{"id":"https://openalex.org/W4399906548","doi":"https://doi.org/10.1093/bioinformatics/btae376","title":"DDN3.0: determining significant rewiring of biological network structure with differential dependency networks","display_name":"DDN3.0: determining significant rewiring of biological network structure with differential dependency networks","publication_year":2024,"publication_date":"2024-06-01","ids":{"openalex":"https://openalex.org/W4399906548","doi":"https://doi.org/10.1093/bioinformatics/btae376","pmid":"https://pubmed.ncbi.nlm.nih.gov/38902940"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae376","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae376","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae376/58290772/btae376.pdf","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://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae376/58290772/btae376.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5104668817","display_name":"Yi Fu","orcid":"https://orcid.org/0000-0002-1922-2100"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yi Fu","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University , Arlington, VA 22203, United States"],"raw_orcid":"https://orcid.org/0000-0002-1922-2100","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University , Arlington, VA 22203, United States","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046890926","display_name":"Yingzhou Lu","orcid":"https://orcid.org/0009-0008-7774-6018"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yingzhou Lu","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University , Arlington, VA 22203, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University , Arlington, VA 22203, United States","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104668418","display_name":"Yizhi Wang","orcid":"https://orcid.org/0000-0001-9456-0743"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yizhi Wang","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University , Arlington, VA 22203, United States"],"raw_orcid":"https://orcid.org/0000-0001-9456-0743","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University , Arlington, VA 22203, United States","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102203376","display_name":"Bai Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bai Zhang","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University , Arlington, VA 22203, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University , Arlington, VA 22203, United States","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100390145","display_name":"Zhen Zhang","orcid":"https://orcid.org/0000-0001-8448-5663"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhen Zhang","raw_affiliation_strings":["Department of Pathology, Johns Hopkins Medical Institutions , Baltimore, MD 21231, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Johns Hopkins Medical Institutions , Baltimore, MD 21231, United States","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076006520","display_name":"Guoqiang Yu","orcid":"https://orcid.org/0000-0002-6743-7413"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guoqiang Yu","raw_affiliation_strings":["Department of Automation, Tsinghua University , Beijing 100084, P.R. China","Department of Automation, Tsinghua University, Beijing, 100084, P. R. China"],"raw_orcid":"https://orcid.org/0000-0002-6743-7413","affiliations":[{"raw_affiliation_string":"Department of Automation, Tsinghua University , Beijing 100084, P.R. China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Department of Automation, Tsinghua University, Beijing, 100084, P. R. China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100343306","display_name":"Chunyu Liu","orcid":"https://orcid.org/0000-0002-5986-4415"},"institutions":[{"id":"https://openalex.org/I20388574","display_name":"SUNY Upstate Medical University","ror":"https://ror.org/040kfrw16","country_code":"US","type":"education","lineage":["https://openalex.org/I20388574"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chunyu Liu","raw_affiliation_strings":["Department of Psychiatry, SUNY Upstate Medical University , Syracuse, NY 13210, United States"],"raw_orcid":"https://orcid.org/0000-0002-5986-4415","affiliations":[{"raw_affiliation_string":"Department of Psychiatry, SUNY Upstate Medical University , Syracuse, NY 13210, United States","institution_ids":["https://openalex.org/I20388574"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011322600","display_name":"Robert Clarke","orcid":"https://orcid.org/0000-0002-9278-0854"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I223919290","display_name":"Hormel (United States)","ror":"https://ror.org/03wnt7k73","country_code":"US","type":"company","lineage":["https://openalex.org/I223919290"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Clarke","raw_affiliation_strings":["The Hormel Institute, University of Minnesota , Austin, MN 55912, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Hormel Institute, University of Minnesota , Austin, MN 55912, United States","institution_ids":["https://openalex.org/I223919290","https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071844909","display_name":"David M. Herrington","orcid":"https://orcid.org/0000-0002-7670-6400"},"institutions":[{"id":"https://openalex.org/I47251452","display_name":"Wake Forest University","ror":"https://ror.org/0207ad724","country_code":"US","type":"education","lineage":["https://openalex.org/I47251452"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David M Herrington","raw_affiliation_strings":["Department of Internal Medicine, Wake Forest University , Winston-Salem, NC 27157, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, Wake Forest University , Winston-Salem, NC 27157, United States","institution_ids":["https://openalex.org/I47251452"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100372002","display_name":"Yue Wang","orcid":"https://orcid.org/0000-0002-1788-1102"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yue Wang","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University , Arlington, VA 22203, United States"],"raw_orcid":"https://orcid.org/0000-0002-1788-1102","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University , Arlington, VA 22203, United States","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.2452,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.88110492,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"40","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9027000069618225,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9027000069618225,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.03539999946951866,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.014299999922513962,"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":0.7031315565109253},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.6638694405555725},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6153634786605835},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.5458720922470093},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.46990177035331726},{"id":"https://openalex.org/keywords/dependency","display_name":"Dependency (UML)","score":0.4354855716228485},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42483651638031006},{"id":"https://openalex.org/keywords/hyperparameter","display_name":"Hyperparameter","score":0.4188287556171417},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.39577120542526245},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3039172291755676},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2427041232585907},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21382862329483032}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7031315565109253},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.6638694405555725},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6153634786605835},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.5458720922470093},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.46990177035331726},{"id":"https://openalex.org/C19768560","wikidata":"https://www.wikidata.org/wiki/Q320727","display_name":"Dependency (UML)","level":2,"score":0.4354855716228485},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42483651638031006},{"id":"https://openalex.org/C8642999","wikidata":"https://www.wikidata.org/wiki/Q4171168","display_name":"Hyperparameter","level":2,"score":0.4188287556171417},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.39577120542526245},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3039172291755676},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2427041232585907},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21382862329483032},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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":"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":"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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae376","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae376","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae376/58290772/btae376.pdf","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:38902940","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38902940","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:pubmedcentral.nih.gov:11199198","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11199198","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11199198/pdf/btae376.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae376","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae376","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae376/58290772/btae376.pdf","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/G1184232923","display_name":null,"funder_award_id":"CA271891","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7435554953","display_name":null,"funder_award_id":"HL111362","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7480935274","display_name":null,"funder_award_id":"MH110504","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7895013820","display_name":null,"funder_award_id":"NS123719","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4399906548.pdf"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W2010824638","https://openalex.org/W2040847667","https://openalex.org/W2070672503","https://openalex.org/W2095833325","https://openalex.org/W2108156593","https://openalex.org/W2112795434","https://openalex.org/W2139329624","https://openalex.org/W2165009258","https://openalex.org/W2464880876","https://openalex.org/W2493614923","https://openalex.org/W2949806030","https://openalex.org/W3114099828","https://openalex.org/W3128088296"],"related_works":["https://openalex.org/W2901655697","https://openalex.org/W2727283706","https://openalex.org/W1525985997","https://openalex.org/W108107911","https://openalex.org/W118100147","https://openalex.org/W2952963846","https://openalex.org/W2161626927","https://openalex.org/W2135602072","https://openalex.org/W2013286793","https://openalex.org/W2023465156"],"abstract_inverted_index":{"MOTIVATION:":[0],"Complex":[1],"diseases":[2],"are":[3,64,74,210],"often":[4,174],"caused":[5],"and":[6,29,43,67,98,118,143,158,173,207],"characterized":[7],"by":[8],"misregulation":[9],"of":[10,22,40,96,146,181,197],"multiple":[11,136],"biological":[12,23],"pathways.":[13],"Differential":[14],"network":[15,24,52,61,86,100,180],"analysis":[16,53,87],"aims":[17],"to":[18,69,132,139],"detect":[19],"significant":[20],"rewiring":[21],"structures":[25,62,101],"under":[26,102],"different":[27,103],"conditions":[28],"has":[30],"become":[31],"an":[32,83],"important":[33],"tool":[34,110],"for":[35,188],"understanding":[36],"the":[37,108],"molecular":[38,184],"etiology":[39],"disease":[41],"progression":[42],"therapeutic":[44],"response.":[45],"With":[46],"few":[47],"exceptions,":[48],"most":[49],"existing":[50],"differential":[51,56,85],"tools":[54],"perform":[55],"tests":[57],"on":[58],"separately":[59],"learned":[60],"that":[63,92,111,162],"computationally":[65],"expensive":[66],"prone":[68],"collapse":[70],"when":[71],"grouped":[72],"samples":[73],"limited":[75],"or":[76],"less":[77],"consistent.":[78],"RESULTS:":[79],"We":[80,105],"previously":[81],"developed":[82],"accurate":[84],"method-differential":[88],"dependency":[89],"networks":[90],"(DDN),":[91],"enables":[93],"joint":[94],"learning":[95,141],"common":[97],"rewired":[99,183],"conditions.":[104],"now":[106],"introduce":[107],"DDN3.0":[109,163,198],"improves":[112],"this":[113],"framework":[114],"with":[115,126],"three":[116],"new":[117],"highly":[119],"efficient":[120],"algorithms,":[121],"namely,":[122],"unbiased":[123],"model":[124],"estimation":[125],"a":[127,171,179,208],"weighted":[128],"error":[129],"measure":[130],"applicable":[131],"imbalance":[133],"sample":[134],"groups,":[135],"acceleration":[137],"strategies":[138],"improve":[140],"efficiency,":[142],"data-driven":[144],"determination":[145],"proper":[147],"hyperparameters.":[148],"The":[149,194],"comparative":[150],"experimental":[151],"results":[152],"obtained":[153],"from":[154],"both":[155],"realistic":[156],"simulations":[157],"case":[159],"studies":[160],"show":[161],"can":[164],"help":[165],"biologists":[166],"more":[167],"accurately":[168],"identify,":[169],"in":[170],"study-specific":[172],"unknown":[175],"conserved":[176],"regulatory":[177],"circuitry,":[178],"significantly":[182],"players":[185],"potentially":[186],"responsible":[187],"phenotypic":[189],"transitions.":[190],"AVAILABILITY":[191],"AND":[192],"IMPLEMENTATION:":[193],"Python":[195],"package":[196],"is":[199],"freely":[200],"available":[201],"at":[202,212],"https://github.com/cbil-vt/DDN3.":[203],"A":[204],"user's":[205],"guide":[206],"vignette":[209],"provided":[211],"https://ddn-30.readthedocs.io/.":[213]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
