{"id":"https://openalex.org/W2155949509","doi":"https://doi.org/10.1093/bioinformatics/bts585","title":"Optimal design of stimulus experiments for robust discrimination of biochemical reaction networks","display_name":"Optimal design of stimulus experiments for robust discrimination of biochemical reaction networks","publication_year":2012,"publication_date":"2012-10-09","ids":{"openalex":"https://openalex.org/W2155949509","doi":"https://doi.org/10.1093/bioinformatics/bts585","mag":"2155949509","pmid":"https://pubmed.ncbi.nlm.nih.gov/23047554"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts585","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts585","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/23/3089/18530350/bts585.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/23/3089/18530350/bts585.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020438172","display_name":"Robert Flassig","orcid":"https://orcid.org/0000-0002-7092-1046"},"institutions":[{"id":"https://openalex.org/I95793202","display_name":"Otto-von-Guericke-Universit\u00e4t Magdeburg","ror":"https://ror.org/00ggpsq73","country_code":"DE","type":"education","lineage":["https://openalex.org/I95793202"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"R. J. Flassig","raw_affiliation_strings":["Otto-von-Guericke University, Process Systems Engineering, Universit\u00e4tsplatz 2, D-39106 Magdeburg, Germany. flassig@mpi-magdeburg.mpg.de"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Otto-von-Guericke University, Process Systems Engineering, Universit\u00e4tsplatz 2, D-39106 Magdeburg, Germany. flassig@mpi-magdeburg.mpg.de","institution_ids":["https://openalex.org/I95793202"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036444315","display_name":"Kai Sundmacher","orcid":"https://orcid.org/0000-0003-3251-0593"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"K. Sundmacher","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.8813,"has_fulltext":false,"cited_by_count":32,"citation_normalized_percentile":{"value":0.85727776,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"28","issue":"23","first_page":"3089","last_page":"3096"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.7434999942779541,"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":0.7434999942779541,"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/T10791","display_name":"Advanced Control Systems Optimization","score":0.1527000069618225,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.05480000004172325,"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/ode","display_name":"Ode","score":0.7034062147140503},{"id":"https://openalex.org/keywords/linearization","display_name":"Linearization","score":0.6993199586868286},{"id":"https://openalex.org/keywords/nonlinear-system","display_name":"Nonlinear system","score":0.6700396537780762},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5837169885635376},{"id":"https://openalex.org/keywords/ordinary-differential-equation","display_name":"Ordinary differential equation","score":0.5060922503471375},{"id":"https://openalex.org/keywords/operating-point","display_name":"Operating point","score":0.42305877804756165},{"id":"https://openalex.org/keywords/control-theory","display_name":"Control theory (sociology)","score":0.4219893217086792},{"id":"https://openalex.org/keywords/matlab","display_name":"MATLAB","score":0.41406798362731934},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.40207773447036743},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.32818979024887085},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.27736803889274597},{"id":"https://openalex.org/keywords/differential-equation","display_name":"Differential equation","score":0.2091732621192932},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1649831235408783},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.0945284366607666}],"concepts":[{"id":"https://openalex.org/C34862557","wikidata":"https://www.wikidata.org/wiki/Q178985","display_name":"Ode","level":2,"score":0.7034062147140503},{"id":"https://openalex.org/C11210021","wikidata":"https://www.wikidata.org/wiki/Q1520713","display_name":"Linearization","level":3,"score":0.6993199586868286},{"id":"https://openalex.org/C158622935","wikidata":"https://www.wikidata.org/wiki/Q660848","display_name":"Nonlinear system","level":2,"score":0.6700396537780762},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5837169885635376},{"id":"https://openalex.org/C51544822","wikidata":"https://www.wikidata.org/wiki/Q465274","display_name":"Ordinary differential equation","level":3,"score":0.5060922503471375},{"id":"https://openalex.org/C22762622","wikidata":"https://www.wikidata.org/wiki/Q628904","display_name":"Operating point","level":2,"score":0.42305877804756165},{"id":"https://openalex.org/C47446073","wikidata":"https://www.wikidata.org/wiki/Q5165890","display_name":"Control theory (sociology)","level":3,"score":0.4219893217086792},{"id":"https://openalex.org/C2780365114","wikidata":"https://www.wikidata.org/wiki/Q169478","display_name":"MATLAB","level":2,"score":0.41406798362731934},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.40207773447036743},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.32818979024887085},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.27736803889274597},{"id":"https://openalex.org/C78045399","wikidata":"https://www.wikidata.org/wiki/Q11214","display_name":"Differential equation","level":2,"score":0.2091732621192932},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1649831235408783},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0945284366607666},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C2775924081","wikidata":"https://www.wikidata.org/wiki/Q55608371","display_name":"Control (management)","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts585","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts585","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/23/3089/18530350/bts585.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23047554","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23047554","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pure.mpg.de:item_2060805","is_oa":true,"landing_page_url":"http://hdl.handle.net/11858/00-001M-0000-0024-3E82-0","pdf_url":"http://hdl.handle.net/11858/00-001M-0000-0024-3E82-0","source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:2517382","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3516143","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts585","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts585","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/23/3089/18530350/bts585.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities","score":0.6100000143051147}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2155949509.pdf"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W62429925","https://openalex.org/W75245544","https://openalex.org/W129305155","https://openalex.org/W202383464","https://openalex.org/W312352384","https://openalex.org/W579748205","https://openalex.org/W579842789","https://openalex.org/W1485426748","https://openalex.org/W1638774395","https://openalex.org/W1965420754","https://openalex.org/W1965554146","https://openalex.org/W1979892077","https://openalex.org/W1990065094","https://openalex.org/W1997537051","https://openalex.org/W2003195392","https://openalex.org/W2011970986","https://openalex.org/W2012001954","https://openalex.org/W2016811449","https://openalex.org/W2016950925","https://openalex.org/W2039339087","https://openalex.org/W2039477419","https://openalex.org/W2042439614","https://openalex.org/W2043073266","https://openalex.org/W2043256931","https://openalex.org/W2045534984","https://openalex.org/W2048971218","https://openalex.org/W2051594535","https://openalex.org/W2059246518","https://openalex.org/W2074869363","https://openalex.org/W2104379479","https://openalex.org/W2110690917","https://openalex.org/W2112036188","https://openalex.org/W2121990344","https://openalex.org/W2131070718","https://openalex.org/W2138192576","https://openalex.org/W2139417466","https://openalex.org/W2144197118","https://openalex.org/W2151531457","https://openalex.org/W2152431703","https://openalex.org/W2156154713","https://openalex.org/W2159902206","https://openalex.org/W2168648059","https://openalex.org/W2171565916","https://openalex.org/W2301746362","https://openalex.org/W2507060499","https://openalex.org/W2525131151","https://openalex.org/W2595741664","https://openalex.org/W3003413895","https://openalex.org/W3106932903","https://openalex.org/W3203779568","https://openalex.org/W6610904127","https://openalex.org/W6647786800","https://openalex.org/W6661676928","https://openalex.org/W6662789159","https://openalex.org/W6682443497","https://openalex.org/W6725076964"],"related_works":["https://openalex.org/W3082668976","https://openalex.org/W2517973022","https://openalex.org/W1543121148","https://openalex.org/W1580703421","https://openalex.org/W2996841952","https://openalex.org/W2618518959","https://openalex.org/W2231364979","https://openalex.org/W4295745414","https://openalex.org/W4288093367","https://openalex.org/W4382202915"],"abstract_inverted_index":{"MOTIVATION:":[0],"Biochemical":[1],"reaction":[2,194],"networks":[3],"in":[4,204,246],"the":[5,20,26,59,129,137,141,145,151,155,175,198,201,205,218,224,244],"form":[6],"of":[7,22,29,39,140,207,226,243],"coupled":[8],"ordinary":[9],"differential":[10],"equations":[11],"(ODEs)":[12],"provide":[13],"a":[14,36,84,161],"powerful":[15],"modeling":[16],"tool":[17],"for":[18,57,90,117,190,236],"understanding":[19],"dynamics":[21],"biochemical":[23],"processes.":[24],"During":[25],"early":[27],"phase":[28],"modeling,":[30],"scientists":[31],"have":[32,67],"to":[33,53,96,165,184,233],"deal":[34],"with":[35,182,223],"large":[37,234],"pool":[38],"competing":[40],"nonlinear":[41,138,177,192],"models.":[42],"At":[43],"this":[44,109],"point,":[45],"discrimination":[46,92,163],"experiments":[47,121],"can":[48,93,230],"be":[49,94,231],"designed":[50],"and":[51,187],"conducted":[52],"obtain":[54],"optimal":[55,86,114,119],"data":[56,257],"selecting":[58],"most":[60],"plausible":[61],"model.":[62],"Since":[63,217],"biological":[64,193],"ODE":[65,146],"models":[66,98],"widely":[68,208],"distributed":[69,209],"parameters":[70],"due":[71],"to,":[72],"e.g.":[73],"biologic":[74],"variability":[75],"or":[76],"experimental":[77,87,238],"variations,":[78],"model":[79,91,125,131,156,170,227],"responses":[80],"become":[81],"distributed.":[82],"Therefore,":[83],"robust":[85,124,162,237],"design":[88,178,188],"(OED)":[89],"used":[95],"discriminate":[97],"based":[99],"on":[100],"their":[101],"response":[102,132,171],"probability":[103],"distribution":[104],"functions":[105],"(PDFs).":[106],"RESULTS:":[107],"In":[108],"work,":[110],"we":[111,148,173],"present":[112],"an":[113],"control-based":[115],"methodology":[116],"designing":[118],"stimulus":[120],"aimed":[122],"at":[123,250,261],"discrimination.":[126],"For":[127],"estimating":[128],"time-varying":[130],"PDF,":[133],"which":[134],"results":[135],"from":[136],"propagation":[139],"parameter":[142,210],"PDF":[143],"under":[144],"dynamics,":[147],"suggest":[149],"using":[150],"sigma-point":[152,199,219],"approach.":[153],"Using":[154],"overlap":[157],"(expected":[158],"likelihood)":[159],"as":[160],"criterion":[164],"measure":[166],"dissimilarities":[167],"between":[168],"expected":[169],"PDFs,":[172],"benchmark":[174],"proposed":[176],"approach":[179,203,220],"against":[180],"linearization":[181,202],"respect":[183],"prediction":[185],"accuracy":[186],"quality":[189],"two":[191],"networks.":[195],"As":[196],"shown,":[197],"outperforms":[200],"case":[206],"sets":[211],"and/or":[212],"existing":[213],"multiple":[214],"steady":[215],"states.":[216],"scales":[221],"linearly":[222],"number":[225],"parameter,":[228],"it":[229],"applied":[232],"systems":[235],"planning.":[239],"AVAILABILITY:":[240],"An":[241],"implementation":[242],"method":[245],"MATLAB/AMPL":[247],"is":[248],"available":[249,260],"http://www.uni-magdeburg.de/ivt/svt/person/rf/roed.html.":[251],"CONTACT:":[252],"flassig@mpi-magdeburg.mpg.de":[253],"SUPPLEMENTARY":[254],"INFORMATION:":[255],"Supplementary":[256],"are":[258,259],"Bioinformatics":[262],"online.":[263]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"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":2018,"cited_by_count":6},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}