu","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Georgia, Athens, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Georgia, Athens, USA","institution_ids":["https://openalex.org/I165733156"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5062568388"],"corresponding_institution_ids":["https://openalex.org/I165733156"],"apc_list":null,"apc_paid":null,"fwci":0.1325,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.5256564,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"15","issue":null,"first_page":"23","last_page":"24"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9983999729156494,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9983999729156494,"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":0.996999979019165,"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":0.9950000047683716,"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/computational-biology","display_name":"Computational biology","score":0.7212322950363159},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7161526679992676},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.6058525443077087},{"id":"https://openalex.org/keywords/operon","display_name":"Operon","score":0.5639654994010925},{"id":"https://openalex.org/keywords/decipher","display_name":"DECIPHER","score":0.5448631048202515},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5160033702850342},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.4916420578956604},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.46919557452201843},{"id":"https://openalex.org/keywords/archaea","display_name":"Archaea","score":0.4585423767566681},{"id":"https://openalex.org/keywords/computational-genomics","display_name":"Computational genomics","score":0.4416678547859192},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.33512240648269653},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.28890225291252136},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2668859362602234},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19506794214248657},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17246049642562866},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.08667856454849243}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7212322950363159},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7161526679992676},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.6058525443077087},{"id":"https://openalex.org/C203075996","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operon","level":4,"score":0.5639654994010925},{"id":"https://openalex.org/C164614171","wikidata":"https://www.wikidata.org/wiki/Q5204775","display_name":"DECIPHER","level":2,"score":0.5448631048202515},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5160033702850342},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4916420578956604},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.46919557452201843},{"id":"https://openalex.org/C550995028","wikidata":"https://www.wikidata.org/wiki/Q10872","display_name":"Archaea","level":3,"score":0.4585423767566681},{"id":"https://openalex.org/C39238701","wikidata":"https://www.wikidata.org/wiki/Q2091816","display_name":"Computational genomics","level":5,"score":0.4416678547859192},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33512240648269653},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.28890225291252136},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2668859362602234},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19506794214248657},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17246049642562866},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.08667856454849243},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/grc.2006.1635749","is_oa":false,"landing_page_url":"https://doi.org/10.1109/grc.2006.1635749","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2006 IEEE International Conference on Granular Computing","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1490264010","https://openalex.org/W1994692113","https://openalex.org/W2029112298","https://openalex.org/W2056584222","https://openalex.org/W2096731969","https://openalex.org/W2102199998","https://openalex.org/W2133298156","https://openalex.org/W2135567384","https://openalex.org/W4246227956","https://openalex.org/W6674388619"],"related_works":["https://openalex.org/W2115350162","https://openalex.org/W2330145053","https://openalex.org/W4249875204","https://openalex.org/W2416520078","https://openalex.org/W4242620632","https://openalex.org/W4256069380","https://openalex.org/W4379618494","https://openalex.org/W2113606293","https://openalex.org/W2344924242","https://openalex.org/W2409656713"],"abstract_inverted_index":{"The":[0,419,543,583],"rapid":[1],"increase":[2],"in":[3,150,252,353,405,520,564,600,610,667],"the":[4,18,54,67,117,166,175,398,406,458,521,538,565,569,586,611,625,668,702,727,741],"number":[5,301,314,320,580,664],"of":[6,21,28,60,66,85,94,116,127,177,181,198,228,233,245,259,282,302,309,315,321,357,376,384,413,422,429,523,541,546,557,581,585,617,627,636,665,681,731],"sequenced":[7],"microbial":[8,49,74,97,111,134,211,253,261,417,685],"genomes":[9,212,455,686],"provides":[10,224,425],"unprecedented":[11],"opportunities":[12],"to":[13,16,58,108,125,289,345,396,416,436,454,498,554,560,646,649,657,683,700,721,737],"computational":[14],"biologists":[15],"decipher":[17],"genomic":[19,50,56,75,98,121,135,283,532,725],"structures":[20,51,57,76,99,122,251],"these":[22,202,495,572],"microbes":[23],"through":[24,81,103,373,462],"development":[25,82],"and":[26,52,77,83,100,113,123,130,153,191,236,248,334,531,638,708,711,729],"application":[27,84,115],"advanced":[29,86],"comparative":[30,87,256,374],"genome":[31,88,257,670],"analysis":[32,89,375,694,718],"tools.":[33],"In":[34,324],"this":[35,673,717],"presentation,":[36],"we":[37,42,204,263,296,326,392,676],"describe":[38],"a":[39,141,179,225,269,272,280,300,312,318,339,347,426,512,558,578,595,601,631,650,663],"systematic":[40,92],"study":[41,64,93],"have":[43,138,185,205,264,286,297,327,337,360,467,509,607,622,677],"been":[44,186,446],"carrying":[45],"out":[46],"on":[47,157],"deciphering":[48,73],"linking":[53],"discovered":[55,118],"prediction":[59,126,170,183,199,208,232,352,356,404],"metabolic":[61,101,305,414,420,679,706,732],"pathways.":[62,542,620],"This":[63,219],"consists":[65],"following":[68],"three":[69],"main":[70],"components:":[71],"(a)":[72],"discovering":[78],"new":[79,722],"ones":[80],"tools,":[90],"(b)":[91],"relationships":[95,119,331],"between":[96,120,332,705],"pathways":[102,107,124,129,235,306,415,421,453,680,707],"mapping":[104,412,451,489,517,525,539,549,630,654],"all":[105,494],"KEGG":[106,423,452,618,682],"over":[109],"300":[110],"genomes,":[112,262,379],"(c)":[114],"biological":[128,234,290],"networks.":[131],"A.":[132],"Deciphering":[133],"structures:":[136],"We":[137,359,389,466,508,621,714],"recently":[139,265,362,468,510,623],"developed":[140,363,511],"computer":[142,348,400,513],"program":[143,167,349,401,514],"JPOP":[144],"(1,2)":[145],"for":[146,209,230,343,350,367,386,402,450,516],"operon":[147,182,207],"structure":[148,533],"predictions":[149,292],"both":[151,527],"prokaryotic":[152],"archaea":[154],"genomes.":[155,254,438],"Testing":[156],"E.":[158],"coli.":[159],"data":[160,214,220],"with":[161],"experimental":[162],"validation":[163],"indicates":[164],"that":[165,299,391,470,551,571,591,594,603,659,716],"has":[168,444],"an":[169,364,447],"accuracy":[171,540],"about":[172,724],"80%.":[173],"Since":[174],"publication":[176],"JPOP,":[178],"couple":[180],"programs":[184],"published":[187],"including":[188],"VIMSS":[189],"(10)":[190],"Pathway":[192],"Tools":[193],"(11),":[194],"reaching":[195],"similar":[196],"levels":[197],"accuracy.":[200],"Using":[201,672],"programs,":[203],"made":[206,308],"300+":[210,260,684],"(all":[213],"are":[215,307,575,660,688],"available":[216,689],"upon":[217,690],"request).":[218,691],"set":[221],"not":[222,445,486],"only":[223],"rich":[226,427],"source":[227,428],"information":[229,385,506,530],"our":[231],"networks":[237],"(see":[238],"section":[239],"C),":[240],"but":[241],"also":[242,361],"facilitates":[243],"investigation":[244],"higher":[246],"level":[247],"less":[249],"understood":[250],"Through":[255],"analyses":[258],"firmly":[266],"established":[267,328,338],"uber-operon,":[268],"concept":[270],"introduced":[271],"few":[273,743],"years":[274],"ago":[275],"by":[276,653],"other":[277,456],"authors,":[278],"as":[279,477,492],"layer":[281],"structures,":[284,726],"which":[285,336,431,734],"direct":[287,615],"implications":[288],"pathway":[291,524,548,559,597,633],"(3).":[293,323],"For":[294],"example,":[295],"demonstrated":[298,469],"well":[303],"studied":[304],"(genes":[310],"of)":[311],"small":[313],"uber-operons":[316,333],"(versus":[317],"large":[319],"operons)":[322],"addition,":[325],"some":[329],"interesting":[330],"regulons,":[335],"solid":[340],"stepping":[341],"stone":[342],"us":[344],"develop":[346,397],"regulon":[351,387,403,712],"general":[354,703],"via":[355],"uber-operons.":[358],"effective":[365,448],"paradigm":[366],"predicting":[368],"cis":[369],"regulatory":[370],"elements":[371],"(4),":[372],"closed":[377],"related":[378],"providing":[380],"another":[381],"important":[382],"piece":[383],"prediction.":[388],"expect":[390,715],"will":[393,719],"be":[394,433,738],"able":[395],"first":[399],"very":[407,441],"near":[408],"future.":[409],"B.":[410],"Systematic":[411],"genomes:":[418],"database":[424],"information,":[430,534],"can":[432],"directly":[434],"mapped":[435,573,678],"individual":[437,605,655],"However":[439],"until":[440],"recently,":[442],"there":[443],"way":[449],"than":[457,642],"simple":[459],"minded":[460],"approach":[461],"sequence":[463,504,528],"similarity":[464,505,529],"search.":[465],"BLAST":[471],"search":[472,484],"or":[473,482],"its":[474,604],"variations/generalizations":[475],"such":[476],"bi-direction":[478],"best":[479],"hit":[480],"(BDBH)":[481],"COG":[483],"do":[485],"provide":[487],"satisfactory":[488],"results":[490],"(5)":[491],"virtually":[493],"methods":[496],"attempt":[497],"find":[499],"orthologous":[500,518],"gene":[501],"relationship":[502,704],"using":[503,526],"alone.":[507],"P-MAP":[515,547,588],"genes":[519,556,563,574,608,644,658],"context":[522],"having":[535],"substantially":[536],"improved":[537],"basic":[544],"idea":[545],"is":[550,590,598,695,735],"it":[552,592],"attempts":[553],"map":[555],"their":[561],"homologous":[562],"target":[566,651,669],"genome,":[567,613,652],"under":[568,697],"condition":[570],"grouped":[576,661],"into":[577,662],"(small)":[579],"operons.":[582],"limitation":[584],"current":[587],"algorithm":[589],"assumes":[593],"template":[596,612],"given":[599],"form":[602],"components":[606],"assigned":[609,645],"limiting":[614],"applications":[616],"(template)":[619],"generalized":[624],"framework":[626],"P-MAP,":[628],"allowing":[629],"generic":[632],"model":[634],"(consisting":[635],"enzymes":[637,656],"enzymatic":[639],"reasons":[640],"rather":[641],"specific":[643],"each":[647],"enzyme)":[648],"operons":[666],"(6).":[671],"novel":[674],"capability,":[675],"(data":[687],"A":[692],"detailed":[693],"currently":[696],"way,":[698],"attempting":[699],"understand":[701],"operon,":[709],"uber-operon":[710],"structures.":[713],"lead":[720],"understanding":[723],"organization":[728],"evolution":[730],"pathways,":[733],"expected":[736],"done":[739],"within":[740],"next":[742],"weeks.":[744]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
