{"id":"https://openalex.org/W2940498855","doi":"https://doi.org/10.1186/s13015-019-0145-8","title":"Repairing Boolean logical models from time-series data using Answer Set Programming","display_name":"Repairing Boolean logical models from time-series data using Answer Set Programming","publication_year":2019,"publication_date":"2019-03-25","ids":{"openalex":"https://openalex.org/W2940498855","doi":"https://doi.org/10.1186/s13015-019-0145-8","mag":"2940498855","pmid":"https://pubmed.ncbi.nlm.nih.gov/30962813"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-019-0145-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-019-0145-8","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-019-0145-8","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-019-0145-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079288097","display_name":"Alexandre Lemos","orcid":"https://orcid.org/0000-0002-3876-1011"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Alexandre Lemos","raw_affiliation_strings":["INESC-ID/Instituto Superior T\u00e9cnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisbon, Portugal","INESC-ID/Instituto Superior T\u00e9cnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029, Lisbon, Portugal"],"affiliations":[{"raw_affiliation_string":"INESC-ID/Instituto Superior T\u00e9cnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisbon, Portugal","institution_ids":["https://openalex.org/I121345201"]},{"raw_affiliation_string":"INESC-ID/Instituto Superior T\u00e9cnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029, Lisbon, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058622165","display_name":"In\u00eas Lynce","orcid":"https://orcid.org/0000-0003-4868-415X"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"In\u00eas Lynce","raw_affiliation_strings":["INESC-ID/Instituto Superior T\u00e9cnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisbon, Portugal","INESC-ID/Instituto Superior T\u00e9cnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029, Lisbon, Portugal"],"affiliations":[{"raw_affiliation_string":"INESC-ID/Instituto Superior T\u00e9cnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisbon, Portugal","institution_ids":["https://openalex.org/I121345201"]},{"raw_affiliation_string":"INESC-ID/Instituto Superior T\u00e9cnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029, Lisbon, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025560387","display_name":"Pedro T. Monteiro","orcid":"https://orcid.org/0000-0002-7934-5495"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Pedro T. Monteiro","raw_affiliation_strings":["INESC-ID/Instituto Superior T\u00e9cnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisbon, Portugal","INESC-ID/Instituto Superior T\u00e9cnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029, Lisbon, Portugal"],"affiliations":[{"raw_affiliation_string":"INESC-ID/Instituto Superior T\u00e9cnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisbon, Portugal","institution_ids":["https://openalex.org/I121345201"]},{"raw_affiliation_string":"INESC-ID/Instituto Superior T\u00e9cnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029, Lisbon, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5079288097"],"corresponding_institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":0.3435,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.58837489,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"14","issue":"1","first_page":"9","last_page":"9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9983999729156494,"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":0.9983999729156494,"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/T11010","display_name":"Logic, Reasoning, and Knowledge","score":0.9861000180244446,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9830999970436096,"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":0.7828050851821899},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6114886999130249},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.5889853835105896},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5640239119529724},{"id":"https://openalex.org/keywords/answer-set-programming","display_name":"Answer set programming","score":0.5630126595497131},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5512583255767822},{"id":"https://openalex.org/keywords/asynchronous-communication","display_name":"Asynchronous communication","score":0.4708021879196167},{"id":"https://openalex.org/keywords/boolean-network","display_name":"Boolean network","score":0.46894997358322144},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.43255746364593506},{"id":"https://openalex.org/keywords/series","display_name":"Series (stratigraphy)","score":0.4126267731189728},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.41133207082748413},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38453471660614014},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33552563190460205},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2830442786216736},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.20396891236305237},{"id":"https://openalex.org/keywords/boolean-function","display_name":"Boolean function","score":0.20111235976219177}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7828050851821899},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6114886999130249},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.5889853835105896},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5640239119529724},{"id":"https://openalex.org/C182620335","wikidata":"https://www.wikidata.org/wiki/Q2852531","display_name":"Answer set programming","level":3,"score":0.5630126595497131},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5512583255767822},{"id":"https://openalex.org/C151319957","wikidata":"https://www.wikidata.org/wiki/Q752739","display_name":"Asynchronous communication","level":2,"score":0.4708021879196167},{"id":"https://openalex.org/C134444547","wikidata":"https://www.wikidata.org/wiki/Q585230","display_name":"Boolean network","level":3,"score":0.46894997358322144},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.43255746364593506},{"id":"https://openalex.org/C143724316","wikidata":"https://www.wikidata.org/wiki/Q312468","display_name":"Series (stratigraphy)","level":2,"score":0.4126267731189728},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.41133207082748413},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38453471660614014},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33552563190460205},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2830442786216736},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.20396891236305237},{"id":"https://openalex.org/C187455244","wikidata":"https://www.wikidata.org/wiki/Q942353","display_name":"Boolean function","level":2,"score":0.20111235976219177},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13015-019-0145-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-019-0145-8","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-019-0145-8","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:30962813","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30962813","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:doaj.org/article:138fa9c047de4cdc8259d301b600596d","is_oa":true,"landing_page_url":"https://doaj.org/article/138fa9c047de4cdc8259d301b600596d","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"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":"Algorithms for Molecular Biology, Vol 14, Iss 1, Pp 1-16 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5436541","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6434824","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6434824","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6434824","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13015-019-0145-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-019-0145-8","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-019-0145-8","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G309696157","display_name":null,"funder_award_id":"UID/CEC/50021/2013","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G6299983296","display_name":null,"funder_award_id":"PTDC/","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G6700943011","display_name":null,"funder_award_id":"UID/CEC/50021/2019","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G7922353001","display_name":null,"funder_award_id":"PTDC/EEI-CTP/2914/2014","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320323424","display_name":"Universidade de Lisboa","ror":"https://ror.org/01c27hj86"},{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320335226","display_name":"Instituto Superior T\u00e9cnico","ror":"https://ror.org/01c27hj86"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2940498855.pdf","grobid_xml":"https://content.openalex.org/works/W2940498855.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W344332445","https://openalex.org/W1482498688","https://openalex.org/W1489988510","https://openalex.org/W1493657719","https://openalex.org/W1595652621","https://openalex.org/W1603219320","https://openalex.org/W2005486846","https://openalex.org/W2011835017","https://openalex.org/W2013942866","https://openalex.org/W2018519939","https://openalex.org/W2031369606","https://openalex.org/W2065782501","https://openalex.org/W2073246651","https://openalex.org/W2096813836","https://openalex.org/W2107189447","https://openalex.org/W2113465369","https://openalex.org/W2115552299","https://openalex.org/W2118449583","https://openalex.org/W2122902176","https://openalex.org/W2126877057","https://openalex.org/W2129325583","https://openalex.org/W2132935366","https://openalex.org/W2136559804","https://openalex.org/W2142400903","https://openalex.org/W2160939581","https://openalex.org/W2174399230","https://openalex.org/W2209982993","https://openalex.org/W2213556458","https://openalex.org/W2335478831","https://openalex.org/W2408617648","https://openalex.org/W2436013910","https://openalex.org/W2489327984","https://openalex.org/W2514850942","https://openalex.org/W2529634546","https://openalex.org/W2580749482","https://openalex.org/W2594490426","https://openalex.org/W2693300196","https://openalex.org/W2963234253","https://openalex.org/W4206370914","https://openalex.org/W4211177236","https://openalex.org/W4212799367","https://openalex.org/W4253456425"],"related_works":["https://openalex.org/W2468279273","https://openalex.org/W2354198838","https://openalex.org/W1989130879","https://openalex.org/W2103419012","https://openalex.org/W2988126442","https://openalex.org/W2116677773","https://openalex.org/W1974414866","https://openalex.org/W2063982682","https://openalex.org/W2802923427","https://openalex.org/W2150695558"],"abstract_inverted_index":{"The":[0],"method":[1],"was":[2],"validated":[3],"using":[4],"known":[5],"biological":[6],"models":[7,15],"from":[8,17],"different":[9],"species,":[10],"as":[11,13],"well":[12],"synthetic":[14],"obtained":[16],"randomly":[18],"generated":[19],"networks.":[20],"We":[21],"discuss":[22],"the":[23,29,33],"method's":[24],"limitations":[25],"regarding":[26],"each":[27],"of":[28],"updating":[30],"schemes":[31],"and":[32],"considered":[34],"minimization":[35],"algorithm.":[36]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
