{"id":"https://openalex.org/W2793609744","doi":"https://doi.org/10.1109/tcbb.2018.2804393","title":"A Comparative Study of Network Motifs in the Integrated Transcriptional Regulation and Protein Interaction Networks of &lt;italic&gt;Shewanella&lt;/italic&gt;","display_name":"A Comparative Study of Network Motifs in the Integrated Transcriptional Regulation and Protein Interaction Networks of &lt;italic&gt;Shewanella&lt;/italic&gt;","publication_year":2018,"publication_date":"2018-02-09","ids":{"openalex":"https://openalex.org/W2793609744","doi":"https://doi.org/10.1109/tcbb.2018.2804393","mag":"2793609744","pmid":"https://pubmed.ncbi.nlm.nih.gov/29994366"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2018.2804393","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2804393","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5060336238","display_name":"Dewu Ding","orcid":null},"institutions":[{"id":"https://openalex.org/I200946902","display_name":"Yichun University","ror":"https://ror.org/05h4th693","country_code":"CN","type":"education","lineage":["https://openalex.org/I200946902"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Dewu Ding","raw_affiliation_strings":["School of Mathematics and Computer Science, Yichun University, Yichun, Jiangxi, P.R. China"],"affiliations":[{"raw_affiliation_string":"School of Mathematics and Computer Science, Yichun University, Yichun, Jiangxi, P.R. China","institution_ids":["https://openalex.org/I200946902"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082259816","display_name":"Xiao Sun","orcid":"https://orcid.org/0000-0003-1048-7775"},"institutions":[{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]},{"id":"https://openalex.org/I4387154005","display_name":"State Key Laboratory of Digital Medical Engineering","ror":"https://ror.org/03ab0at74","country_code":null,"type":"facility","lineage":["https://openalex.org/I4387154005","https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiao Sun","raw_affiliation_strings":["State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, P.R. China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, P.R. China","institution_ids":["https://openalex.org/I76569877","https://openalex.org/I4387154005"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5060336238"],"corresponding_institution_ids":["https://openalex.org/I200946902"],"apc_list":null,"apc_paid":null,"fwci":0.3913,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.60148037,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"16","issue":"1","first_page":"163","last_page":"171"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11231","display_name":"Microbial Fuel Cells and Bioremediation","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2305","display_name":"Environmental Engineering"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11231","display_name":"Microbial Fuel Cells and Bioremediation","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2305","display_name":"Environmental Engineering"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11784","display_name":"CO2 Reduction Techniques and Catalysts","score":0.9933000206947327,"subfield":{"id":"https://openalex.org/subfields/2105","display_name":"Renewable Energy, Sustainability and the Environment"},"field":{"id":"https://openalex.org/fields/21","display_name":"Energy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10303","display_name":"Photosynthetic Processes and Mechanisms","score":0.9919999837875366,"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/shewanella-oneidensis","display_name":"Shewanella oneidensis","score":0.9558115601539612},{"id":"https://openalex.org/keywords/shewanella","display_name":"Shewanella","score":0.753276526927948},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5084134936332703},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.47541314363479614},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46520692110061646},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4292134940624237},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3649156987667084},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.3188124895095825}],"concepts":[{"id":"https://openalex.org/C2781170380","wikidata":"https://www.wikidata.org/wiki/Q4049396","display_name":"Shewanella oneidensis","level":3,"score":0.9558115601539612},{"id":"https://openalex.org/C2778824058","wikidata":"https://www.wikidata.org/wiki/Q3243676","display_name":"Shewanella","level":3,"score":0.753276526927948},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5084134936332703},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.47541314363479614},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46520692110061646},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4292134940624237},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3649156987667084},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.3188124895095825},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020592","descriptor_name":"Shewanella","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020592","descriptor_name":"Shewanella","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020592","descriptor_name":"Shewanella","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2018.2804393","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2804393","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29994366","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29994366","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.5299999713897705}],"awards":[{"id":"https://openalex.org/G8496386714","display_name":null,"funder_award_id":"61472078","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W1533994546","https://openalex.org/W1592232350","https://openalex.org/W1965917470","https://openalex.org/W1967490380","https://openalex.org/W1968596431","https://openalex.org/W1971254121","https://openalex.org/W1972792790","https://openalex.org/W1984189354","https://openalex.org/W1986111357","https://openalex.org/W1989277878","https://openalex.org/W1994328828","https://openalex.org/W1997052232","https://openalex.org/W2001018770","https://openalex.org/W2023889921","https://openalex.org/W2027819618","https://openalex.org/W2037248648","https://openalex.org/W2038012561","https://openalex.org/W2038045995","https://openalex.org/W2054331129","https://openalex.org/W2057152187","https://openalex.org/W2059713400","https://openalex.org/W2061425021","https://openalex.org/W2067847918","https://openalex.org/W2070350400","https://openalex.org/W2084695584","https://openalex.org/W2086044927","https://openalex.org/W2096173332","https://openalex.org/W2098045561","https://openalex.org/W2105924489","https://openalex.org/W2106923147","https://openalex.org/W2108559568","https://openalex.org/W2112262143","https://openalex.org/W2116194650","https://openalex.org/W2122964133","https://openalex.org/W2123124546","https://openalex.org/W2123649954","https://openalex.org/W2126606094","https://openalex.org/W2133301971","https://openalex.org/W2142284828","https://openalex.org/W2152269861","https://openalex.org/W2153624566","https://openalex.org/W2156425900","https://openalex.org/W2156586206","https://openalex.org/W2161917555","https://openalex.org/W2166742266","https://openalex.org/W2341672742","https://openalex.org/W2599750594","https://openalex.org/W2599799592","https://openalex.org/W2898057000","https://openalex.org/W2949374631","https://openalex.org/W3199943451","https://openalex.org/W4285719527","https://openalex.org/W6632196570","https://openalex.org/W6735010770","https://openalex.org/W6800717233"],"related_works":["https://openalex.org/W2126383458","https://openalex.org/W1986111357","https://openalex.org/W2360862540","https://openalex.org/W4281704995","https://openalex.org/W1965596097","https://openalex.org/W2036697821","https://openalex.org/W2143431457","https://openalex.org/W3172417719","https://openalex.org/W2783647467","https://openalex.org/W2051742391"],"abstract_inverted_index":{"The":[0,72],"Shewanella":[1,47,92,151],"species":[2],"shows":[3],"a":[4,9,106,141,147],"remarkable":[5],"respiratory":[6],"versatility":[7],"with":[8,140],"great":[10],"variety":[11],"of":[12,75,112],"extracellular":[13],"electron":[14],"acceptors":[15],"(termed":[16],"Extracellular":[17],"Electron":[18],"Transfer,":[19],"EET).":[20],"To":[21],"explore":[22],"relevant":[23],"mechanisms":[24],"from":[25],"the":[26,32,52,62,76,83,91,101,109,129,136],"network":[27,53,63],"motif":[28,102,137],"view,":[29],"we":[30,97],"constructed":[31],"integrated":[33,57,70],"networks":[34],"that":[35,61,86],"combined":[36],"transcriptional":[37],"regulation":[38],"interactions":[39,43],"(TRIs)":[40],"and":[41,50,127],"protein-protein":[42],"(PPIs)":[44],"for":[45,119],"13":[46],"species,":[48],"identified":[49],"compared":[51],"motifs":[54,64,79],"in":[55,68,90,108,135,150],"these":[56,69],"networks.":[58,71],"We":[59],"found":[60,98],"were":[65,87],"evolutionary":[66],"conserved":[67,78],"functional":[73],"significance":[74],"highly":[77],"was":[80],"discussed,":[81],"especially":[82],"important":[84],"ones":[85],"potentially":[88],"involved":[89,134],"EET":[93],"processes.":[94],"More":[95],"importantly,":[96],"that:":[99],"1)":[100],"co-regulated":[103],"PPI":[104],"took":[105],"role":[107,149],"\"standby":[110],"mode\"":[111],"protein":[113],"utilization,":[114],"which":[115,133],"will":[116],"be":[117],"helpful":[118],"cells":[120],"to":[121,124],"rapidly":[122],"response":[123],"environmental":[125],"changes;":[126],"2)":[128],"type":[130],"II":[131],"cofactors,":[132],"TRI":[138],"interacting":[139],"third":[142],"protein,":[143],"mainly":[144],"carried":[145],"out":[146],"signalling":[148],"oneidensis":[152],"MR-1.":[153]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2018-03-29T00:00:00"}
