{"id":"https://openalex.org/W2110266641","doi":"https://doi.org/10.1109/tcbb.2014.2377733","title":"Optimal Experimental Design for Gene Regulatory Networks in the Presence of Uncertainty","display_name":"Optimal Experimental Design for Gene Regulatory Networks in the Presence of Uncertainty","publication_year":2014,"publication_date":"2014-12-04","ids":{"openalex":"https://openalex.org/W2110266641","doi":"https://doi.org/10.1109/tcbb.2014.2377733","mag":"2110266641","pmid":"https://pubmed.ncbi.nlm.nih.gov/26357334"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2014.2377733","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2377733","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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/A5053317035","display_name":"Roozbeh Dehghannasiri","orcid":"https://orcid.org/0000-0001-7413-3437"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Roozbeh Dehghannasiri","raw_affiliation_strings":["Department of Electrical and Computer Engineering and the Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering and the Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081620315","display_name":"Byung-Jun Yoon","orcid":"https://orcid.org/0000-0001-9328-1101"},"institutions":[{"id":"https://openalex.org/I4210144839","display_name":"Hamad bin Khalifa University","ror":"https://ror.org/03eyq4y97","country_code":"QA","type":"education","lineage":["https://openalex.org/I4210144839"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["QA","US"],"is_corresponding":false,"raw_author_name":"Byung-Jun Yoon","raw_affiliation_strings":["College of Science, Engineering, and Technology, Hamad bin Khalifa University (HBKU), Doha, Qatar","Department of Electrical and Computer Engineering and the Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Science, Engineering, and Technology, Hamad bin Khalifa University (HBKU), Doha, Qatar","institution_ids":["https://openalex.org/I4210144839"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering and the Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112221423","display_name":"Edward R. Dougherty","orcid":null},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Edward R. Dougherty","raw_affiliation_strings":["Department of Electrical and Computer Engineering and the Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering and the Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX","institution_ids":["https://openalex.org/I91045830"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2645,"currency":"USD","value_usd":2645},"apc_paid":null,"fwci":2.9866,"has_fulltext":false,"cited_by_count":71,"citation_normalized_percentile":{"value":0.92044985,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"12","issue":"4","first_page":"938","last_page":"950"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9995999932289124,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9995999932289124,"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/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9866999983787537,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9695000052452087,"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/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6937341690063477},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.684586763381958},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6730867624282837},{"id":"https://openalex.org/keywords/prioritization","display_name":"Prioritization","score":0.48001307249069214},{"id":"https://openalex.org/keywords/risk-analysis","display_name":"Risk analysis (engineering)","score":0.3628179728984833},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.34034428000450134},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23630517721176147},{"id":"https://openalex.org/keywords/management-science","display_name":"Management science","score":0.1302659511566162},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1299910843372345},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.11997225880622864},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10299983620643616},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09294843673706055}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6937341690063477},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.684586763381958},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6730867624282837},{"id":"https://openalex.org/C2777615720","wikidata":"https://www.wikidata.org/wiki/Q11888847","display_name":"Prioritization","level":2,"score":0.48001307249069214},{"id":"https://openalex.org/C112930515","wikidata":"https://www.wikidata.org/wiki/Q4389547","display_name":"Risk analysis (engineering)","level":1,"score":0.3628179728984833},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.34034428000450134},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23630517721176147},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.1302659511566162},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1299910843372345},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.11997225880622864},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10299983620643616},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09294843673706055},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2014.2377733","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2377733","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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:26357334","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26357334","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":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.44999998807907104,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1561649271","https://openalex.org/W1965387924","https://openalex.org/W1971266246","https://openalex.org/W1972155227","https://openalex.org/W2049480816","https://openalex.org/W2051835055","https://openalex.org/W2055075302","https://openalex.org/W2058794142","https://openalex.org/W2069034916","https://openalex.org/W2077229799","https://openalex.org/W2090882632","https://openalex.org/W2095712283","https://openalex.org/W2105291362","https://openalex.org/W2111123076","https://openalex.org/W2113169045","https://openalex.org/W2114518254","https://openalex.org/W2121782762","https://openalex.org/W2125210796","https://openalex.org/W2130721915","https://openalex.org/W2132935366","https://openalex.org/W2133851381","https://openalex.org/W2134717973","https://openalex.org/W2136559804","https://openalex.org/W2136636278","https://openalex.org/W2138031337","https://openalex.org/W2140941551","https://openalex.org/W2144578442","https://openalex.org/W2146206618","https://openalex.org/W2152563826","https://openalex.org/W2156377786","https://openalex.org/W2159638256","https://openalex.org/W2160220288","https://openalex.org/W2160533336","https://openalex.org/W2165350808","https://openalex.org/W2166122445","https://openalex.org/W2166162270","https://openalex.org/W2168399023","https://openalex.org/W2530014580","https://openalex.org/W2795495912","https://openalex.org/W3097925195","https://openalex.org/W3103871524","https://openalex.org/W4232528534","https://openalex.org/W4388252848","https://openalex.org/W4388257666"],"related_works":["https://openalex.org/W2506292322","https://openalex.org/W4283209547","https://openalex.org/W4367627632","https://openalex.org/W2466517183","https://openalex.org/W2950199998","https://openalex.org/W2560421304","https://openalex.org/W2951387065","https://openalex.org/W2134575910","https://openalex.org/W4385727351","https://openalex.org/W4306798985"],"abstract_inverted_index":{"Of":[0],"major":[1],"interest":[2],"to":[3,14,20,25,58,74,99,127,149,169],"translational":[4,82],"genomics":[5],"is":[6,33,56,85],"the":[7,26,46,100,108,118,137,146,153,166,171,176,182,185],"intervention":[8],"in":[9,18,94,175],"gene":[10,196],"regulatory":[11,197],"networks":[12],"(GRNs)":[13],"affect":[15],"cell":[16],"behavior;":[17],"particular,":[19],"alter":[21],"pathological":[22],"phenotypes.":[23],"Owing":[24],"complexity":[27],"of":[28,43,110,120,124,184],"GRNs,":[29],"accurate":[30],"network":[31,77,111,178],"inference":[32],"practically":[34],"challenging":[35],"and":[36,48,92,194],"GRN":[37,88],"models":[38],"often":[39],"contain":[40],"considerable":[41],"amounts":[42],"uncertainty.":[44,78],"Considering":[45],"cost":[47,102,109,123],"time":[49],"required":[50],"for":[51,63,132],"conducting":[52,152],"biological":[53],"experiments,":[54],"it":[55,84,104],"desirable":[57],"have":[59],"a":[60,81,95,129],"systematic":[61],"method":[62,187],"prioritizing":[64],"potential":[65,140,168],"experiments":[66,141],"so":[67],"that":[68,87,97,103],"an":[69,162],"experiment":[70,164],"can":[71,160],"be":[72,90],"chosen":[73],"optimally":[75],"reduce":[76,170],"Moreover,":[79],"from":[80],"perspective":[83],"crucial":[86],"uncertainty":[89,125,173],"quantified":[91],"reduced":[93],"manner":[96],"pertains":[98],"operational":[101],"induces,":[105],"such":[106],"as":[107],"intervention.":[112],"In":[113,136],"this":[114,157],"work,":[115],"we":[116],"utilize":[117],"concept":[119],"mean":[121],"objective":[122],"(MOCU)":[126],"propose":[128],"novel":[130],"framework":[131],"optimal":[133,163],"experimental":[134],"design.":[135],"proposed":[138,186],"framework,":[139],"are":[142],"prioritized":[143],"based":[144,191],"on":[145,156,192],"MOCU":[147],"expected":[148],"remain":[150],"after":[151],"experiment.":[154],"Based":[155],"prioritization,":[158],"one":[159],"select":[161],"with":[165],"largest":[167],"pertinent":[172],"present":[174],"current":[177],"model.":[179],"We":[180],"demonstrate":[181],"effectiveness":[183],"via":[188],"extensive":[189],"simulations":[190],"synthetic":[193],"real":[195],"networks.":[198]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":5}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
