{"id":"https://openalex.org/W4412957524","doi":"https://doi.org/10.1093/bioinformatics/btaf352","title":"Double optimal transport for differential gene regulatory network inference with unpaired samples","display_name":"Double optimal transport for differential gene regulatory network inference with unpaired samples","publication_year":2025,"publication_date":"2025-08-01","ids":{"openalex":"https://openalex.org/W4412957524","doi":"https://doi.org/10.1093/bioinformatics/btaf352","pmid":"https://pubmed.ncbi.nlm.nih.gov/40757912"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf352","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf352","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btaf352","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100722835","display_name":"Mengyu Li","orcid":"https://orcid.org/0000-0002-5286-7525"},"institutions":[{"id":"https://openalex.org/I78988378","display_name":"Renmin University of China","ror":"https://ror.org/041pakw92","country_code":"CN","type":"education","lineage":["https://openalex.org/I78988378"]},{"id":"https://openalex.org/I4210096250","display_name":"Beijing Institute of Big Data Research","ror":"https://ror.org/00s1sz824","country_code":"CN","type":"facility","lineage":["https://openalex.org/I20231570","https://openalex.org/I37796252","https://openalex.org/I4210096250"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Mengyu Li","raw_affiliation_strings":["Institute of Statistics and Big Data, Renmin University of China , Beijing 100872,","Institute of Statistics and Big Data, Renmin University of China, Beijing 100872, China"],"affiliations":[{"raw_affiliation_string":"Institute of Statistics and Big Data, Renmin University of China , Beijing 100872,","institution_ids":["https://openalex.org/I78988378","https://openalex.org/I4210096250"]},{"raw_affiliation_string":"Institute of Statistics and Big Data, Renmin University of China, Beijing 100872, China","institution_ids":["https://openalex.org/I78988378"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080509522","display_name":"Bencong Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bencong Zhu","raw_affiliation_strings":["Department of Statistics, The Chinese University of Hong Kong , Hong Kong 999077,","Department of Statistics, The Chinese University of Hong Kong, Hong Kong 999077, China"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, The Chinese University of Hong Kong , Hong Kong 999077,","institution_ids":["https://openalex.org/I177725633"]},{"raw_affiliation_string":"Department of Statistics, The Chinese University of Hong Kong, Hong Kong 999077, China","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102923021","display_name":"Cheng Meng","orcid":"https://orcid.org/0000-0002-7111-0966"},"institutions":[{"id":"https://openalex.org/I4210096250","display_name":"Beijing Institute of Big Data Research","ror":"https://ror.org/00s1sz824","country_code":"CN","type":"facility","lineage":["https://openalex.org/I20231570","https://openalex.org/I37796252","https://openalex.org/I4210096250"]},{"id":"https://openalex.org/I78988378","display_name":"Renmin University of China","ror":"https://ror.org/041pakw92","country_code":"CN","type":"education","lineage":["https://openalex.org/I78988378"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cheng Meng","raw_affiliation_strings":["Center for Applied Statistics, Institute of Statistics and Big Data, Renmin University of China , Beijing 100872,","Center for Applied Statistics, Institute of Statistics and Big Data, Renmin University of China, Beijing 100872, China"],"affiliations":[{"raw_affiliation_string":"Center for Applied Statistics, Institute of Statistics and Big Data, Renmin University of China , Beijing 100872,","institution_ids":["https://openalex.org/I78988378","https://openalex.org/I4210096250"]},{"raw_affiliation_string":"Center for Applied Statistics, Institute of Statistics and Big Data, Renmin University of China, Beijing 100872, China","institution_ids":["https://openalex.org/I78988378"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060018541","display_name":"Xiaodan Fan","orcid":"https://orcid.org/0000-0002-2744-9030"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaodan Fan","raw_affiliation_strings":["Department of Statistics, The Chinese University of Hong Kong , Hong Kong 999077,","Department of Statistics, The Chinese University of Hong Kong, Hong Kong 999077, China"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, The Chinese University of Hong Kong , Hong Kong 999077,","institution_ids":["https://openalex.org/I177725633"]},{"raw_affiliation_string":"Department of Statistics, The Chinese University of Hong Kong, Hong Kong 999077, China","institution_ids":["https://openalex.org/I177725633"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100722835"],"corresponding_institution_ids":["https://openalex.org/I4210096250","https://openalex.org/I78988378"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.17916686,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9955999851226807,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9879999756813049,"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/computer-science","display_name":"Computer science","score":0.7131384611129761},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6887804269790649},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6741106510162354},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5792209506034851},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4621162712574005},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37242186069488525},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2770431935787201},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.27199792861938477},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.25475624203681946},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1659514307975769},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10416391491889954}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7131384611129761},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6887804269790649},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6741106510162354},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5792209506034851},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4621162712574005},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37242186069488525},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2770431935787201},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27199792861938477},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25475624203681946},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1659514307975769},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10416391491889954},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000090063","descriptor_name":"Proto-Oncogene Mas","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000090063","descriptor_name":"Proto-Oncogene Mas","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000090063","descriptor_name":"Proto-Oncogene Mas","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000090063","descriptor_name":"Proto-Oncogene Mas","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000090063","descriptor_name":"Proto-Oncogene Mas","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D013274","descriptor_name":"Stomach Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013274","descriptor_name":"Stomach Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013274","descriptor_name":"Stomach Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013274","descriptor_name":"Stomach Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013274","descriptor_name":"Stomach Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013274","descriptor_name":"Stomach Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013274","descriptor_name":"Stomach Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013274","descriptor_name":"Stomach Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013274","descriptor_name":"Stomach Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013274","descriptor_name":"Stomach Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"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":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf352","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf352","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40757912","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40757912","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:12342166","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12342166","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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/btaf352","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf352","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W1573602524","https://openalex.org/W1585160083","https://openalex.org/W1920348529","https://openalex.org/W2007490905","https://openalex.org/W2030119035","https://openalex.org/W2036996178","https://openalex.org/W2061425021","https://openalex.org/W2076477598","https://openalex.org/W2076513103","https://openalex.org/W2085116222","https://openalex.org/W2106555403","https://openalex.org/W2126345910","https://openalex.org/W2132555912","https://openalex.org/W2134179844","https://openalex.org/W2165009258","https://openalex.org/W2165190832","https://openalex.org/W2173732482","https://openalex.org/W2337819340","https://openalex.org/W2465098683","https://openalex.org/W2552017669","https://openalex.org/W2559588208","https://openalex.org/W2899545492","https://openalex.org/W2900099657","https://openalex.org/W2931120067","https://openalex.org/W2998917483","https://openalex.org/W3047682456","https://openalex.org/W3082556740","https://openalex.org/W3089458470","https://openalex.org/W3094335680","https://openalex.org/W3104417128","https://openalex.org/W3127245931","https://openalex.org/W3158738859","https://openalex.org/W3177878434","https://openalex.org/W3199285124","https://openalex.org/W3214180234","https://openalex.org/W4210832122","https://openalex.org/W4213459226","https://openalex.org/W4282932623","https://openalex.org/W4283726337","https://openalex.org/W4287866560","https://openalex.org/W4296024012","https://openalex.org/W4308834225","https://openalex.org/W4312190814","https://openalex.org/W4313829323","https://openalex.org/W4316653897","https://openalex.org/W4321615643","https://openalex.org/W4380551942","https://openalex.org/W4380715272","https://openalex.org/W4382022265","https://openalex.org/W4387774515","https://openalex.org/W4391661458","https://openalex.org/W4409683720","https://openalex.org/W4410201440","https://openalex.org/W6774184294","https://openalex.org/W6779738240","https://openalex.org/W6784503993","https://openalex.org/W6804393327","https://openalex.org/W6853595279"],"related_works":["https://openalex.org/W2389214306","https://openalex.org/W2965083567","https://openalex.org/W4235240664","https://openalex.org/W1838576100","https://openalex.org/W2095886385","https://openalex.org/W2950199998","https://openalex.org/W2560421304","https://openalex.org/W2951387065","https://openalex.org/W4385727351","https://openalex.org/W4306798985"],"abstract_inverted_index":{"A":[0],"Python":[1],"library":[2],"that":[3],"implements":[4],"the":[5],"proposed":[6],"method":[7],"is":[8],"available":[9],"at":[10],"https://github.com/Mengyu8042/ot-grn.":[11]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
