{"id":"https://openalex.org/W2032978045","doi":"https://doi.org/10.1109/iccabs.2012.6182639","title":"A robust, library-based, optimization-driven method for automatic gene circuit design","display_name":"A robust, library-based, optimization-driven method for automatic gene circuit design","publication_year":2012,"publication_date":"2012-02-01","ids":{"openalex":"https://openalex.org/W2032978045","doi":"https://doi.org/10.1109/iccabs.2012.6182639","mag":"2032978045"},"language":"en","primary_location":{"id":"doi:10.1109/iccabs.2012.6182639","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2012.6182639","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS)","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/A5098500719","display_name":"Linh Hunyh","orcid":null},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Linh Hunyh","raw_affiliation_strings":["Department of Computer Science & UC Davis Genome Center, University of California, Davis, Davis, CA, USA","Department of Computer Science & UC Davis Genome Center, University of California, Davis, 95620, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science & UC Davis Genome Center, University of California, Davis, Davis, CA, USA","institution_ids":["https://openalex.org/I84218800"]},{"raw_affiliation_string":"Department of Computer Science & UC Davis Genome Center, University of California, Davis, 95620, USA#TAB#","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004351739","display_name":"Ilias Tagkopoulos","orcid":"https://orcid.org/0000-0003-1104-7616"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ilias Tagkopoulos","raw_affiliation_strings":["Department of Computer Science & UC Davis Genome Center, University of California, Davis, Davis, CA, USA","Department of Computer Science & UC Davis Genome Center, University of California, Davis, 95620, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science & UC Davis Genome Center, University of California, Davis, Davis, CA, USA","institution_ids":["https://openalex.org/I84218800"]},{"raw_affiliation_string":"Department of Computer Science & UC Davis Genome Center, University of California, Davis, 95620, USA#TAB#","institution_ids":["https://openalex.org/I84218800"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5098500719"],"corresponding_institution_ids":["https://openalex.org/I84218800"],"apc_list":null,"apc_paid":null,"fwci":0.1313,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.50899903,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9994000196456909,"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":0.9994000196456909,"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":0.9970999956130981,"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":0.9909999966621399,"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/computer-science","display_name":"Computer science","score":0.7029731273651123},{"id":"https://openalex.org/keywords/synthetic-biology","display_name":"Synthetic biology","score":0.599723219871521},{"id":"https://openalex.org/keywords/electronic-circuit","display_name":"Electronic circuit","score":0.5929453372955322},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.5441608428955078},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.536579966545105},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5299181938171387},{"id":"https://openalex.org/keywords/convergence","display_name":"Convergence (economics)","score":0.4758448600769043},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.43152594566345215},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.423740953207016},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.3940238058567047},{"id":"https://openalex.org/keywords/electronic-engineering","display_name":"Electronic engineering","score":0.34520918130874634},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18077966570854187},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1643829643726349},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1280083954334259},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12257090210914612}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7029731273651123},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.599723219871521},{"id":"https://openalex.org/C134146338","wikidata":"https://www.wikidata.org/wiki/Q1815901","display_name":"Electronic circuit","level":2,"score":0.5929453372955322},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.5441608428955078},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.536579966545105},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5299181938171387},{"id":"https://openalex.org/C2777303404","wikidata":"https://www.wikidata.org/wiki/Q759757","display_name":"Convergence (economics)","level":2,"score":0.4758448600769043},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.43152594566345215},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.423740953207016},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.3940238058567047},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.34520918130874634},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18077966570854187},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1643829643726349},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1280083954334259},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12257090210914612},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"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},{"id":"https://openalex.org/C50522688","wikidata":"https://www.wikidata.org/wiki/Q189833","display_name":"Economic growth","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/iccabs.2012.6182639","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2012.6182639","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1537056303","https://openalex.org/W2001741445","https://openalex.org/W2013330518","https://openalex.org/W2016235466","https://openalex.org/W2019998456","https://openalex.org/W2029237398","https://openalex.org/W2039679384","https://openalex.org/W2077480167","https://openalex.org/W2080233018","https://openalex.org/W2084405349","https://openalex.org/W2106876741","https://openalex.org/W2130912501","https://openalex.org/W2134759932","https://openalex.org/W2158979830","https://openalex.org/W2167879794","https://openalex.org/W2168142693","https://openalex.org/W6632207536"],"related_works":["https://openalex.org/W3141738981","https://openalex.org/W2099102792","https://openalex.org/W4254255930","https://openalex.org/W634364059","https://openalex.org/W4377564965","https://openalex.org/W2009687716","https://openalex.org/W4205129443","https://openalex.org/W1987791267","https://openalex.org/W71063077","https://openalex.org/W2011675579"],"abstract_inverted_index":{"Automatic":[0],"design":[1,160],"of":[2,16,55,66,161],"synthetic":[3,10,34,100,134],"circuits":[4,35,101,163],"is":[5,149],"a":[6,39,49,70,78,90,94,116,127,133,150,153],"major":[7],"challenge":[8],"in":[9,24,89,126],"biology,":[11],"which":[12],"promises":[13],"rapid":[14,128],"development":[15],"standardized,":[17],"scalable,":[18],"and":[19,43,52,77,93,115,129,141,168],"modular":[20],"designs.":[21],"Current":[22],"methods":[23],"the":[25,53,63,86,138,158],"field":[26],"mostly":[27],"rely":[28],"on":[29],"heuristic":[30],"algorithms":[31],"for":[32,157],"finding":[33],"that":[36,102,136],"function":[37],"within":[38],"specific":[40],"parameter":[41],"range,":[42],"user-defined":[44,75,165],"constraints.":[45,169],"Here,":[46],"we":[47],"introduce":[48],"three-phase":[50],"framework,":[51],"technique":[54],"mixed":[56],"integer":[57],"nonlinear":[58],"programming":[59],"(MINLP)":[60],"to":[61,69,132],"find":[62],"optimal":[64],"assignment":[65],"biological":[67,162],"parts":[68],"fixed":[71],"circuit":[72,135],"topology,":[73],"given":[74],"constraints":[76],"desired":[79,139],"steady-state":[80],"or":[81],"temporal":[82,142,166],"profile.":[83],"We":[84],"evaluated":[85],"proposed":[87],"framework":[88,124,156],"toggle":[91],"switch":[92],"band":[95],"detector":[96],"circuit,":[97],"two":[98],"non-linear":[99],"have":[103],"been":[104],"experimentally":[105,110],"constructed":[106],"before.":[107],"By":[108],"using":[109],"characterized":[111],"mutant":[112],"promoter":[113],"libraries":[114],"user":[117],"defined":[118],"topology":[119],"as":[120],"inputs,":[121],"our":[122],"optimization":[123],"results":[125],"reproducible":[130],"convergence":[131],"exhibits":[137],"characteristics":[140],"expression":[143],"profiles.":[144],"The":[145],"work":[146],"described":[147],"here":[148],"step":[151],"towards":[152],"unifying,":[154],"biologically-relevant":[155],"automated":[159],"with":[164],"profiles":[167]},"counts_by_year":[{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
