{"id":"https://openalex.org/W2092598996","doi":"https://doi.org/10.1109/tcbb.2014.2362531","title":"A Property-Driven Methodology for Formal Analysis of Synthetic Biology Systems","display_name":"A Property-Driven Methodology for Formal Analysis of Synthetic Biology Systems","publication_year":2014,"publication_date":"2014-10-09","ids":{"openalex":"https://openalex.org/W2092598996","doi":"https://doi.org/10.1109/tcbb.2014.2362531","mag":"2092598996","pmid":"https://pubmed.ncbi.nlm.nih.gov/26357223"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2014.2362531","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2362531","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":true,"oa_status":"green","oa_url":"https://bradscholars.brad.ac.uk/bitstreams/579d7229-3a04-440a-9774-1553e8d4c1ac/download","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037997843","display_name":"Savas Konur","orcid":"https://orcid.org/0000-0002-0642-9452"},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Savas Konur","raw_affiliation_strings":["Department of Computer Science, University of Sheffield, Sheffield, United Kingdom","Department of Computer Science, University of Sheffield, Sheffield, United Kingdom,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Sheffield, Sheffield, United Kingdom","institution_ids":["https://openalex.org/I91136226"]},{"raw_affiliation_string":"Department of Computer Science, University of Sheffield, Sheffield, United Kingdom,","institution_ids":["https://openalex.org/I91136226"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032331047","display_name":"Marian Gheorghe","orcid":"https://orcid.org/0000-0002-2409-4959"},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Marian Gheorghe","raw_affiliation_strings":["Department of Computer Science, University of Sheffield, Sheffield, United Kingdom","Department of Computer Science, University of Sheffield, Sheffield, United Kingdom,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Sheffield, Sheffield, United Kingdom","institution_ids":["https://openalex.org/I91136226"]},{"raw_affiliation_string":"Department of Computer Science, University of Sheffield, Sheffield, United Kingdom,","institution_ids":["https://openalex.org/I91136226"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I91136226"],"apc_list":{"value":2645,"currency":"USD","value_usd":2645},"apc_paid":null,"fwci":0.8073,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.71680896,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"12","issue":"2","first_page":"360","last_page":"371"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9976000189781189,"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":0.9976000189781189,"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/T10142","display_name":"Formal Methods in Verification","score":0.9955999851226807,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.9901000261306763,"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/synthetic-biology","display_name":"Synthetic biology","score":0.7631615400314331},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.6594343185424805},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6261993646621704},{"id":"https://openalex.org/keywords/formal-methods","display_name":"Formal methods","score":0.5904418230056763},{"id":"https://openalex.org/keywords/model-checking","display_name":"Model checking","score":0.5371158123016357},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5231884121894836},{"id":"https://openalex.org/keywords/generator","display_name":"Generator (circuit theory)","score":0.4833931028842926},{"id":"https://openalex.org/keywords/perspective","display_name":"Perspective (graphical)","score":0.46913406252861023},{"id":"https://openalex.org/keywords/modelling-biological-systems","display_name":"Modelling biological systems","score":0.4384315609931946},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3693997263908386},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.33307725191116333},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.32607966661453247},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2082584798336029},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.20536404848098755},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2011171281337738},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.11403441429138184},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.09749111533164978}],"concepts":[{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.7631615400314331},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.6594343185424805},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6261993646621704},{"id":"https://openalex.org/C75606506","wikidata":"https://www.wikidata.org/wiki/Q1049183","display_name":"Formal methods","level":2,"score":0.5904418230056763},{"id":"https://openalex.org/C110251889","wikidata":"https://www.wikidata.org/wiki/Q1569697","display_name":"Model checking","level":2,"score":0.5371158123016357},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5231884121894836},{"id":"https://openalex.org/C2780992000","wikidata":"https://www.wikidata.org/wiki/Q17016113","display_name":"Generator (circuit theory)","level":3,"score":0.4833931028842926},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.46913406252861023},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.4384315609931946},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3693997263908386},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.33307725191116333},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.32607966661453247},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2082584798336029},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.20536404848098755},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2011171281337738},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.11403441429138184},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.09749111533164978},{"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/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","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":4,"locations":[{"id":"doi:10.1109/tcbb.2014.2362531","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2362531","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:26357223","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26357223","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":"Journal Article"},{"id":"pmh:oai:bradscholars.brad.ac.uk:10454/8708.2","is_oa":false,"landing_page_url":"https://bradscholars.brad.ac.uk/handle/10454/8708.2","pdf_url":null,"source":{"id":"https://openalex.org/S4306401846","display_name":"Bradford Scholars (University of Bradford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139894009","host_organization_name":"University of Bradford","host_organization_lineage":["https://openalex.org/I139894009"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:bradscholars.brad.ac.uk:10454/8708","is_oa":true,"landing_page_url":"http://hdl.handle.net/10454/8708","pdf_url":"https://bradscholars.brad.ac.uk/bitstreams/579d7229-3a04-440a-9774-1553e8d4c1ac/download","source":{"id":"https://openalex.org/S4306401846","display_name":"Bradford Scholars (University of Bradford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139894009","host_organization_name":"University of Bradford","host_organization_lineage":["https://openalex.org/I139894009"],"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":"Article"}],"best_oa_location":{"id":"pmh:oai:bradscholars.brad.ac.uk:10454/8708","is_oa":true,"landing_page_url":"http://hdl.handle.net/10454/8708","pdf_url":"https://bradscholars.brad.ac.uk/bitstreams/579d7229-3a04-440a-9774-1553e8d4c1ac/download","source":{"id":"https://openalex.org/S4306401846","display_name":"Bradford Scholars (University of Bradford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139894009","host_organization_name":"University of Bradford","host_organization_lineage":["https://openalex.org/I139894009"],"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":"Article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1430276424","display_name":null,"funder_award_id":"PN-II-ID-PCE-2011-3-0688","funder_id":"https://openalex.org/F4320308292","funder_display_name":"Corporation for National and Community Service"},{"id":"https://openalex.org/G1524875618","display_name":null,"funder_award_id":"EP/I031812/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G502459198","display_name":null,"funder_award_id":"EP/I031642/2","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G7816206975","display_name":"ROADBLOCK: Towards Programmable Defensive Bacterial Coatings &amp; Skins","funder_award_id":"EP/I031812/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G939259430","display_name":null,"funder_award_id":"EP/I031642/2","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320308292","display_name":"Corporation for National and Community Service","ror":"https://ror.org/00p8rjs69"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2092598996.pdf","grobid_xml":"https://content.openalex.org/works/W2092598996.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W93312097","https://openalex.org/W138443365","https://openalex.org/W139209134","https://openalex.org/W139322006","https://openalex.org/W206643225","https://openalex.org/W251988146","https://openalex.org/W1489391022","https://openalex.org/W1504952131","https://openalex.org/W1520566118","https://openalex.org/W1566900355","https://openalex.org/W1576177385","https://openalex.org/W1599416730","https://openalex.org/W1748979965","https://openalex.org/W1804287018","https://openalex.org/W1859458367","https://openalex.org/W1922112848","https://openalex.org/W1977624796","https://openalex.org/W1983350265","https://openalex.org/W1984936841","https://openalex.org/W1996832037","https://openalex.org/W2002956917","https://openalex.org/W2005998857","https://openalex.org/W2022607335","https://openalex.org/W2042321087","https://openalex.org/W2060551079","https://openalex.org/W2065754558","https://openalex.org/W2081556416","https://openalex.org/W2084154666","https://openalex.org/W2092008396","https://openalex.org/W2103256803","https://openalex.org/W2110062879","https://openalex.org/W2110908283","https://openalex.org/W2111759547","https://openalex.org/W2115309705","https://openalex.org/W2117949454","https://openalex.org/W2118039525","https://openalex.org/W2126855067","https://openalex.org/W2131463591","https://openalex.org/W2131992538","https://openalex.org/W2138153242","https://openalex.org/W2139768072","https://openalex.org/W2141881497","https://openalex.org/W2148895036","https://openalex.org/W2152863619","https://openalex.org/W2158708642","https://openalex.org/W2172140874","https://openalex.org/W2185071254","https://openalex.org/W2322912787","https://openalex.org/W2587122255","https://openalex.org/W2672830324","https://openalex.org/W4285719527","https://openalex.org/W6608519349","https://openalex.org/W6609519101","https://openalex.org/W6633876618","https://openalex.org/W6638434051","https://openalex.org/W6639015652","https://openalex.org/W6640078909","https://openalex.org/W6700970844"],"related_works":["https://openalex.org/W2338895903","https://openalex.org/W2024161258","https://openalex.org/W1911418903","https://openalex.org/W3044523069","https://openalex.org/W2126646394","https://openalex.org/W1982249722","https://openalex.org/W3144585500","https://openalex.org/W2057769265","https://openalex.org/W1987445442","https://openalex.org/W2211443823"],"abstract_inverted_index":{"This":[0],"paper":[1],"proposes":[2],"a":[3],"formal":[4],"methodology":[5,31],"to":[6,34,47,54],"analyse":[7,56],"bio-systems,":[8],"in":[9],"particular":[10],"synthetic":[11,36,60],"biology":[12,61],"systems.":[13,62],"An":[14],"integrative":[15],"analysis":[16],"perspective":[17],"combining":[18],"different":[19,25],"model":[20],"checking":[21],"approaches":[22],"based":[23],"on":[24],"property":[26],"categories":[27],"is":[28,32],"provided.":[29],"The":[30],"applied":[33],"the":[35,49],"pulse":[37],"generator":[38],"system":[39],"and":[40],"several":[41],"verification":[42],"experiments":[43],"are":[44],"carried":[45],"out":[46],"demonstrate":[48],"use":[50],"of":[51,59],"our":[52],"approach":[53],"formally":[55],"various":[57],"aspects":[58]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2}],"updated_date":"2026-08-25T07:29:55.448023","created_date":"2025-10-10T00:00:00"}
