{"id":"https://openalex.org/W3129036873","doi":"https://doi.org/10.3390/e23020170","title":"ELIHKSIR Web Server: Evolutionary Links Inferred for Histidine Kinase Sensors Interacting with Response Regulators","display_name":"ELIHKSIR Web Server: Evolutionary Links Inferred for Histidine Kinase Sensors Interacting with Response Regulators","publication_year":2021,"publication_date":"2021-01-30","ids":{"openalex":"https://openalex.org/W3129036873","doi":"https://doi.org/10.3390/e23020170","mag":"3129036873","pmid":"https://pubmed.ncbi.nlm.nih.gov/33573110"},"language":"en","primary_location":{"id":"doi:10.3390/e23020170","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e23020170","pdf_url":"https://www.mdpi.com/1099-4300/23/2/170/pdf?version=1612680538","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1099-4300/23/2/170/pdf?version=1612680538","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066873210","display_name":"Claude Sinner","orcid":"https://orcid.org/0000-0003-2176-685X"},"institutions":[{"id":"https://openalex.org/I162577319","display_name":"The University of Texas at Dallas","ror":"https://ror.org/049emcs32","country_code":"US","type":"education","lineage":["https://openalex.org/I162577319"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Claude Sinner","raw_affiliation_strings":["Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA","institution_ids":["https://openalex.org/I162577319"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016183987","display_name":"Cheyenne Ziegler","orcid":"https://orcid.org/0000-0002-6379-3162"},"institutions":[{"id":"https://openalex.org/I162577319","display_name":"The University of Texas at Dallas","ror":"https://ror.org/049emcs32","country_code":"US","type":"education","lineage":["https://openalex.org/I162577319"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cheyenne Ziegler","raw_affiliation_strings":["Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA","institution_ids":["https://openalex.org/I162577319"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039957653","display_name":"Yun Ho Jung","orcid":"https://orcid.org/0000-0002-1891-5642"},"institutions":[{"id":"https://openalex.org/I162577319","display_name":"The University of Texas at Dallas","ror":"https://ror.org/049emcs32","country_code":"US","type":"education","lineage":["https://openalex.org/I162577319"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yun Ho Jung","raw_affiliation_strings":["Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA","institution_ids":["https://openalex.org/I162577319"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090629959","display_name":"Xianli Jiang","orcid":"https://orcid.org/0000-0003-1697-8575"},"institutions":[{"id":"https://openalex.org/I162577319","display_name":"The University of Texas at Dallas","ror":"https://ror.org/049emcs32","country_code":"US","type":"education","lineage":["https://openalex.org/I162577319"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xianli Jiang","raw_affiliation_strings":["Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA","institution_ids":["https://openalex.org/I162577319"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018611865","display_name":"Faruck Morcos","orcid":"https://orcid.org/0000-0001-6208-1561"},"institutions":[{"id":"https://openalex.org/I162577319","display_name":"The University of Texas at Dallas","ror":"https://ror.org/049emcs32","country_code":"US","type":"education","lineage":["https://openalex.org/I162577319"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Faruck Morcos","raw_affiliation_strings":["Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA","Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA","Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA"],"affiliations":[{"raw_affiliation_string":"Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA","institution_ids":["https://openalex.org/I162577319","https://openalex.org/I4210155419"]},{"raw_affiliation_string":"Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA","institution_ids":["https://openalex.org/I162577319"]},{"raw_affiliation_string":"Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA","institution_ids":["https://openalex.org/I162577319"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5018611865"],"corresponding_institution_ids":["https://openalex.org/I162577319","https://openalex.org/I4210155419"],"apc_list":{"value":2000,"currency":"CHF","value_usd":2165},"apc_paid":{"value":2000,"currency":"CHF","value_usd":2165},"fwci":0.3246,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.54902982,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"23","issue":"2","first_page":"170","last_page":"170"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991000294685364,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9968000054359436,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/response-regulator","display_name":"Response regulator","score":0.7333073019981384},{"id":"https://openalex.org/keywords/regulator","display_name":"Regulator","score":0.6387505531311035},{"id":"https://openalex.org/keywords/crosstalk","display_name":"Crosstalk","score":0.6339964270591736},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6055712699890137},{"id":"https://openalex.org/keywords/histidine-kinase","display_name":"Histidine kinase","score":0.5088418126106262},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49803757667541504},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.49695685505867004},{"id":"https://openalex.org/keywords/phosphorylation","display_name":"Phosphorylation","score":0.4812590777873993},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.45055723190307617},{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.41733086109161377},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3244713842868805},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.20809277892112732},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.1877020001411438},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12324938178062439},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.0875059962272644}],"concepts":[{"id":"https://openalex.org/C2781196521","wikidata":"https://www.wikidata.org/wiki/Q24965710","display_name":"Response regulator","level":4,"score":0.7333073019981384},{"id":"https://openalex.org/C6929976","wikidata":"https://www.wikidata.org/wiki/Q3771881","display_name":"Regulator","level":3,"score":0.6387505531311035},{"id":"https://openalex.org/C169822122","wikidata":"https://www.wikidata.org/wiki/Q230187","display_name":"Crosstalk","level":2,"score":0.6339964270591736},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6055712699890137},{"id":"https://openalex.org/C2778905257","wikidata":"https://www.wikidata.org/wiki/Q1620721","display_name":"Histidine kinase","level":4,"score":0.5088418126106262},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49803757667541504},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49695685505867004},{"id":"https://openalex.org/C11960822","wikidata":"https://www.wikidata.org/wiki/Q242736","display_name":"Phosphorylation","level":2,"score":0.4812590777873993},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.45055723190307617},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.41733086109161377},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3244713842868805},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.20809277892112732},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.1877020001411438},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12324938178062439},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0875059962272644},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3390/e23020170","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e23020170","pdf_url":"https://www.mdpi.com/1099-4300/23/2/170/pdf?version=1612680538","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},{"id":"pmid:33573110","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33573110","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":"Entropy (Basel, Switzerland)","raw_type":null},{"id":"pmh:oai:doaj.org/article:e989b040e8eb4b8b81cd56f48cf362e3","is_oa":true,"landing_page_url":"https://doaj.org/article/e989b040e8eb4b8b81cd56f48cf362e3","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Entropy, Vol 23, Iss 2, p 170 (2021)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/1099-4300/23/2/170/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/e23020170","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Entropy; Volume 23; Issue 2; Pages: 170","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:7911359","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7911359","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Entropy (Basel)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/e23020170","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e23020170","pdf_url":"https://www.mdpi.com/1099-4300/23/2/170/pdf?version=1612680538","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6100000143051147,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G5016678989","display_name":"CAREER:  Developing Novel Models of Sequence Evolution for Protein Design and Molecular Recognition","funder_award_id":"1943442","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5042914008","display_name":null,"funder_award_id":"R35GM133631","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5623625596","display_name":null,"funder_award_id":"---","funder_id":"https://openalex.org/F4320327708","funder_display_name":"University of Texas at Dallas"},{"id":"https://openalex.org/G5921281487","display_name":null,"funder_award_id":"number","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8301358366","display_name":null,"funder_award_id":"MCB-1943442","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320327708","display_name":"University of Texas at Dallas","ror":"https://ror.org/049emcs32"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3129036873.pdf","grobid_xml":"https://content.openalex.org/works/W3129036873.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1577231857","https://openalex.org/W1861406683","https://openalex.org/W1982829391","https://openalex.org/W2008545402","https://openalex.org/W2020243807","https://openalex.org/W2048310584","https://openalex.org/W2080184242","https://openalex.org/W2081929574","https://openalex.org/W2085211779","https://openalex.org/W2096515244","https://openalex.org/W2109613442","https://openalex.org/W2109839728","https://openalex.org/W2134587758","https://openalex.org/W2151831732","https://openalex.org/W2391698393","https://openalex.org/W2395745621","https://openalex.org/W2417059200","https://openalex.org/W2461611684","https://openalex.org/W2551582013","https://openalex.org/W2626396625","https://openalex.org/W2766246727","https://openalex.org/W2888162369","https://openalex.org/W2898402099","https://openalex.org/W2950410860","https://openalex.org/W2997802784","https://openalex.org/W3136918052","https://openalex.org/W4210623056","https://openalex.org/W6784891704"],"related_works":["https://openalex.org/W2141612196","https://openalex.org/W1535625299","https://openalex.org/W2964461511","https://openalex.org/W2010394763","https://openalex.org/W2110343075","https://openalex.org/W2278025825","https://openalex.org/W2093358630","https://openalex.org/W2166247218","https://openalex.org/W2085792075","https://openalex.org/W2024804257"],"abstract_inverted_index":{"Two-component":[0],"systems":[1],"(TCS)":[2],"are":[3,162],"signaling":[4],"machinery":[5],"that":[6],"consist":[7],"of":[8,42,62,76,166,175,183],"a":[9,59,73,97,181],"histidine":[10],"kinases":[11],"(HK)":[12],"and":[13,90,107,115,155,187],"response":[14,28],"regulator":[15,29],"(RR).":[16,30],"When":[17],"an":[18],"environmental":[19],"change":[20],"is":[21],"detected,":[22],"the":[23,40,78,132,144,150,157],"HK":[24],"phosphorylates":[25],"its":[26],"cognate":[27,32],"While":[31],"interactions":[33,44,51,86],"were":[34,118,137],"considered":[35],"orthogonal,":[36],"experimental":[37],"evidence":[38],"shows":[39],"prevalence":[41],"crosstalk":[43,50],"between":[45],"non-cognate":[46],"HK-RR":[47],"pairs.":[48],"Currently,":[49],"have":[52],"been":[53],"demonstrated":[54],"for":[55,72,87,125],"TCS":[56,70,88,167,184,191],"proteins":[57,89,154],"in":[58,84,131],"limited":[60],"number":[61],"organisms.":[63],"By":[64],"providing":[65],"specificity":[66,95,133],"predictions":[67],"across":[68],"entire":[69],"networks":[71,168],"large":[74],"variety":[75,182],"organisms,":[77],"ELIHKSIR":[79,145,176],"web":[80,146],"server":[81],"assists":[82],"users":[83,178],"identifying":[85],"their":[91],"mutants.":[92],"To":[93],"generate":[94],"scores,":[96],"global":[98],"probabilistic":[99],"model":[100],"was":[101],"used":[102,120],"to":[103,121,139,149,152,169,179,189],"identify":[104],"interfacial":[105],"couplings":[106,114],"local":[108,116],"fields":[109,117],"from":[110],"sequence":[111],"information.":[112],"These":[113,135],"then":[119],"construct":[122],"Hamiltonian":[123],"scores":[124],"positions":[126],"with":[127],"encoded":[128],"specificity,":[129],"resulting":[130,158],"score.":[134],"methods":[136],"applied":[138],"6676":[140],"organisms":[141],"available":[142],"on":[143],"server.":[147],"Due":[148],"ability":[151],"mutate":[153],"display":[156],"network":[159,185],"changes,":[160],"there":[161],"nearly":[163],"endless":[164],"combinations":[165],"analyze":[170],"using":[171],"ELIHKSIR.":[172],"The":[173],"functionality":[174],"allows":[177],"perform":[180],"analyses":[186],"visualizations":[188],"support":[190],"research":[192],"efforts.":[193]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}