{"id":"https://openalex.org/W2168569373","doi":"https://doi.org/10.1093/bioinformatics/btp200","title":"A general computational method for robustness analysis with applications to synthetic gene networks","display_name":"A general computational method for robustness analysis with applications to synthetic gene networks","publication_year":2009,"publication_date":"2009-05-27","ids":{"openalex":"https://openalex.org/W2168569373","doi":"https://doi.org/10.1093/bioinformatics/btp200","mag":"2168569373","pmid":"https://pubmed.ncbi.nlm.nih.gov/19477984"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp200","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp200","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i169/48990823/bioinformatics_25_12_i169.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/25/12/i169/48990823/bioinformatics_25_12_i169.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013710352","display_name":"Aur\u00e9lien Rizk","orcid":null},"institutions":[{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Aur\u00e9lien Rizk","raw_affiliation_strings":["INRIA Paris-Rocquencourt, 78153 Le Chesnay Cedex, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRIA Paris-Rocquencourt, 78153 Le Chesnay Cedex, France","institution_ids":["https://openalex.org/I1326498283"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051551664","display_name":"Gr\u00e9gory Batt","orcid":"https://orcid.org/0000-0003-1697-139X"},"institutions":[{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Gregory Batt","raw_affiliation_strings":["INRIA Paris-Rocquencourt, 78153 Le Chesnay Cedex, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRIA Paris-Rocquencourt, 78153 Le Chesnay Cedex, France","institution_ids":["https://openalex.org/I1326498283"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000983836","display_name":"Fran\u00e7ois Fages","orcid":"https://orcid.org/0000-0001-5650-8266"},"institutions":[{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Fran\u00e7ois Fages","raw_affiliation_strings":["INRIA Paris-Rocquencourt, 78153 Le Chesnay Cedex, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRIA Paris-Rocquencourt, 78153 Le Chesnay Cedex, France","institution_ids":["https://openalex.org/I1326498283"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003525513","display_name":"Sylvain Soliman","orcid":"https://orcid.org/0000-0001-5525-7418"},"institutions":[{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Sylvain Soliman","raw_affiliation_strings":["INRIA Paris-Rocquencourt, 78153 Le Chesnay Cedex, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRIA Paris-Rocquencourt, 78153 Le Chesnay Cedex, France","institution_ids":["https://openalex.org/I1326498283"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5051551664"],"corresponding_institution_ids":["https://openalex.org/I1326498283"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.5298,"has_fulltext":true,"cited_by_count":113,"citation_normalized_percentile":{"value":0.9364375,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"25","issue":"12","first_page":"i169","last_page":"i178"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9908999800682068,"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":0.9908999800682068,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.003000000026077032,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.0005000000237487257,"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/robustness","display_name":"Robustness (evolution)","score":0.8453357219696045},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6918593645095825},{"id":"https://openalex.org/keywords/timer","display_name":"Timer","score":0.647404670715332},{"id":"https://openalex.org/keywords/cascade","display_name":"Cascade","score":0.6146765947341919},{"id":"https://openalex.org/keywords/synthetic-biology","display_name":"Synthetic biology","score":0.4963448643684387},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.20347633957862854},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16258221864700317},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10421997308731079},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07042083144187927}],"concepts":[{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.8453357219696045},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6918593645095825},{"id":"https://openalex.org/C2776633867","wikidata":"https://www.wikidata.org/wiki/Q186612","display_name":"Timer","level":3,"score":0.647404670715332},{"id":"https://openalex.org/C34146451","wikidata":"https://www.wikidata.org/wiki/Q5048094","display_name":"Cascade","level":2,"score":0.6146765947341919},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.4963448643684387},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.20347633957862854},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16258221864700317},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10421997308731079},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07042083144187927},{"id":"https://openalex.org/C173018170","wikidata":"https://www.wikidata.org/wiki/Q165678","display_name":"Microcontroller","level":2,"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/C42360764","wikidata":"https://www.wikidata.org/wiki/Q83588","display_name":"Chemical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","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":6,"locations":[{"id":"doi:10.1093/bioinformatics/btp200","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp200","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i169/48990823/bioinformatics_25_12_i169.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19477984","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19477984","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:CiteSeerX.psu:10.1.1.156.2881","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.156.2881","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://pauillac.inria.fr/~fages/Papers/RBFS09ismb.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.358.4089","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.358.4089","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/68/4e/Bioinformatics_2009_Jun_15_25(12)_i169-i178.tar.gz","raw_type":"text"},{"id":"pmh:oai:HAL:inria-00419708v1","is_oa":false,"landing_page_url":"https://inria.hal.science/inria-00419708","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2009, 25 (12), pp.il69--il78. &#x27E8;10.1093/bioinformatics/btp200&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:1855985","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2687954","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp200","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp200","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i169/48990823/bioinformatics_25_12_i169.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320313934","display_name":"Institut national de recherche en informatique et en automatique (INRIA)","ror":"https://ror.org/02kvxyf05"},{"id":"https://openalex.org/F4320323910","display_name":"Institut National de la Recherche Agronomique","ror":"https://ror.org/01x3gbx83"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2168569373.pdf","grobid_xml":"https://content.openalex.org/works/W2168569373.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W1483606732","https://openalex.org/W1494737186","https://openalex.org/W1506101803","https://openalex.org/W1532361198","https://openalex.org/W1535073122","https://openalex.org/W1590804833","https://openalex.org/W1623155147","https://openalex.org/W1979833590","https://openalex.org/W1982583288","https://openalex.org/W2000163865","https://openalex.org/W2003512951","https://openalex.org/W2037689113","https://openalex.org/W2055613433","https://openalex.org/W2058618427","https://openalex.org/W2062873592","https://openalex.org/W2066440682","https://openalex.org/W2079604837","https://openalex.org/W2084332810","https://openalex.org/W2090249495","https://openalex.org/W2092309107","https://openalex.org/W2100790213","https://openalex.org/W2103331163","https://openalex.org/W2110071847","https://openalex.org/W2112036188","https://openalex.org/W2117056464","https://openalex.org/W2119510512","https://openalex.org/W2121149194","https://openalex.org/W2128952742","https://openalex.org/W2131463591","https://openalex.org/W2132750992","https://openalex.org/W2132817950","https://openalex.org/W2133254839","https://openalex.org/W2135852310","https://openalex.org/W2137510998","https://openalex.org/W2139629468","https://openalex.org/W2141977920","https://openalex.org/W2142072523","https://openalex.org/W2143197862","https://openalex.org/W2147777139","https://openalex.org/W2166499263","https://openalex.org/W2170592382","https://openalex.org/W2171501814","https://openalex.org/W2396555304","https://openalex.org/W3011730451","https://openalex.org/W4211017114","https://openalex.org/W6635515983","https://openalex.org/W6636501790","https://openalex.org/W6665183450","https://openalex.org/W6684974061"],"related_works":["https://openalex.org/W2113348537","https://openalex.org/W1570447736","https://openalex.org/W2367062657","https://openalex.org/W4281635263","https://openalex.org/W2121898229","https://openalex.org/W4376605043","https://openalex.org/W2102710619","https://openalex.org/W2398603113","https://openalex.org/W2356212209","https://openalex.org/W2168569373"],"abstract_inverted_index":{"MOTIVATION:":[0],"Robustness":[1,30],"is":[2,18,31,127],"the":[3,13,21,42,101,105,133,136,162],"capacity":[4],"of":[5,15,24,45,48,64,104,107,117,124,135,139,159],"a":[6,10,46,61,91,108,114,140,149],"system":[7],"to":[8,68,81,113],"maintain":[9],"function":[11,71],"in":[12,34,73,97],"face":[14],"perturbations.":[16,118],"It":[17],"essential":[19],"for":[20,100,152],"correct":[22],"functioning":[23],"natural":[25],"and":[26,80,85,94,121,131,161],"engineered":[27],"biological":[28,49,70,122,150],"systems.":[29],"generally":[32],"defined":[33],"an":[35,95],"ad":[36],"hoc,":[37],"problem-dependent":[38],"manner,":[39],"thus":[40],"hampering":[41],"fruitful":[43],"development":[44],"theory":[47],"robustness,":[50],"recently":[51],"advocated":[52],"by":[53,129],"Kitano.":[54],"RESULTS:":[55],"In":[56],"this":[57],"article,":[58],"we":[59,89],"propose":[60,90],"general":[62],"definition":[63],"robustness":[65,106,134],"that":[66,144],"applies":[67],"any":[69],"expressible":[72],"temporal":[74,78],"logic":[75],"LTL":[76],"(linear":[77],"logic),":[79],"broad":[82],"model":[83,165],"classes":[84],"perturbation":[86],"types.":[87],"Moreover,":[88],"computational":[92],"approach":[93,126],"implementation":[96],"BIOCHAM":[98,160],"2.8":[99,158],"automated":[102],"estimation":[103],"given":[109,115],"behavior":[110,138],"with":[111],"respect":[112],"set":[116],"The":[119],"applicability":[120],"relevance":[123],"our":[125],"demonstrated":[128],"testing":[130],"improving":[132],"timed":[137],"synthetic":[141,153],"transcriptional":[142,163],"cascade":[143,164],"could":[145],"be":[146],"used":[147],"as":[148],"timer":[151],"biology":[154],"applications.":[155],"AVAILABILITY:":[156],"Version":[157],"are":[166],"available":[167],"at":[168],"http://contraintes.inria.fr/BIOCHAM/.":[169]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":14},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":15},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":6}],"updated_date":"2026-08-08T01:25:22.217667","created_date":"2025-10-10T00:00:00"}
