{"id":"https://openalex.org/W2051572912","doi":"https://doi.org/10.1109/bibe.2007.4375625","title":"MotifNetwork: A Grid-enabled Workflow for High-throughput Domain Analysis of Biological Sequences: Implications for annotation and study of phylogeny, protein interactions, and intraspecies variation","display_name":"MotifNetwork: A Grid-enabled Workflow for High-throughput Domain Analysis of Biological Sequences: Implications for annotation and study of phylogeny, protein interactions, and intraspecies variation","publication_year":2007,"publication_date":"2007-10-01","ids":{"openalex":"https://openalex.org/W2051572912","doi":"https://doi.org/10.1109/bibe.2007.4375625","mag":"2051572912"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2007.4375625","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2007.4375625","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE 7th International Symposium 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/A5031569253","display_name":"Jeffrey L. Tilson","orcid":null},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I69048370","display_name":"Renaissance Computing Institute","ror":"https://ror.org/01s91ey96","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535","https://openalex.org/I170897317","https://openalex.org/I69048370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey L. Tilson","raw_affiliation_strings":["Renaissance Computing Institute,Computational Biology, University of Illinois, Urbana-Champaign, USA","University of Illinois at Urbana-Champaign, Urbana-Champaign#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Renaissance Computing Institute,Computational Biology, University of Illinois, Urbana-Champaign, USA","institution_ids":["https://openalex.org/I69048370","https://openalex.org/I157725225"]},{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, Urbana-Champaign#TAB#","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014574127","display_name":"Gloria Rendon","orcid":null},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I4210135837","display_name":"National Center for Supercomputing Applications","ror":"https://ror.org/03r10zj06","country_code":"US","type":"facility","lineage":["https://openalex.org/I157725225","https://openalex.org/I4210135837"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gloria Rendon","raw_affiliation_strings":["National Center for Supercomputing Applications, University of Illinois, Urbana-Champaign, USA","University of Illinois at Urbana Champaign"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Supercomputing Applications, University of Illinois, Urbana-Champaign, USA","institution_ids":["https://openalex.org/I4210135837","https://openalex.org/I157725225"]},{"raw_affiliation_string":"University of Illinois at Urbana Champaign","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000980399","display_name":"Mao-Feng Ger","orcid":null},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mao-Feng Ger","raw_affiliation_strings":["Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, USA","University of Illinois at Urbana Champaign"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"University of Illinois at Urbana Champaign","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062408256","display_name":"Eric Jakobsson","orcid":"https://orcid.org/0000-0002-7892-5295"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I19908199","display_name":"National Center for Supercomputing Applications","ror":"https://ror.org/03g9ch715","country_code":"BG","type":"facility","lineage":["https://openalex.org/I19908199"]},{"id":"https://openalex.org/I4210135837","display_name":"National Center for Supercomputing Applications","ror":"https://ror.org/03r10zj06","country_code":"US","type":"facility","lineage":["https://openalex.org/I157725225","https://openalex.org/I4210135837"]}],"countries":["BG","US"],"is_corresponding":false,"raw_author_name":"Eric Jakobsson","raw_affiliation_strings":["National Center for Supercomputing Applications, Center for Biophysics and Computational Biology,Computational Biology, University of Illinois, Urbana-Champaign, USA","National Center for Supercomputing Applications, University of Illinois, Urbana-Champaign; Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Supercomputing Applications, Center for Biophysics and Computational Biology,Computational Biology, University of Illinois, Urbana-Champaign, USA","institution_ids":["https://openalex.org/I4210135837","https://openalex.org/I157725225"]},{"raw_affiliation_string":"National Center for Supercomputing Applications, University of Illinois, Urbana-Champaign; Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign","institution_ids":["https://openalex.org/I19908199"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.673,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.68494176,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"5","issue":null,"first_page":"620","last_page":"627"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9937000274658203,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9848999977111816,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5998628735542297},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5773848295211792},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5578293204307556},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.5104802846908569},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5101564526557922},{"id":"https://openalex.org/keywords/biological-database","display_name":"Biological database","score":0.5075184106826782},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4987671375274658},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4886834919452667},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4648880362510681},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4598563313484192},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.43881338834762573},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43207627534866333},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.42364850640296936},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.42279738187789917},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4181049168109894},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2984127104282379},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.24208661913871765},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.11653217673301697}],"concepts":[{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5998628735542297},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5773848295211792},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5578293204307556},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.5104802846908569},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5101564526557922},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.5075184106826782},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4987671375274658},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4886834919452667},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4648880362510681},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4598563313484192},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.43881338834762573},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43207627534866333},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.42364850640296936},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.42279738187789917},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4181049168109894},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2984127104282379},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.24208661913871765},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.11653217673301697},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","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},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibe.2007.4375625","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2007.4375625","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE 7th International Symposium on BioInformatics and BioEngineering","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1510543252","https://openalex.org/W1555993967","https://openalex.org/W1974139890","https://openalex.org/W2022366078","https://openalex.org/W2030314076","https://openalex.org/W2064940205","https://openalex.org/W2106468692","https://openalex.org/W2109497857","https://openalex.org/W2119195082","https://openalex.org/W2148877470","https://openalex.org/W2158714788","https://openalex.org/W2166699767","https://openalex.org/W2167846577","https://openalex.org/W2168103533","https://openalex.org/W3148640261","https://openalex.org/W4237715662","https://openalex.org/W6677787809"],"related_works":["https://openalex.org/W24843447","https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W3170299350","https://openalex.org/W2218034408","https://openalex.org/W2368410102","https://openalex.org/W2392921965","https://openalex.org/W2605676258","https://openalex.org/W2086443788"],"abstract_inverted_index":{"Traditionally,":[0],"bioinformatics":[1],"has":[2],"been":[3],"organized":[4],"around":[5],"the":[6,80,86,98,102,106,147],"concepts":[7],"of":[8,20,33,47,62,97,101,109,125,143],"genes":[9],"and":[10,23,31,45,56,67,69,105,114],"gene":[11,63,65,68,87],"products,":[12],"typically":[13],"proteins.":[14],"Proteins":[15],"are":[16,24,51],"represented":[17],"as":[18,54],"sequences":[19],"amino":[21,35],"acids":[22],"analyzed":[25],"against":[26],"each":[27,118],"other":[28],"by":[29,123],"alignment":[30],"similarity":[32],"their":[34,43],"acids.":[36],"However":[37],"proteins":[38],"contain":[39],"subsequences":[40,50],"that":[41],"define":[42],"activity":[44],"mode":[46],"regulation.":[48],"These":[49],"referred":[52],"to":[53,76,132],"\"domains\"":[55],"\"motifs\".":[57],"For":[58],"understanding":[59],"many":[60],"aspects":[61],"function,":[64],"interaction,":[66],"organism":[70],"evolution,":[71],"there":[72],"is":[73,91,146],"an":[74],"advantage":[75],"focusing":[77],"analysis":[78,90],"on":[79,85,129],"domain/motif":[81],"level":[82],"rather":[83],"than":[84],"level.":[88],"Such":[89],"inherently":[92],"highly":[93],"computationally":[94],"intensive":[95],"because":[96],"exponential":[99],"growth":[100],"protein":[103],"databases":[104],"combinatorial":[107],"number":[108],"ways":[110],"in":[111],"which":[112],"domains":[113],"motifs":[115],"interact":[116],"with":[117],"other.":[119],"Here":[120],"we":[121],"report,":[122],"means":[124],"a":[126,134],"biological":[127],"example,":[128],"our":[130],"efforts":[131],"build":[133],"user-friendly":[135],"environment":[136,145],"for":[137],"facilitating":[138],"such":[139],"analysis.":[140],"The":[141],"name":[142],"this":[144],"MotifNetwork.":[148]},"counts_by_year":[{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}