{"id":"https://openalex.org/W2001698737","doi":"https://doi.org/10.1109/tcbb.2014.2372790","title":"Systematic Biological Filter Design with a Desired I/O Filtering Response Based on Promoter-RBS Libraries","display_name":"Systematic Biological Filter Design with a Desired I/O Filtering Response Based on Promoter-RBS Libraries","publication_year":2014,"publication_date":"2014-11-20","ids":{"openalex":"https://openalex.org/W2001698737","doi":"https://doi.org/10.1109/tcbb.2014.2372790","mag":"2001698737","pmid":"https://pubmed.ncbi.nlm.nih.gov/26357282"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2014.2372790","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2372790","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/A5109931967","display_name":"Chih\u2010Yuan Hsu","orcid":null},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Chih-Yuan Hsu","raw_affiliation_strings":["Lab of Control and Systems Biology, Department of Electrical Engineering","Lab of Genetic Circuit Design, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lab of Control and Systems Biology, Department of Electrical Engineering","institution_ids":[]},{"raw_affiliation_string":"Lab of Genetic Circuit Design, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023171570","display_name":"Zhen-Ming Pan","orcid":null},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Zhen-Ming Pan","raw_affiliation_strings":["Lab of Control and Systems Biology, National Tsing Hua University, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lab of Control and Systems Biology, National Tsing Hua University, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026686544","display_name":"Rei-Hsing Hu","orcid":null},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Rei-Hsing Hu","raw_affiliation_strings":["Lab of Genetic Circuit Design, National Tsing Hua University, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lab of Genetic Circuit Design, National Tsing Hua University, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103036910","display_name":"Chih-Chun Chang","orcid":"https://orcid.org/0000-0002-2891-8804"},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Chih-Chun Chang","raw_affiliation_strings":["Lab of Genetic Circuit Design, National Tsing Hua University, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lab of Genetic Circuit Design, National Tsing Hua University, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071219800","display_name":"Hsiao-Chun Cheng","orcid":null},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Hsiao-Chun Cheng","raw_affiliation_strings":["Lab of Genetic Circuit Design, National Tsing Hua University, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lab of Genetic Circuit Design, National Tsing Hua University, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101909683","display_name":"Che Lin","orcid":"https://orcid.org/0000-0002-8564-5793"},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Che Lin","raw_affiliation_strings":["Institute of Communications Engineering, National Tsing Hua University, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Communications Engineering, National Tsing Hua University, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038219293","display_name":"Bor\u2010Sen Chen","orcid":"https://orcid.org/0000-0003-1644-6106"},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Bor-Sen Chen","raw_affiliation_strings":["Lab of Control and Systems Biology, Department of Electrical Engineering","Lab of Genetic Circuit Design, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lab of Control and Systems Biology, Department of Electrical Engineering","institution_ids":[]},{"raw_affiliation_string":"Lab of Genetic Circuit Design, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I25846049"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I25846049"],"apc_list":null,"apc_paid":null,"fwci":0.39,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.59645098,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"12","issue":"3","first_page":"712","last_page":"725"},"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":0.9957000017166138,"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":0.989799976348877,"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/cascade","display_name":"Cascade","score":0.7338331341743469},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.6638185381889343},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.4645167887210846},{"id":"https://openalex.org/keywords/synthetic-biology","display_name":"Synthetic biology","score":0.4485052824020386},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43346500396728516},{"id":"https://openalex.org/keywords/control-theory","display_name":"Control theory (sociology)","score":0.41860780119895935},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3621554970741272},{"id":"https://openalex.org/keywords/electronic-engineering","display_name":"Electronic engineering","score":0.3330753743648529},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.3116747736930847},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20737719535827637},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.20241165161132812},{"id":"https://openalex.org/keywords/control","display_name":"Control (management)","score":0.1680087447166443},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.07594761252403259},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.07098916172981262}],"concepts":[{"id":"https://openalex.org/C34146451","wikidata":"https://www.wikidata.org/wiki/Q5048094","display_name":"Cascade","level":2,"score":0.7338331341743469},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.6638185381889343},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.4645167887210846},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.4485052824020386},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43346500396728516},{"id":"https://openalex.org/C47446073","wikidata":"https://www.wikidata.org/wiki/Q5165890","display_name":"Control theory (sociology)","level":3,"score":0.41860780119895935},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3621554970741272},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.3330753743648529},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.3116747736930847},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20737719535827637},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.20241165161132812},{"id":"https://openalex.org/C2775924081","wikidata":"https://www.wikidata.org/wiki/Q55608371","display_name":"Control (management)","level":2,"score":0.1680087447166443},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.07594761252403259},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.07098916172981262},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","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}],"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2014.2372790","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2372790","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:26357282","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26357282","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":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2294976436","display_name":null,"funder_award_id":"NSC 103-2745-E-007-001-ASP","funder_id":"https://openalex.org/F4320321040","funder_display_name":"National Science Council"},{"id":"https://openalex.org/G31183732","display_name":null,"funder_award_id":"NSC-102-2745-E-007-001-ASP","funder_id":"https://openalex.org/F4320321040","funder_display_name":"National Science Council"}],"funders":[{"id":"https://openalex.org/F4320321040","display_name":"National Science Council","ror":"https://ror.org/02kv4zf79"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1492868033","https://openalex.org/W1547106545","https://openalex.org/W1645305843","https://openalex.org/W1965205049","https://openalex.org/W1977624796","https://openalex.org/W1982228455","https://openalex.org/W1985555064","https://openalex.org/W1989983571","https://openalex.org/W1991081400","https://openalex.org/W2000109449","https://openalex.org/W2001426985","https://openalex.org/W2013330518","https://openalex.org/W2021405930","https://openalex.org/W2022891974","https://openalex.org/W2023525048","https://openalex.org/W2027576577","https://openalex.org/W2028569720","https://openalex.org/W2028603053","https://openalex.org/W2032408161","https://openalex.org/W2041985017","https://openalex.org/W2043096047","https://openalex.org/W2044968161","https://openalex.org/W2045095831","https://openalex.org/W2047360542","https://openalex.org/W2047882868","https://openalex.org/W2057993765","https://openalex.org/W2071523283","https://openalex.org/W2082398508","https://openalex.org/W2089022150","https://openalex.org/W2089832080","https://openalex.org/W2091731123","https://openalex.org/W2105631762","https://openalex.org/W2105662588","https://openalex.org/W2106876741","https://openalex.org/W2113226210","https://openalex.org/W2130912501","https://openalex.org/W2132207273","https://openalex.org/W2132828256","https://openalex.org/W2134759932","https://openalex.org/W2143258942","https://openalex.org/W2144588155","https://openalex.org/W2149778176","https://openalex.org/W2159712401","https://openalex.org/W2166401033","https://openalex.org/W2167879794","https://openalex.org/W2325072505","https://openalex.org/W2480256690","https://openalex.org/W2904250082","https://openalex.org/W3023540311","https://openalex.org/W4211125927","https://openalex.org/W4233374826"],"related_works":["https://openalex.org/W2153719181","https://openalex.org/W1971748923","https://openalex.org/W2060986072","https://openalex.org/W1566155057","https://openalex.org/W2052574922","https://openalex.org/W2065045110","https://openalex.org/W64588465","https://openalex.org/W3120641340","https://openalex.org/W2117825986","https://openalex.org/W3134067061"],"abstract_inverted_index":{"In":[0,32],"this":[1],"study,":[2],"robust":[3,83,163],"biological":[4,39,84,99,125,153,166],"filters":[5,85],"with":[6],"an":[7,136],"external":[8],"control":[9,178],"to":[10,49,145,182],"match":[11,187],"a":[12,27,44,56,74,152,162,177],"desired":[13,148],"input/output":[14],"(I/O)":[15],"filtering":[16,192],"response":[17,59],"are":[18,96],"engineered":[19,169],"based":[20,156],"on":[21,157],"the":[22,33,38,62,65,106,121,147,158,172,184,189],"well-characterized":[23,93],"promoter-RBS":[24,94,113,138,173],"libraries":[25,95,175],"and":[26,54,104,108,135,176],"cascade":[28,131],"gene":[29,132],"circuit":[30],"topology.":[31],"field":[34],"of":[35,64,82,111,123,151],"synthetic":[36,124],"biology,":[37],"filter":[40,100,126,167],"system":[41],"serves":[42],"as":[43],"powerful":[45],"detector":[46],"or":[47,71],"sensor":[48],"sense":[50],"different":[51],"molecular":[52,67],"signals":[53],"produces":[55],"specific":[57],"output":[58],"only":[60],"if":[61],"concentration":[63,180],"input":[66],"signal":[68],"is":[69,86,127,140,168],"higher":[70],"lower":[72],"than":[73],"specified":[75,190],"threshold.":[76],"The":[77],"proposed":[78,159],"systematic":[79,160],"design":[80,101],"method":[81],"summarized":[87],"into":[88,129],"three":[89,130],"steps.":[90],"Firstly,":[91],"several":[92],"established":[97],"for":[98,142,188],"by":[102,170],"identifying":[103],"collecting":[105],"quantitative":[107],"qualitative":[109],"characteristics":[110],"their":[112],"components":[114],"via":[115],"nonlinear":[116],"parameter":[117],"estimation":[118],"method.":[119],"Then,":[120],"topology":[122],"decomposed":[128],"regulatory":[133],"modules,":[134],"appropriate":[137],"library":[139,181],"selected":[141],"each":[143],"module":[144],"achieve":[146,183],"I/O":[149,191],"specification":[150],"filter.":[154],"Finally,":[155],"method,":[161],"externally":[164],"tunable":[165],"searching":[171],"component":[174],"inducer":[179],"optimal":[185],"reference":[186],"response.":[193]},"counts_by_year":[{"year":2016,"cited_by_count":3}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
