{"id":"https://openalex.org/W3012628579","doi":"https://doi.org/10.1007/978-3-030-51372-6_11","title":"Rewriting Theory for the Life Sciences: A Unifying Theory of CTMC Semantics","display_name":"Rewriting Theory for the Life Sciences: A Unifying Theory of CTMC Semantics","publication_year":2020,"publication_date":"2020-01-01","ids":{"openalex":"https://openalex.org/W3012628579","doi":"https://doi.org/10.1007/978-3-030-51372-6_11","mag":"3012628579"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-030-51372-6_11","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-030-51372-6_11","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2003.09395","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016179123","display_name":"Nicolas Behr","orcid":"https://orcid.org/0000-0002-8738-5040"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I4210098463","display_name":"Center for Research and Interdisciplinarity","ror":"https://ror.org/00zbj9525","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210098463"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Nicolas Behr","raw_affiliation_strings":["Center for Research and Interdisciplinarity (CRI), Universite de Paris, INSERM U1284, Paris, France"],"raw_orcid":"https://orcid.org/0000-0002-8738-5040","affiliations":[{"raw_affiliation_string":"Center for Research and Interdisciplinarity (CRI), Universite de Paris, INSERM U1284, Paris, France","institution_ids":["https://openalex.org/I4210098463","https://openalex.org/I204730241","https://openalex.org/I154526488"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077182970","display_name":"Jean Krivine","orcid":"https://orcid.org/0000-0001-7261-7462"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I4210117673","display_name":"Institut de Recherche en Informatique Fondamentale","ror":"https://ror.org/02krdtz55","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210089394","https://openalex.org/I4210117673","https://openalex.org/I4210139971"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jean Krivine","raw_affiliation_strings":["Institut de Recherche en Informatique Fondamentale (IRIF), Universit\u00e9 de Paris, CNRS UMR 8243, Paris Cedex 13, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut de Recherche en Informatique Fondamentale (IRIF), Universit\u00e9 de Paris, CNRS UMR 8243, Paris Cedex 13, France","institution_ids":["https://openalex.org/I4210117673","https://openalex.org/I204730241","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jakob L. Andersen","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jakob L. Andersen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":null,"display_name":"Daniel Merkle","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Daniel Merkle","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5016179123"],"corresponding_institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210098463"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":null,"fwci":0.0836,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.43178933,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"884","issue":null,"first_page":"185","last_page":"115"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9865999817848206,"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":0.9865999817848206,"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/T12029","display_name":"DNA and Biological Computing","score":0.9757999777793884,"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/T11450","display_name":"Model-Driven Software Engineering Techniques","score":0.9634000062942505,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/rewriting","display_name":"Rewriting","score":0.9564675092697144},{"id":"https://openalex.org/keywords/formalism","display_name":"Formalism (music)","score":0.5880080461502075},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.570472002029419},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5556733012199402},{"id":"https://openalex.org/keywords/confluence","display_name":"Confluence","score":0.5125343799591064},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.5073582530021667},{"id":"https://openalex.org/keywords/algebra-over-a-field","display_name":"Algebra over a field","score":0.4197773337364197},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.35330772399902344},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3180044889450073},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2743077278137207},{"id":"https://openalex.org/keywords/pure-mathematics","display_name":"Pure mathematics","score":0.25564882159233093}],"concepts":[{"id":"https://openalex.org/C154690210","wikidata":"https://www.wikidata.org/wiki/Q1668499","display_name":"Rewriting","level":2,"score":0.9564675092697144},{"id":"https://openalex.org/C73301696","wikidata":"https://www.wikidata.org/wiki/Q5469984","display_name":"Formalism (music)","level":3,"score":0.5880080461502075},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.570472002029419},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5556733012199402},{"id":"https://openalex.org/C77906462","wikidata":"https://www.wikidata.org/wiki/Q1140902","display_name":"Confluence","level":2,"score":0.5125343799591064},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.5073582530021667},{"id":"https://openalex.org/C136119220","wikidata":"https://www.wikidata.org/wiki/Q1000660","display_name":"Algebra over a field","level":2,"score":0.4197773337364197},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35330772399902344},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3180044889450073},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2743077278137207},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.25564882159233093},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C558565934","wikidata":"https://www.wikidata.org/wiki/Q2743","display_name":"Musical","level":2,"score":0.0}],"mesh":[],"locations_count":9,"locations":[{"id":"doi:10.1007/978-3-030-51372-6_11","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-030-51372-6_11","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},{"id":"doi:10.1016/j.tcs.2021.07.026","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.tcs.2021.07.026","pdf_url":null,"source":{"id":"https://openalex.org/S90727058","display_name":"Theoretical Computer Science","issn_l":"0304-3975","issn":["0304-3975","1879-2294"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Theoretical Computer Science","raw_type":"journal-article"},{"id":"pmh:oai:sdu.dk:openaire_cris_publications/dbd990cf-d7b6-4fc3-8bd7-218c43396bfb","is_oa":false,"landing_page_url":"https://portal.findresearcher.sdu.dk/da/publications/dbd990cf-d7b6-4fc3-8bd7-218c43396bfb","pdf_url":null,"source":{"id":"https://openalex.org/S4306400423","display_name":"University of Southern Denmark Research Portal (University of Southern Denmark)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I177969490","host_organization_name":"University of Southern Denmark","host_organization_lineage":["https://openalex.org/I177969490"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Behr, N, Krivine, J, Andersen, J L & Merkle, D 2021, 'Rewriting theory for the life sciences : A unifying theory of CTMC semantics', Theoretical Computer Science, vol. 884, pp. 68-115. https://doi.org/10.1016/j.tcs.2021.07.026","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:arXiv.org:2003.09395","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2003.09395","pdf_url":"https://arxiv.org/pdf/2003.09395","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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"},{"id":"mag:3012628579","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/2003.09395v2","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"pmh:oai:HAL:hal-02920023v1","is_oa":true,"landing_page_url":"https://hal.science/hal-02920023","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"International Conference on Graph Transformation 2020, Jun 2020, Bergen, Norway. pp.185-202, &#x27E8;10.1007/978-3-030-51372-6_11&#x27E9;","raw_type":"Conference papers"},{"id":"pmh:oai:HAL:hal-03835365v1","is_oa":false,"landing_page_url":"https://hal.science/hal-03835365","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":"Theoretical Computer Science, 2021, 884, pp.68-115. &#x27E8;10.1016/j.tcs.2021.07.026&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:7314866","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7314866","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Graph Transformation","raw_type":"Text"},{"id":"doi:10.48550/arxiv.2003.09395","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2003.09395","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2003.09395","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2003.09395","pdf_url":"https://arxiv.org/pdf/2003.09395","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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"},"sustainable_development_goals":[{"display_name":"Responsible consumption and production","score":0.49000000953674316,"id":"https://metadata.un.org/sdg/12"}],"awards":[{"id":"https://openalex.org/G1032663478","display_name":null,"funder_award_id":"NNF19OC0057834","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G2166313133","display_name":null,"funder_award_id":"DFF-0135-00420B","funder_id":"https://openalex.org/F4320338218","funder_display_name":"Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences"},{"id":"https://openalex.org/G2533613479","display_name":null,"funder_award_id":"DFF-7014-00041","funder_id":"https://openalex.org/F4320338218","funder_display_name":"Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences"}],"funders":[{"id":"https://openalex.org/F4320322928","display_name":"Danmarks Frie Forskningsfond","ror":"https://ror.org/02sptwz63"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"},{"id":"https://openalex.org/F4320327387","display_name":"Danmarks Frie Forskningsfond","ror":null},{"id":"https://openalex.org/F4320338218","display_name":"Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W184396603","https://openalex.org/W1510054038","https://openalex.org/W1548957673","https://openalex.org/W1589305078","https://openalex.org/W1787979754","https://openalex.org/W1836559177","https://openalex.org/W1843363608","https://openalex.org/W1892851289","https://openalex.org/W1972476072","https://openalex.org/W1986649132","https://openalex.org/W2027857026","https://openalex.org/W2028130113","https://openalex.org/W2030190879","https://openalex.org/W2040860090","https://openalex.org/W2054776476","https://openalex.org/W2079370090","https://openalex.org/W2104525378","https://openalex.org/W2106925277","https://openalex.org/W2117043211","https://openalex.org/W2126852846","https://openalex.org/W2260741225","https://openalex.org/W2466928235","https://openalex.org/W2467494155","https://openalex.org/W2487649280","https://openalex.org/W2585447181","https://openalex.org/W2737885945","https://openalex.org/W2772491215","https://openalex.org/W2807744179","https://openalex.org/W2938043835","https://openalex.org/W2938952696","https://openalex.org/W2942407691","https://openalex.org/W2946983868","https://openalex.org/W2963912089","https://openalex.org/W2963964585","https://openalex.org/W3037418945","https://openalex.org/W3082689362","https://openalex.org/W3098051788","https://openalex.org/W3105422096","https://openalex.org/W4205605414","https://openalex.org/W4205916380","https://openalex.org/W6603252803","https://openalex.org/W6626735091","https://openalex.org/W6635029139","https://openalex.org/W6635261825","https://openalex.org/W6636058210","https://openalex.org/W6638030428","https://openalex.org/W6638613852","https://openalex.org/W6638766259","https://openalex.org/W6639527639","https://openalex.org/W6675861790","https://openalex.org/W6678677553","https://openalex.org/W6692837339","https://openalex.org/W6696743178","https://openalex.org/W6719611203","https://openalex.org/W6719974709","https://openalex.org/W6734383943","https://openalex.org/W6752725924","https://openalex.org/W6761464382","https://openalex.org/W6762956106","https://openalex.org/W6781790302","https://openalex.org/W6785179808","https://openalex.org/W6786230864","https://openalex.org/W6805832723"],"related_works":["https://openalex.org/W3037418945","https://openalex.org/W3170839469","https://openalex.org/W3129098456","https://openalex.org/W153083962","https://openalex.org/W2938952696","https://openalex.org/W3085882190","https://openalex.org/W3109435874","https://openalex.org/W2046868815","https://openalex.org/W3098051788","https://openalex.org/W2040598439","https://openalex.org/W3092058530","https://openalex.org/W3143469549","https://openalex.org/W2922196358","https://openalex.org/W2779136310","https://openalex.org/W2144940322","https://openalex.org/W2591718150","https://openalex.org/W2047273923","https://openalex.org/W2155770035","https://openalex.org/W2185509723","https://openalex.org/W2596768015"],"abstract_inverted_index":null,"counts_by_year":[{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
