{"id":"https://openalex.org/W4416690969","doi":"https://doi.org/10.1371/journal.pcbi.1013743","title":"TransMarker: Unveiling dynamic network biomarkers in cancer progression through cross-state graph alignment and optimal transport","display_name":"TransMarker: Unveiling dynamic network biomarkers in cancer progression through cross-state graph alignment and optimal transport","publication_year":2025,"publication_date":"2025-11-24","ids":{"openalex":"https://openalex.org/W4416690969","doi":"https://doi.org/10.1371/journal.pcbi.1013743","pmid":"https://pubmed.ncbi.nlm.nih.gov/41284725"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013743","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013743","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1013743","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065781818","display_name":"Fatemeh Keikha","orcid":"https://orcid.org/0000-0003-1760-6394"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Fatemeh Keikha","raw_affiliation_strings":["Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008268821","display_name":"Chuanyuan Wang","orcid":"https://orcid.org/0000-0002-3206-1372"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chuanyuan Wang","raw_affiliation_strings":["Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051273783","display_name":"Zhixia Yang","orcid":"https://orcid.org/0000-0003-0446-4278"},"institutions":[{"id":"https://openalex.org/I96908189","display_name":"Xinjiang University","ror":"https://ror.org/059gw8r13","country_code":"CN","type":"education","lineage":["https://openalex.org/I96908189"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhixia Yang","raw_affiliation_strings":["College of Mathematics and Systems Science, Xinjiang University, Urumqi, Xinjiang, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Mathematics and Systems Science, Xinjiang University, Urumqi, Xinjiang, China","institution_ids":["https://openalex.org/I96908189"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001552700","display_name":"Zhi\u2010Ping Liu","orcid":"https://orcid.org/0000-0001-7742-9161"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I96908189","display_name":"Xinjiang University","ror":"https://ror.org/059gw8r13","country_code":"CN","type":"education","lineage":["https://openalex.org/I96908189"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhi-Ping Liu","raw_affiliation_strings":["College of Mathematics and Systems Science, Xinjiang University, Urumqi, Xinjiang, China","Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong, China","National Center for Applied Mathematics, Shandong University, Jinan, Shandong, China"],"raw_orcid":"https://orcid.org/0000-0001-7742-9161","affiliations":[{"raw_affiliation_string":"College of Mathematics and Systems Science, Xinjiang University, Urumqi, Xinjiang, China","institution_ids":["https://openalex.org/I96908189"]},{"raw_affiliation_string":"Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"National Center for Applied Mathematics, Shandong University, Jinan, Shandong, China","institution_ids":["https://openalex.org/I154099455"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5065781818"],"corresponding_institution_ids":["https://openalex.org/I154099455"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.30493955,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"21","issue":"11","first_page":"e1013743","last_page":"e1013743"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5364000201225281,"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":0.5364000201225281,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.3587999939918518,"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":0.028300000354647636,"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/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6148999929428101},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5263000130653381},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.4821000099182129},{"id":"https://openalex.org/keywords/biomarker-discovery","display_name":"Biomarker discovery","score":0.4675999879837036},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.447299987077713},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.4269999861717224},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.41749998927116394},{"id":"https://openalex.org/keywords/biomarker","display_name":"Biomarker","score":0.3668000102043152},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.35850000381469727}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6327999830245972},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6148999929428101},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5401999950408936},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5263000130653381},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4821000099182129},{"id":"https://openalex.org/C124535831","wikidata":"https://www.wikidata.org/wiki/Q4915074","display_name":"Biomarker discovery","level":4,"score":0.4675999879837036},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.447299987077713},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.4269999861717224},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.41749998927116394},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4147000014781952},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3840999901294708},{"id":"https://openalex.org/C2781197716","wikidata":"https://www.wikidata.org/wiki/Q864574","display_name":"Biomarker","level":2,"score":0.3668000102043152},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3596000075340271},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.35850000381469727},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.35019999742507935},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.3221000134944916},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.321399986743927},{"id":"https://openalex.org/C158207573","wikidata":"https://www.wikidata.org/wiki/Q5747224","display_name":"Heterogeneous network","level":4,"score":0.3151000142097473},{"id":"https://openalex.org/C13540734","wikidata":"https://www.wikidata.org/wiki/Q5318996","display_name":"Dynamic network analysis","level":2,"score":0.3127000033855438},{"id":"https://openalex.org/C2777002142","wikidata":"https://www.wikidata.org/wiki/Q5031432","display_name":"Cancer biomarkers","level":3,"score":0.30219998955726624},{"id":"https://openalex.org/C34947359","wikidata":"https://www.wikidata.org/wiki/Q665189","display_name":"Complex network","level":2,"score":0.30140000581741333},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.28850001096725464},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.2831999957561493},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.2793999910354614},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.262800008058548},{"id":"https://openalex.org/C3017616150","wikidata":"https://www.wikidata.org/wiki/Q1069330","display_name":"Diagnostic biomarker","level":3,"score":0.25769999623298645},{"id":"https://openalex.org/C74197172","wikidata":"https://www.wikidata.org/wiki/Q1195339","display_name":"Directed acyclic graph","level":2,"score":0.25600001215934753},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.2508000135421753}],"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":"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","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":"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":3,"locations":[{"id":"doi:10.1371/journal.pcbi.1013743","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013743","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:41284725","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41284725","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:84a7accf55af4f5aa56b66694aff24f5","is_oa":true,"landing_page_url":"https://doaj.org/article/84a7accf55af4f5aa56b66694aff24f5","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":"PLoS Computational Biology, Vol 21, Iss 11, p e1013743 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013743","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013743","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1552419163","display_name":null,"funder_award_id":"92374107","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5248026891","display_name":null,"funder_award_id":"62373216","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W1606375300","https://openalex.org/W1987219048","https://openalex.org/W2049923776","https://openalex.org/W2097749765","https://openalex.org/W2117692326","https://openalex.org/W2122708083","https://openalex.org/W2134596328","https://openalex.org/W2171115585","https://openalex.org/W2177221460","https://openalex.org/W2473462735","https://openalex.org/W2517756917","https://openalex.org/W2559588208","https://openalex.org/W2768700270","https://openalex.org/W2773934967","https://openalex.org/W2775791231","https://openalex.org/W2794480084","https://openalex.org/W2944311410","https://openalex.org/W2951531839","https://openalex.org/W2952590793","https://openalex.org/W2961453427","https://openalex.org/W2969229043","https://openalex.org/W2980135568","https://openalex.org/W3006545951","https://openalex.org/W3106518003","https://openalex.org/W3123028737","https://openalex.org/W3135888762","https://openalex.org/W3214798941","https://openalex.org/W4200111727","https://openalex.org/W4280521296","https://openalex.org/W4310732282","https://openalex.org/W4383377618","https://openalex.org/W4386452973","https://openalex.org/W4389166577","https://openalex.org/W4396829599","https://openalex.org/W4404699593","https://openalex.org/W4409481553","https://openalex.org/W4410348639","https://openalex.org/W4410738144"],"related_works":[],"abstract_inverted_index":{"The":[0],"identification":[1],"of":[2,84,180,212],"state":[3,92,122,167],"specific":[4],"biomarkers":[5,80,156,239],"that":[6,221],"reflect":[7],"dynamic":[8,79],"changes":[9,140],"in":[10,72,97,160,200],"gene":[11,111],"regulatory":[12,65,73,152,223],"networks":[13],"is":[14],"critical":[15],"for":[16,31,115,120,165,235],"understanding":[17],"cancer":[18],"progression":[19,243],"and":[20,46,128,176,190,204,228,240],"enhancing":[21],"diagnostic":[22],"precision.":[23],"While":[24],"multilayer":[25,99,196],"network":[26,164,197],"models":[27],"have":[28],"been":[29],"proposed":[30],"analyzing":[32],"disease":[33,50,76,91,166,242],"evolution,":[34],"most":[35],"existing":[36,195],"methods":[37],"rely":[38],"solely":[39],"on":[40,173],"topological":[41],"features,":[42],"neglecting":[43],"structural":[44,129],"rewiring":[45],"expression":[47,107,226],"variability":[48],"across":[49,187],"states.":[51],"In":[52],"this":[53],"study,":[54],"we":[55],"introduce":[56],"TransMarker,":[57],"a":[58,94,98,144,161,232],"framework":[59],"designed":[60],"to":[61,108,184,215],"detect":[62],"genes":[63],"with":[64,69,105,138],"role":[66],"transitions,":[67],"those":[68],"meaningful":[70,238],"shifts":[71,130],"roles":[74],"during":[75],"progression,":[77],"as":[78,93],"via":[81,133],"cross-state":[82,229],"alignment":[83,230],"multi-state":[85],"single-cell":[86],"data.":[87],"TransMarker":[88,193],"encodes":[89],"each":[90,116,121,213],"distinct":[95],"layer":[96],"graph,":[100],"integrating":[101],"prior":[102],"interaction":[103],"data":[104],"state-specific":[106],"construct":[109],"attributed":[110],"networks.":[112],"Contextualized":[113],"embeddings":[114],"stage":[117],"are":[118,131,141,157],"generated":[119],"using":[123,143],"Graph":[124],"Attention":[125],"Networks":[126],"(GATs),":[127],"quantified":[132],"Gromov-Wasserstein":[134],"optimal":[135],"transport.":[136],"Genes":[137],"significant":[139],"ranked":[142],"Dynamic":[145],"Network":[146],"Index":[147],"(DNI),":[148],"which":[149],"captures":[150],"their":[151],"variability.":[153],"These":[154],"prioritized":[155],"then":[158],"applied":[159],"deep":[162],"neural":[163],"classification.":[168],"We":[169],"validate":[170],"our":[171],"approach":[172],"synthetic":[174],"simulated":[175],"real":[177],"world":[178],"dataset":[179],"gastric":[181],"adenocarcinoma":[182],"(GAC),":[183],"evaluate":[185],"performance":[186],"diverse":[188],"scenarios":[189],"assess":[191],"generalizability.":[192],"outperforms":[194],"ranking":[198],"techniques":[199],"classification":[201],"accuracy,":[202],"robustness,":[203],"biomarker":[205],"relevance.":[206],"Ablation":[207],"studies":[208],"confirm":[209],"the":[210],"contribution":[211],"step":[214],"overall":[216],"performance.":[217],"Our":[218],"findings":[219],"suggest":[220],"combining":[222],"rewiring,":[224],"temporal":[225],"dynamics,":[227],"provides":[231],"powerful":[233],"strategy":[234],"identifying":[236],"biologically":[237],"modeling":[241],"at":[244],"single":[245],"cell":[246],"resolution.":[247]},"counts_by_year":[],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-11-25T00:00:00"}
