{"id":"https://openalex.org/W2342722535","doi":"https://doi.org/10.1109/bhi.2016.7455962","title":"A reliable alternative of OptKnock for desirable mutant microbial strains","display_name":"A reliable alternative of OptKnock for desirable mutant microbial strains","publication_year":2016,"publication_date":"2016-02-01","ids":{"openalex":"https://openalex.org/W2342722535","doi":"https://doi.org/10.1109/bhi.2016.7455962","mag":"2342722535"},"language":"en","primary_location":{"id":"doi:10.1109/bhi.2016.7455962","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bhi.2016.7455962","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI)","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/A5076338403","display_name":"Meltem Apaydin","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":true,"raw_author_name":"Meltem Apaydin","raw_affiliation_strings":["Dept. of Electrical and Computer Engineering, Texas A&M University, TX, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Electrical and Computer Engineering, Texas A&M University, TX, USA","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100732720","display_name":"Bo Zeng","orcid":"https://orcid.org/0000-0002-8689-4281"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bo Zeng","raw_affiliation_strings":["Dept. of Industrial Engineering, University of Pittsburgh, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Industrial Engineering, University of Pittsburgh, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073946580","display_name":"Xiaoning Qian","orcid":"https://orcid.org/0000-0002-4347-2476"},"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":"Xiaoning Qian","raw_affiliation_strings":["Dept. of Electrical and Computer Engineering, Texas A&M University, TX, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Electrical and Computer Engineering, Texas A&M University, TX, USA","institution_ids":["https://openalex.org/I91045830"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5076338403"],"corresponding_institution_ids":["https://openalex.org/I91045830"],"apc_list":null,"apc_paid":null,"fwci":0.1667,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.62090144,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"4","issue":null,"first_page":"573","last_page":"576"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998000264167786,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998000264167786,"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/T10476","display_name":"Algal biology and biofuel production","score":0.9797000288963318,"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/T10171","display_name":"Biofuel production and bioconversion","score":0.9717000126838684,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.638601541519165},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5148240923881531},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4271775782108307},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40678372979164124},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.3283020853996277},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2932237982749939},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2387056052684784},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.14165276288986206},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10623541474342346},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07843160629272461}],"concepts":[{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.638601541519165},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5148240923881531},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4271775782108307},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40678372979164124},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.3283020853996277},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2932237982749939},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2387056052684784},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.14165276288986206},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10623541474342346},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07843160629272461}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bhi.2016.7455962","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bhi.2016.7455962","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1977241851","https://openalex.org/W1980875662","https://openalex.org/W1984096521","https://openalex.org/W1993319399","https://openalex.org/W2006672203","https://openalex.org/W2023617120","https://openalex.org/W2062245653","https://openalex.org/W2070534023","https://openalex.org/W2102164505","https://openalex.org/W2130364940","https://openalex.org/W2148750928","https://openalex.org/W2153373497","https://openalex.org/W2171403356","https://openalex.org/W2340950576"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2155835698","https://openalex.org/W2076096978","https://openalex.org/W2094337488","https://openalex.org/W2350587855","https://openalex.org/W2044028228","https://openalex.org/W2047730886","https://openalex.org/W2994288809","https://openalex.org/W2077224613","https://openalex.org/W1984834769"],"abstract_inverted_index":{"Genome-scale":[0],"metabolic":[1,252],"models":[2],"have":[3],"lead":[4,281],"to":[5,11,34,39,64,215,282],"the":[6,13,17,23,41,45,66,69,73,76,83,95,103,109,114,117,121,126,152,157,169,172,176,181,191,197,207,220,257,274],"development":[7],"of":[8,19,25,44,48,56,68,116,156,171,219,227],"computational":[9],"methods":[10,31,59],"understand":[12],"underlying":[14],"mechanism":[15],"about":[16],"metabolism":[18],"an":[20],"organism.":[21],"With":[22],"foundation":[24],"Flux":[26],"balance":[27],"analysis":[28],"(FBA),":[29],"optimization":[30,62,85,146,159,178,234,278],"are":[32,262],"developed":[33],"suggest":[35],"optimal":[36,138],"knockout":[37,139,209,239,287],"strategies":[38,140,210],"achieve":[40],"maximum":[42,122],"production":[43,67,92,115],"target":[46],"metabolite":[47],"interest":[49],"including":[50],"industrial":[51],"and":[52,154,180,193,241,254,265,285],"pharmaceutical":[53],"chemicals.":[54],"Many":[55],"these":[57,217],"existing":[58],"employ":[60],"bi-level":[61,145,233,277],"formulations":[63],"maximize":[65],"desired":[70,118],"biochemical":[71,119],"at":[72],"outer-level":[74,194],"while":[75],"organism":[77],"still":[78],"maintains":[79],"living":[80],"modeled":[81],"as":[82,101],"inner-level":[84,158,177,192],"model,":[86],"for":[87,113],"example,":[88],"by":[89,98,201],"maximizing":[90],"biomass":[91,123],"yield":[93],"under":[94,120],"constraints":[96],"imposed":[97],"gene":[99],"knockouts":[100],"in":[102,142,161,211],"well-known":[104],"OptKnock.":[105],"OptKnock":[106,202,246],"always":[107],"selects":[108],"most":[110],"optimistic":[111,221],"flux":[112,128],"condition":[124],"although":[125],"actual":[127,163,208],"can":[129],"be":[130,186,204],"less":[131],"than":[132],"this":[133],"maximum.":[134],"This":[135],"is":[136],"because":[137],"derived":[141],"such":[143],"a":[144,187,225,230,248],"framework":[147],"may":[148,185,203],"heavily":[149],"depend":[150],"on":[151,247],"closeness":[153],"robustness":[155],"model":[160,179,279],"capturing":[162],"cell":[164],"survival":[165],"states.":[166],"By":[167],"examining":[168],"non-uniqueness":[170],"surviving":[173],"mutants":[174,199],"from":[175,206,245],"fact":[182],"that":[183,256,273],"there":[184],"non-cooperative":[188],"environment":[189],"between":[190],"decision":[195],"makers,":[196],"suggested":[198],"produced":[200],"different":[205],"practice.":[212],"In":[213],"order":[214],"prevent":[216],"limitations":[218],"OptKnock,":[222],"we":[223,271],"propose":[224],"modification":[226],"it":[228],"through":[229,259],"novel":[231],"pessimistic":[232,238,260,276],"perspective.":[235],"We":[236],"compute":[237],"solutions":[240,258],"compare":[242],"with":[243],"those":[244],"core":[249],"E.":[250],"coli":[251],"network,":[253],"observe":[255],"view":[261],"more":[263,283],"reliable":[264],"perform":[266],"better.":[267],"For":[268],"future":[269],"research,":[270],"believe":[272],"proposed":[275],"will":[280],"practical":[284],"robust":[286],"strategies.":[288]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}