{"id":"https://openalex.org/W4200084772","doi":"https://doi.org/10.1093/bioinformatics/btab825","title":"pystablemotifs: Python library for attractor identification and control in Boolean networks","display_name":"pystablemotifs: Python library for attractor identification and control in Boolean networks","publication_year":2021,"publication_date":"2021-12-02","ids":{"openalex":"https://openalex.org/W4200084772","doi":"https://doi.org/10.1093/bioinformatics/btab825","pmid":"https://pubmed.ncbi.nlm.nih.gov/34875008"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab825","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab825","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"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":"green","oa_url":"https://scholarsphere.psu.edu/resources/c5c6c107-09cb-401c-93f3-569346db15d1/downloads/20420","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046067017","display_name":"Jordan C. Rozum","orcid":"https://orcid.org/0000-0002-4356-9809"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jordan C Rozum","raw_affiliation_strings":["Department of Physics, The Pennsylvania State University , University Park, PA 16802, USA"],"affiliations":[{"raw_affiliation_string":"Department of Physics, The Pennsylvania State University , University Park, PA 16802, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073550862","display_name":"D\u00e1vid Deritei","orcid":"https://orcid.org/0000-0002-7584-4828"},"institutions":[{"id":"https://openalex.org/I101202996","display_name":"Semmelweis University","ror":"https://ror.org/01g9ty582","country_code":"HU","type":"education","lineage":["https://openalex.org/I101202996"]},{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["HU","US"],"is_corresponding":false,"raw_author_name":"D\u00e1vid Deritei","raw_affiliation_strings":["Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, MA 02115, USA","Department of Molecular Biology, Semmelweis University , Budapest 1085, Hungary"],"affiliations":[{"raw_affiliation_string":"Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I1283280774","https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Molecular Biology, Semmelweis University , Budapest 1085, Hungary","institution_ids":["https://openalex.org/I101202996"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048613102","display_name":"Kyu Hyong Park","orcid":"https://orcid.org/0009-0007-0884-5541"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyu Hyong Park","raw_affiliation_strings":["Department of Physics, The Pennsylvania State University , University Park, PA 16802, USA"],"affiliations":[{"raw_affiliation_string":"Department of Physics, The Pennsylvania State University , University Park, PA 16802, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042886213","display_name":"Jorge G\u00f3mez Tejeda Za\u00f1udo","orcid":"https://orcid.org/0000-0002-1092-0068"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jorge G\u00f3mez Tejeda Za\u00f1udo","raw_affiliation_strings":["Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02115, USA","Eli and Edythe L. Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"],"affiliations":[{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]},{"raw_affiliation_string":"Eli and Edythe L. Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012905268","display_name":"R\u00e9ka Albert","orcid":"https://orcid.org/0000-0002-9485-0828"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"R\u00e9ka Albert","raw_affiliation_strings":["Department of Biology, The Pennsylvania State University , University Park, PA 16802, USA","Department of Physics, The Pennsylvania State University , University Park, PA 16802, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, The Pennsylvania State University , University Park, PA 16802, USA","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Department of Physics, The Pennsylvania State University , University Park, PA 16802, USA","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5012905268","https://openalex.org/A5046067017"],"corresponding_institution_ids":["https://openalex.org/I130769515"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.8219,"has_fulltext":true,"cited_by_count":58,"citation_normalized_percentile":{"value":0.94895992,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"38","issue":"5","first_page":"1465","last_page":"1466"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9847999811172485,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9732999801635742,"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/attractor","display_name":"Attractor","score":0.8796482086181641},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8243910074234009},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7712193131446838},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6146650910377502},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5228241682052612},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.4863884747028351},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.48015302419662476},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4652707576751709},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.44690579175949097},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3948880434036255},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.27914732694625854},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21614289283752441},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1260489821434021}],"concepts":[{"id":"https://openalex.org/C164380108","wikidata":"https://www.wikidata.org/wiki/Q507187","display_name":"Attractor","level":2,"score":0.8796482086181641},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8243910074234009},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7712193131446838},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6146650910377502},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5228241682052612},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.4863884747028351},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.48015302419662476},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4652707576751709},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.44690579175949097},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3948880434036255},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.27914732694625854},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21614289283752441},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1260489821434021},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab825","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab825","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34875008","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34875008","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:scholarsphere.psu.edu:9691aa62-9e9e-43cc-8951-b4331dcff16c","is_oa":true,"landing_page_url":"https://scholarsphere.psu.edu/resources/9691aa62-9e9e-43cc-8951-b4331dcff16c","pdf_url":"https://scholarsphere.psu.edu/resources/c5c6c107-09cb-401c-93f3-569346db15d1/downloads/20420","source":{"id":"https://openalex.org/S4306401507","display_name":"ScholarSphere (Penn State Libraries)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I3130638595","host_organization_name":"Pangasinan State University","host_organization_lineage":["https://openalex.org/I3130638595"],"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:scholarsphere.psu.edu:9691aa62-9e9e-43cc-8951-b4331dcff16c","is_oa":true,"landing_page_url":"https://scholarsphere.psu.edu/resources/9691aa62-9e9e-43cc-8951-b4331dcff16c","pdf_url":"https://scholarsphere.psu.edu/resources/c5c6c107-09cb-401c-93f3-569346db15d1/downloads/20420","source":{"id":"https://openalex.org/S4306401507","display_name":"ScholarSphere (Penn State Libraries)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I3130638595","host_organization_name":"Pangasinan State University","host_organization_lineage":["https://openalex.org/I3130638595"],"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/G2141835443","display_name":"III: Small: Collaborative Research: Network Analysis and Anomaly Detection via Global Curvatures","funder_award_id":"1814405","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2197203347","display_name":null,"funder_award_id":"Award","funder_id":"https://openalex.org/F4320306536","funder_display_name":"V Foundation for Cancer Research"},{"id":"https://openalex.org/G2462515792","display_name":null,"funder_award_id":"IIS 1814405 to R.A.","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2888295325","display_name":null,"funder_award_id":"D2015-039","funder_id":"https://openalex.org/F4320332898","funder_display_name":"Stand Up To Cancer"},{"id":"https://openalex.org/G3603220033","display_name":null,"funder_award_id":"D2015-039","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5263746854","display_name":null,"funder_award_id":"D2015-039","funder_id":"https://openalex.org/F4320306536","funder_display_name":"V Foundation for Cancer Research"},{"id":"https://openalex.org/G5553358577","display_name":null,"funder_award_id":"IIS 1814405","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6439859455","display_name":null,"funder_award_id":"1715826","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7085905232","display_name":null,"funder_award_id":"PHY 1545832","funder_id":"https://openalex.org/F4320332898","funder_display_name":"Stand Up To Cancer"},{"id":"https://openalex.org/G7232745676","display_name":null,"funder_award_id":"MCB 1715826","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7382407927","display_name":null,"funder_award_id":"PHY 1545832","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7995573518","display_name":"Collaborative Research: Rational Design of Anticancer Drug Combinations using Dynamic Multidimensional Theory","funder_award_id":"1545832","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306536","display_name":"V Foundation for Cancer Research","ror":"https://ror.org/00kbbk236"},{"id":"https://openalex.org/F4320332898","display_name":"Stand Up To Cancer","ror":"https://ror.org/01dmpb598"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4200084772.pdf","grobid_xml":"https://content.openalex.org/works/W4200084772.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W2018519939","https://openalex.org/W2035036685","https://openalex.org/W2053367939","https://openalex.org/W2094025864","https://openalex.org/W2113268441","https://openalex.org/W2417863416","https://openalex.org/W2544038273","https://openalex.org/W2786241182","https://openalex.org/W3048705798","https://openalex.org/W3080647147","https://openalex.org/W3099614534","https://openalex.org/W3147279858","https://openalex.org/W3181363992"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W3049714198","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W2960434112","https://openalex.org/W4287027380","https://openalex.org/W2789551765"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":20},{"year":2022,"cited_by_count":20}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}