{"id":"https://openalex.org/W1987369697","doi":"https://doi.org/10.1145/1839764.1839775","title":"Understanding signalling networks as collections of signal transduction pathways","display_name":"Understanding signalling networks as collections of signal transduction pathways","publication_year":2010,"publication_date":"2010-09-29","ids":{"openalex":"https://openalex.org/W1987369697","doi":"https://doi.org/10.1145/1839764.1839775","mag":"1987369697"},"language":"en","primary_location":{"id":"doi:10.1145/1839764.1839775","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1839764.1839775","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th International Conference on Computational Methods in Systems Biology","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/A5071721902","display_name":"Robin Donaldson","orcid":null},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Robin Donaldson","raw_affiliation_strings":["University of Glasgow, Glasgow, UK"],"affiliations":[{"raw_affiliation_string":"University of Glasgow, Glasgow, UK","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090498111","display_name":"Carolyn Talcott","orcid":"https://orcid.org/0000-0003-2845-7144"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]},{"id":"https://openalex.org/I4210099336","display_name":"Menlo School","ror":"https://ror.org/01240pn49","country_code":"US","type":"education","lineage":["https://openalex.org/I4210099336"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carolyn Talcott","raw_affiliation_strings":["SRI International, Menlo Park, CA","SRI International, Menlo Park,CA#TAB#"],"affiliations":[{"raw_affiliation_string":"SRI International, Menlo Park, CA","institution_ids":["https://openalex.org/I1298353152","https://openalex.org/I4210099336"]},{"raw_affiliation_string":"SRI International, Menlo Park,CA#TAB#","institution_ids":["https://openalex.org/I1298353152","https://openalex.org/I4210099336"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047480366","display_name":"Merrill Knapp","orcid":"https://orcid.org/0000-0003-1939-8672"},"institutions":[{"id":"https://openalex.org/I4210099336","display_name":"Menlo School","ror":"https://ror.org/01240pn49","country_code":"US","type":"education","lineage":["https://openalex.org/I4210099336"]},{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Merrill Knapp","raw_affiliation_strings":["SRI International, Menlo Park, CA","SRI International, Menlo Park,CA#TAB#"],"affiliations":[{"raw_affiliation_string":"SRI International, Menlo Park, CA","institution_ids":["https://openalex.org/I1298353152","https://openalex.org/I4210099336"]},{"raw_affiliation_string":"SRI International, Menlo Park,CA#TAB#","institution_ids":["https://openalex.org/I1298353152","https://openalex.org/I4210099336"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015862123","display_name":"Muffy Calder","orcid":"https://orcid.org/0000-0001-5033-7232"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Muffy Calder","raw_affiliation_strings":["University of Glasgow, Glasgow, UK"],"affiliations":[{"raw_affiliation_string":"University of Glasgow, Glasgow, UK","institution_ids":["https://openalex.org/I7882870"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5071721902"],"corresponding_institution_ids":["https://openalex.org/I7882870"],"apc_list":null,"apc_paid":null,"fwci":0.1355,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.52568248,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"86","last_page":"95"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9987999796867371,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9854999780654907,"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/signalling","display_name":"Signalling","score":0.7622373104095459},{"id":"https://openalex.org/keywords/signal-transduction","display_name":"Signal transduction","score":0.6899589896202087},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5258912444114685},{"id":"https://openalex.org/keywords/signalling-pathways","display_name":"Signalling pathways","score":0.45912349224090576},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.4375176727771759},{"id":"https://openalex.org/keywords/petri-net","display_name":"Petri net","score":0.4209986925125122},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31460756063461304},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.29906463623046875},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.24806728959083557},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1417866051197052}],"concepts":[{"id":"https://openalex.org/C39743133","wikidata":"https://www.wikidata.org/wiki/Q3262595","display_name":"Signalling","level":2,"score":0.7622373104095459},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.6899589896202087},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5258912444114685},{"id":"https://openalex.org/C3018449070","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signalling pathways","level":3,"score":0.45912349224090576},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.4375176727771759},{"id":"https://openalex.org/C38677869","wikidata":"https://www.wikidata.org/wiki/Q724168","display_name":"Petri net","level":2,"score":0.4209986925125122},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31460756063461304},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.29906463623046875},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.24806728959083557},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1417866051197052},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/1839764.1839775","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1839764.1839775","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th International Conference on Computational Methods in Systems Biology","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.298.4709","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.298.4709","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.dcs.gla.ac.uk/~muffy/papers/cmsb2010.2.pdf","raw_type":"text"},{"id":"pmh:oai:eprints.gla.ac.uk:39280","is_oa":false,"landing_page_url":"http://eprints.gla.ac.uk/39280/","pdf_url":null,"source":{"id":"https://openalex.org/S4210235606","display_name":"ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam)","issn_l":"2622-8912","issn":["2622-8912","2622-8920"],"is_oa":false,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference Proceedings"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1690115124","display_name":null,"funder_award_id":"CA-112970","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2955406896","display_name":null,"funder_award_id":"EP/E032745/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G7733252309","display_name":null,"funder_award_id":"IIS-0513857","funder_id":"https://openalex.org/F4320337389","funder_display_name":"Division of Information and Intelligent Systems"}],"funders":[{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337389","display_name":"Division of Information and Intelligent Systems","ror":"https://ror.org/053a2cp42"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W68069235","https://openalex.org/W333135988","https://openalex.org/W1482381349","https://openalex.org/W1504007491","https://openalex.org/W1509607930","https://openalex.org/W1515942843","https://openalex.org/W1604675118","https://openalex.org/W1943502734","https://openalex.org/W1964012101","https://openalex.org/W1976195354","https://openalex.org/W2002405581","https://openalex.org/W2065952296","https://openalex.org/W2078355959","https://openalex.org/W2099039198","https://openalex.org/W2117486132","https://openalex.org/W2122792487","https://openalex.org/W2128276963","https://openalex.org/W2144063122","https://openalex.org/W2144082908","https://openalex.org/W2161621619","https://openalex.org/W2614695056","https://openalex.org/W2620015488","https://openalex.org/W2911741782","https://openalex.org/W4234315090","https://openalex.org/W6628843398","https://openalex.org/W6681451615"],"related_works":["https://openalex.org/W2092427118","https://openalex.org/W2058539798","https://openalex.org/W2947741874","https://openalex.org/W1492131881","https://openalex.org/W2087709298","https://openalex.org/W2165025106","https://openalex.org/W4386778658","https://openalex.org/W2969844295","https://openalex.org/W2987447052","https://openalex.org/W2058327635"],"abstract_inverted_index":{"A":[0,17],"signalling":[1,57,98],"network":[2,5,27,58,99],"is":[3,19,76],"a":[4,11,20,33,36,43,56,61,131],"of":[6,23,42],"reactions":[7],"that":[8,39,59,140],"govern":[9],"how":[10],"cell":[12],"responds":[13],"to":[14,35,51,78,96,121,135],"its":[15],"environment.":[16],"pathway":[18,137],"dynamic":[21],"flow":[22],"\"signal\"":[24],"through":[25],"the":[26,79,94,97,104,126,142],"(signal":[28],"transduction),":[29],"for":[30,133],"example":[31,134],"from":[32],"receptor":[34],"transcription":[37],"factor":[38],"enables":[40],"expression":[41],"gene.":[44],"In":[45],"this":[46],"paper":[47],"we":[48],"introduce
\\na":[49],"method":[50,95],"compute":[52],"all":[53],"pathways":[54,129],"in":[55,103,130],"satisfy":[60],"simple":[62],"property":[63],"constraining":[64],"initial,":[65],"signal":[66,74],"and":[67,88,108,112,124],"intermediate":[68],"states.":[69],"This":[70,116],"method,":[71],"concerned":[72],"with":[73],"transduction,":[75],"compared":[77],"steady":[80],"state":[81],"view":[82],"underlying":[83],"Petri":[84],"net":[85],"place/transition":[86],"invariants":[87],"flux":[89],"balance":[90],"analysis.":[91],"We":[92],"apply":[93],"model":[100],"being":[101],"developed":[102],"Pathway":[105],"Logic":[106],"project":[107],"identify":[109],"knockout/inhibition":[110],"targets":[111,139],"common":[113],"(pathway)":[114],"events.":[115],"approach":[117],"also":[118],"allows":[119],"us":[120],"better":[122],"understand":[123],"formalise":[125],"interaction":[127],"between":[128],"network,":[132],"identifying":[136],"inhibition":[138],"limit":[141],"effect":[143],"on":[144],"unrelated":[145],"pathways.":[146]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}