{"id":"https://openalex.org/W4413453426","doi":"https://doi.org/10.1093/bioinformatics/btaf461","title":"CANA v1.0.0: efficient quantification of canalization in automata networks","display_name":"CANA v1.0.0: efficient quantification of canalization in automata networks","publication_year":2025,"publication_date":"2025-08-23","ids":{"openalex":"https://openalex.org/W4413453426","doi":"https://doi.org/10.1093/bioinformatics/btaf461","pmid":"https://pubmed.ncbi.nlm.nih.gov/40848247"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf461","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf461","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btaf461","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074269131","display_name":"Austin M. Marcus","orcid":"https://orcid.org/0000-0002-1611-8236"},"institutions":[{"id":"https://openalex.org/I123946342","display_name":"Binghamton University","ror":"https://ror.org/008rmbt77","country_code":"US","type":"education","lineage":["https://openalex.org/I123946342"]},{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Austin M Marcus","raw_affiliation_strings":["Center for Complex Biological Systems, University of California Irvine , Irvine, CA 92697,","School of Systems Science and Industrial Engineering, Binghamton University (State University of New York) , Vestal, NY 13850,","School of Systems Science and Industrial Engineering, Binghamton University (State University of New York), Vestal NY, 13850, United States","University of California Irvine Center for Complex Biological Systems, , Irvine, CA 92697,","Binghamton University (State University of New York) School of Systems Science and Industrial Engineering, , Vestal NY, 13850,","Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, United States"],"affiliations":[{"raw_affiliation_string":"Center for Complex Biological Systems, University of California Irvine , Irvine, CA 92697,","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"School of Systems Science and Industrial Engineering, Binghamton University (State University of New York) , Vestal, NY 13850,","institution_ids":["https://openalex.org/I123946342"]},{"raw_affiliation_string":"School of Systems Science and Industrial Engineering, Binghamton University (State University of New York), Vestal NY, 13850, United States","institution_ids":["https://openalex.org/I123946342"]},{"raw_affiliation_string":"University of California Irvine Center for Complex Biological Systems, , Irvine, CA 92697,","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Binghamton University (State University of New York) School of Systems Science and Industrial Engineering, , Vestal NY, 13850,","institution_ids":["https://openalex.org/I123946342"]},{"raw_affiliation_string":"Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, United States","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046067017","display_name":"Jordan C. Rozum","orcid":"https://orcid.org/0000-0002-4356-9809"},"institutions":[{"id":"https://openalex.org/I123946342","display_name":"Binghamton University","ror":"https://ror.org/008rmbt77","country_code":"US","type":"education","lineage":["https://openalex.org/I123946342"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jordan Rozum","raw_affiliation_strings":["School of Systems Science and Industrial Engineering, Binghamton University (State University of New York) , Vestal, NY 13850,","Binghamton University (State University of New York) School of Systems Science and Industrial Engineering, , Vestal NY, 13850,","School of Systems Science and Industrial Engineering, Binghamton University (State University of New York), Vestal NY, 13850, United States"],"affiliations":[{"raw_affiliation_string":"School of Systems Science and Industrial Engineering, Binghamton University (State University of New York) , Vestal, NY 13850,","institution_ids":["https://openalex.org/I123946342"]},{"raw_affiliation_string":"Binghamton University (State University of New York) School of Systems Science and Industrial Engineering, , Vestal NY, 13850,","institution_ids":["https://openalex.org/I123946342"]},{"raw_affiliation_string":"School of Systems Science and Industrial Engineering, Binghamton University (State University of New York), Vestal NY, 13850, United States","institution_ids":["https://openalex.org/I123946342"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5098623185","display_name":"Herbert Sizek","orcid":null},"institutions":[{"id":"https://openalex.org/I25169866","display_name":"Universidade Cat\u00f3lica Portuguesa","ror":"https://ror.org/03b9snr86","country_code":"PT","type":"education","lineage":["https://openalex.org/I25169866"]},{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["PT","US"],"is_corresponding":false,"raw_author_name":"Herbert Sizek","raw_affiliation_strings":["Department of Informatics, Indiana University , Bloomington, IN 47405,","Universidade Cat\u00f3lica Portuguesa, Cat\u00f3lica Biomedical Research Centre , Lisboa, 1649-023,"],"affiliations":[{"raw_affiliation_string":"Department of Informatics, Indiana University , Bloomington, IN 47405,","institution_ids":["https://openalex.org/I4210119109"]},{"raw_affiliation_string":"Universidade Cat\u00f3lica Portuguesa, Cat\u00f3lica Biomedical Research Centre , Lisboa, 1649-023,","institution_ids":["https://openalex.org/I25169866"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065682719","display_name":"Lu\u00eds M. Rocha","orcid":"https://orcid.org/0000-0001-9402-887X"},"institutions":[{"id":"https://openalex.org/I123946342","display_name":"Binghamton University","ror":"https://ror.org/008rmbt77","country_code":"US","type":"education","lineage":["https://openalex.org/I123946342"]},{"id":"https://openalex.org/I25169866","display_name":"Universidade Cat\u00f3lica Portuguesa","ror":"https://ror.org/03b9snr86","country_code":"PT","type":"education","lineage":["https://openalex.org/I25169866"]}],"countries":["PT","US"],"is_corresponding":false,"raw_author_name":"Luis M Rocha","raw_affiliation_strings":["School of Systems Science and Industrial Engineering, Binghamton University (State University of New York) , Vestal, NY 13850,","Universidade Cat\u00f3lica Portuguesa, Cat\u00f3lica Biomedical Research Centre , 1649-023 Lisboa,","Binghamton University (State University of New York) School of Systems Science and Industrial Engineering, , Vestal NY, 13850,","School of Systems Science and Industrial Engineering, Binghamton University (State University of New York), Vestal NY, 13850, United States"],"affiliations":[{"raw_affiliation_string":"School of Systems Science and Industrial Engineering, Binghamton University (State University of New York) , Vestal, NY 13850,","institution_ids":["https://openalex.org/I123946342"]},{"raw_affiliation_string":"Universidade Cat\u00f3lica Portuguesa, Cat\u00f3lica Biomedical Research Centre , 1649-023 Lisboa,","institution_ids":["https://openalex.org/I25169866"]},{"raw_affiliation_string":"Binghamton University (State University of New York) School of Systems Science and Industrial Engineering, , Vestal NY, 13850,","institution_ids":["https://openalex.org/I123946342"]},{"raw_affiliation_string":"School of Systems Science and Industrial Engineering, Binghamton University (State University of New York), Vestal NY, 13850, United States","institution_ids":["https://openalex.org/I123946342"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5074269131"],"corresponding_institution_ids":["https://openalex.org/I123946342","https://openalex.org/I204250578"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.22649308,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"10","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12326","display_name":"Network Packet Processing and Optimization","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12326","display_name":"Network Packet Processing and Optimization","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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/T12072","display_name":"Machine Learning and Algorithms","score":0.9955000281333923,"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/T10142","display_name":"Formal Methods in Verification","score":0.9905999898910522,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6914780139923096},{"id":"https://openalex.org/keywords/automaton","display_name":"Automaton","score":0.5133008360862732},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4256434738636017},{"id":"https://openalex.org/keywords/cellular-automaton","display_name":"Cellular automaton","score":0.4182148873806},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.35192030668258667},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32420071959495544},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2251499593257904}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6914780139923096},{"id":"https://openalex.org/C112505250","wikidata":"https://www.wikidata.org/wiki/Q787116","display_name":"Automaton","level":2,"score":0.5133008360862732},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4256434738636017},{"id":"https://openalex.org/C35527583","wikidata":"https://www.wikidata.org/wiki/Q189156","display_name":"Cellular automaton","level":2,"score":0.4182148873806},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35192030668258667},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32420071959495544},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2251499593257904}],"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":"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":"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf461","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf461","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40848247","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40848247","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:11319915","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12512137","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:repositorio.ucp.pt:10400.14/55409","is_oa":true,"landing_page_url":"http://hdl.handle.net/10400.14/55409","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":null,"raw_type":"research article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf461","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf461","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2800641596","display_name":null,"funder_award_id":"2022.09122.PTDC","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1966053044","https://openalex.org/W1990412515","https://openalex.org/W1997088865","https://openalex.org/W2000982470","https://openalex.org/W2058704592","https://openalex.org/W2076130704","https://openalex.org/W2094902224","https://openalex.org/W2171421390","https://openalex.org/W2176409730","https://openalex.org/W2789248437","https://openalex.org/W2951789849","https://openalex.org/W3082777162","https://openalex.org/W3125815138","https://openalex.org/W3137689056","https://openalex.org/W4321374025","https://openalex.org/W4323073466","https://openalex.org/W4389782980"],"related_works":["https://openalex.org/W2164619678","https://openalex.org/W2113544496","https://openalex.org/W2360313292","https://openalex.org/W2067777412","https://openalex.org/W1669105318","https://openalex.org/W2359527201","https://openalex.org/W2353714615","https://openalex.org/W2141069492","https://openalex.org/W1986870597","https://openalex.org/W2124122503"],"abstract_inverted_index":{"CANA":[0],"source":[1],"is":[2,6,15],"on":[3,16,21],"https://github.com/CASCI-lab/CANA":[4],"and":[5],"installable":[7],"via":[8],"pip":[9],"install":[10],"cana.":[11],"Source":[12],"for":[13],"schematodes":[14],"https://github.com/CASCI-lab/schematodes.":[17],"Analysis":[18],"scripts":[19],"are":[20],"https://github.com/CASCI-lab/symmetryInCellCollective.":[22]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
