{"id":"https://openalex.org/W4401203812","doi":"https://doi.org/10.1186/s12859-024-05871-x","title":"Ant colony optimization for the identification of dysregulated gene subnetworks from expression data","display_name":"Ant colony optimization for the identification of dysregulated gene subnetworks from expression data","publication_year":2024,"publication_date":"2024-08-01","ids":{"openalex":"https://openalex.org/W4401203812","doi":"https://doi.org/10.1186/s12859-024-05871-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/39090538"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05871-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05871-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05871-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05871-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056412439","display_name":"Eileen Marie Hanna","orcid":"https://orcid.org/0000-0002-2093-4586"},"institutions":[{"id":"https://openalex.org/I56306041","display_name":"Lebanese American University","ror":"https://ror.org/00hqkan37","country_code":"LB","type":"education","lineage":["https://openalex.org/I56306041"]}],"countries":["LB"],"is_corresponding":true,"raw_author_name":"Eileen Marie Hanna","raw_affiliation_strings":["Department of Computer Science and Mathematics, Lebanese American University, Byblos, Lebanon. eileenmarie.hanna@lau.edu.lb","Department of Computer Science and Mathematics, Lebanese American University, Byblos, Lebanon"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Mathematics, Lebanese American University, Byblos, Lebanon. eileenmarie.hanna@lau.edu.lb","institution_ids":["https://openalex.org/I56306041"]},{"raw_affiliation_string":"Department of Computer Science and Mathematics, Lebanese American University, Byblos, Lebanon","institution_ids":["https://openalex.org/I56306041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037653002","display_name":"Ghadi El Hasbani","orcid":"https://orcid.org/0000-0003-4171-2891"},"institutions":[{"id":"https://openalex.org/I56306041","display_name":"Lebanese American University","ror":"https://ror.org/00hqkan37","country_code":"LB","type":"education","lineage":["https://openalex.org/I56306041"]}],"countries":["LB"],"is_corresponding":false,"raw_author_name":"Ghadi El Hasbani","raw_affiliation_strings":["Department of Computer Science and Mathematics, Lebanese American University, Byblos, Lebanon"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Mathematics, Lebanese American University, Byblos, Lebanon","institution_ids":["https://openalex.org/I56306041"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047508564","display_name":"Danielle Azar","orcid":"https://orcid.org/0000-0002-6159-3714"},"institutions":[{"id":"https://openalex.org/I56306041","display_name":"Lebanese American University","ror":"https://ror.org/00hqkan37","country_code":"LB","type":"education","lineage":["https://openalex.org/I56306041"]}],"countries":["LB"],"is_corresponding":false,"raw_author_name":"Danielle Azar","raw_affiliation_strings":["Department of Computer Science and Mathematics, Lebanese American University, Byblos, Lebanon"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Mathematics, Lebanese American University, Byblos, Lebanon","institution_ids":["https://openalex.org/I56306041"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5056412439"],"corresponding_institution_ids":["https://openalex.org/I56306041"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.4862,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.61145425,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"25","issue":"1","first_page":"254","last_page":"254"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9061999917030334,"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":0.9061999917030334,"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/T10885","display_name":"Gene expression and cancer classification","score":0.04659999907016754,"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":0.008899999782443047,"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/dna-microarray","display_name":"DNA microarray","score":0.7718667984008789},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6840818524360657},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.649297833442688},{"id":"https://openalex.org/keywords/ant-colony-optimization-algorithms","display_name":"Ant colony optimization algorithms","score":0.6083663702011108},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5442545413970947},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5175444483757019},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.49845361709594727},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.48182955384254456},{"id":"https://openalex.org/keywords/ant","display_name":"ANT","score":0.48029085993766785},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38610297441482544},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.35762274265289307},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3429874777793884},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2322535216808319},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.07208764553070068}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.7718667984008789},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6840818524360657},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.649297833442688},{"id":"https://openalex.org/C40128228","wikidata":"https://www.wikidata.org/wiki/Q460851","display_name":"Ant colony optimization algorithms","level":2,"score":0.6083663702011108},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5442545413970947},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5175444483757019},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.49845361709594727},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.48182955384254456},{"id":"https://openalex.org/C97467695","wikidata":"https://www.wikidata.org/wiki/Q295802","display_name":"ANT","level":2,"score":0.48029085993766785},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38610297441482544},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.35762274265289307},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3429874777793884},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2322535216808319},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.07208764553070068},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001000","descriptor_name":"Ants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001000","descriptor_name":"Ants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001000","descriptor_name":"Ants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001000","descriptor_name":"Ants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001000","descriptor_name":"Ants","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D019636","descriptor_name":"Neurodegenerative Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019636","descriptor_name":"Neurodegenerative Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019636","descriptor_name":"Neurodegenerative Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019636","descriptor_name":"Neurodegenerative Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019636","descriptor_name":"Neurodegenerative Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-024-05871-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05871-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05871-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39090538","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39090538","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11295523","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11295523","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11295523/pdf/12859_2024_Article_5871.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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:0135e1c2516d4dc8bbe8e07ed7e1a59a","is_oa":true,"landing_page_url":"https://doaj.org/article/0135e1c2516d4dc8bbe8e07ed7e1a59a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-30 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05871-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05871-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05871-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2","score":0.5299999713897705}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4401203812.pdf","grobid_xml":"https://content.openalex.org/works/W4401203812.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1578104218","https://openalex.org/W2023066496","https://openalex.org/W2073576377","https://openalex.org/W2074277704","https://openalex.org/W2084533385","https://openalex.org/W2095319945","https://openalex.org/W2100490867","https://openalex.org/W2100980426","https://openalex.org/W2105734437","https://openalex.org/W2108096229","https://openalex.org/W2109044536","https://openalex.org/W2109555487","https://openalex.org/W2110687686","https://openalex.org/W2112811019","https://openalex.org/W2116634113","https://openalex.org/W2119220491","https://openalex.org/W2121619336","https://openalex.org/W2129099812","https://openalex.org/W2130410032","https://openalex.org/W2132022337","https://openalex.org/W2138485499","https://openalex.org/W2143950810","https://openalex.org/W2146026944","https://openalex.org/W2146512944","https://openalex.org/W2149491227","https://openalex.org/W2160697532","https://openalex.org/W2170989872","https://openalex.org/W2542210920","https://openalex.org/W2757523215","https://openalex.org/W2945138188","https://openalex.org/W2968022676","https://openalex.org/W3004747635","https://openalex.org/W3093449011","https://openalex.org/W4292083457","https://openalex.org/W4321169271","https://openalex.org/W4377225074"],"related_works":["https://openalex.org/W2253992237","https://openalex.org/W624076816","https://openalex.org/W849430572","https://openalex.org/W2285878319","https://openalex.org/W594861393","https://openalex.org/W2991307080","https://openalex.org/W3177044606","https://openalex.org/W2244036508","https://openalex.org/W4237535716","https://openalex.org/W2110363036"],"abstract_inverted_index":{"BACKGROUND:":[0],"High-throughput":[1],"experimental":[2],"technologies":[3],"can":[4],"provide":[5],"deeper":[6],"insights":[7],"into":[8],"pathway":[9,46],"perturbations":[10],"in":[11,73,76,91,193,205,264],"biomedical":[12],"studies.":[13,78],"Accordingly,":[14],"their":[15],"usage":[16],"is":[17,272],"central":[18,63],"to":[19,64,125,149,195,213],"the":[20,26,82,106,170,186,257],"identification":[21,131],"of":[22,29,37,84,108,155,172,177,261,267],"molecular":[23],"targets":[24],"and":[25,45,129,136,145,162,175,201,216,259],"subsequent":[27],"development":[28],"suitable":[30],"treatments":[31],"for":[32,55,180],"various":[33],"diseases.":[34],"Classical":[35],"interpretations":[36],"generated":[38],"data,":[39],"such":[40,77],"as":[41],"differential":[42],"gene":[43,85,92,223,230],"expression":[44,224],"analyses,":[47],"disregard":[48],"interconnections":[49,61],"between":[50],"studied":[51],"genes":[52],"when":[53],"looking":[54],"gene-disease":[56],"associations.":[57],"Given":[58],"that":[59,87,185],"these":[60],"are":[62],"cellular":[65],"processes,":[66],"there":[67],"has":[68],"been":[69],"a":[70,109,117,234,238,247],"recent":[71],"interest":[72],"incorporating":[74],"them":[75],"The":[79,220],"latter":[80],"allows":[81],"detection":[83],"modules":[86,104,231,266],"underlie":[88],"complex":[89],"phenotypes":[90],"interaction":[93],"networks.":[94],"Existing":[95],"methods":[96],"either":[97],"impose":[98],"radius-based":[99,140],"restrictions":[100],"or":[101],"freely":[102],"grow":[103],"at":[105,275],"expense":[107],"statistical":[110],"bias":[111],"towards":[112],"large":[113],"modules.":[114],"We":[115,143,168],"propose":[116],"heuristic":[118,239],"method,":[119],"inspired":[120],"by":[121],"Ant":[122,242],"Colony":[123,243],"Optimization,":[124,244],"apply":[126],"gene-level":[127,178],"scoring":[128],"module":[130],"with":[132,233,250],"distance-based":[133,248],"search":[134,249],"constraints":[135],"penalties,":[137],"rather":[138],"than":[139],"constraints.":[141,253],"RESULTS:":[142],"test":[144],"compare":[146],"our":[147,262],"results":[148,204,255],"other":[150],"approaches":[151],"using":[152],"three":[153,165,207],"datasets":[154,208],"different":[156,211],"neurodegenerative":[157],"diseases,":[158],"namely":[159],"Alzheimer's,":[160],"Parkinson's,":[161],"Huntington's,":[163],"over":[164],"independent":[166],"experiments.":[167],"report":[169],"outcomes":[171],"enrichment":[173,203],"analyses":[174],"concordance":[176],"scores":[179],"each":[181],"disease.":[182,236],"Results":[183],"indicate":[184],"proposed":[187],"approach":[188,226],"generally":[189],"shows":[190],"superior":[191],"stability":[192,260],"comparison":[194],"existing":[196],"methods.":[197],"It":[198],"produces":[199],"stable":[200],"meaningful":[202],"all":[206],"which":[209],"have":[210],"case":[212],"control":[214],"proportions":[215],"sample":[217],"sizes.":[218],"CONCLUSION:":[219],"presented":[221],"network-based":[222],"analysis":[225],"successfully":[227],"identifies":[228],"dysregulated":[229],"associated":[232],"certain":[235],"Using":[237],"based":[240],"on":[241],"we":[245],"perform":[246],"no":[251],"radius":[252],"Experimental":[254],"support":[256],"effectiveness":[258],"method":[263],"prioritizing":[265],"high":[268],"relevance.":[269],"Our":[270],"tool":[271],"publicly":[273],"available":[274],"github.com/GhadiElHasbani/ACOxGS.git.":[276]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}