{"id":"https://openalex.org/W4408300361","doi":"https://doi.org/10.1093/bib/bbaf085","title":"Learning directed acyclic graphs for ligands and receptors based on spatially resolved transcriptomic data of ovarian cancer","display_name":"Learning directed acyclic graphs for ligands and receptors based on spatially resolved transcriptomic data of ovarian cancer","publication_year":2025,"publication_date":"2025-03-01","ids":{"openalex":"https://openalex.org/W4408300361","doi":"https://doi.org/10.1093/bib/bbaf085","pmid":"https://pubmed.ncbi.nlm.nih.gov/40062614"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf085","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf085","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf085/62364411/bbaf085.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in 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/bib/article-pdf/26/2/bbaf085/62364411/bbaf085.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049850046","display_name":"Shrabanti Chowdhury","orcid":"https://orcid.org/0000-0001-8429-7822"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shrabanti Chowdhury","raw_affiliation_strings":["Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , 1399 Park Ave, New York, NY 10029 ,","Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1399 Park Ave, New York, NY 10029, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , 1399 Park Ave, New York, NY 10029 ,","institution_ids":["https://openalex.org/I98704320"]},{"raw_affiliation_string":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1399 Park Ave, New York, NY 10029, United States","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060541999","display_name":"Sammy Ferri\u2010Borgogno","orcid":"https://orcid.org/0000-0002-8270-8963"},"institutions":[{"id":"https://openalex.org/I117693200","display_name":"Gynecologic Oncology Group","ror":"https://ror.org/04x187e69","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I117693200"]},{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sammy Ferri-Borgogno","raw_affiliation_strings":["Department of Gynecologic Oncology and Reproductive Medicine , Division of Surgery, , 1155 Pressler St., Houston, TX 77030 ,","The University of Texas MD Anderson Cancer Center , Division of Surgery, , 1155 Pressler St., Houston, TX 77030 ,","Department of Gynecologic Oncology and Reproductive Medicine, Division of Surgery, The University of Texas MD Anderson Cancer Center, 1155 Pressler St., Houston, TX 77030, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Gynecologic Oncology and Reproductive Medicine , Division of Surgery, , 1155 Pressler St., Houston, TX 77030 ,","institution_ids":["https://openalex.org/I117693200"]},{"raw_affiliation_string":"The University of Texas MD Anderson Cancer Center , Division of Surgery, , 1155 Pressler St., Houston, TX 77030 ,","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"Department of Gynecologic Oncology and Reproductive Medicine, Division of Surgery, The University of Texas MD Anderson Cancer Center, 1155 Pressler St., Houston, TX 77030, United States","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026731357","display_name":"Yang Peng","orcid":"https://orcid.org/0000-0002-0630-9506"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peng Yang","raw_affiliation_strings":["Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center , TX ,","Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, TX, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center , TX ,","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, TX, United States","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100354894","display_name":"Wenyi Wang","orcid":"https://orcid.org/0000-0003-0617-9438"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wenyi Wang","raw_affiliation_strings":["Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center , TX ,","Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, TX, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center , TX ,","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, TX, United States","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102003987","display_name":"Jie Peng","orcid":"https://orcid.org/0000-0003-4040-0327"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jie Peng","raw_affiliation_strings":["Department of Statistics, University of California Davis , 399 Crocker Ln, Davis, CA 95616 ,","Department of Statistics, University of California Davis, 399 Crocker Ln, Davis, CA 95616, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of California Davis , 399 Crocker Ln, Davis, CA 95616 ,","institution_ids":["https://openalex.org/I84218800"]},{"raw_affiliation_string":"Department of Statistics, University of California Davis, 399 Crocker Ln, Davis, CA 95616, United States","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010693778","display_name":"Samuel C. Mok","orcid":"https://orcid.org/0000-0001-7013-1805"},"institutions":[{"id":"https://openalex.org/I117693200","display_name":"Gynecologic Oncology Group","ror":"https://ror.org/04x187e69","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I117693200"]},{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samuel C Mok","raw_affiliation_strings":["Department of Gynecologic Oncology and Reproductive Medicine , Division of Surgery, , 1155 Pressler St., Houston, TX 77030 ,","The University of Texas MD Anderson Cancer Center , Division of Surgery, , 1155 Pressler St., Houston, TX 77030 ,","Department of Gynecologic Oncology and Reproductive Medicine, Division of Surgery, The University of Texas MD Anderson Cancer Center, 1155 Pressler St., Houston, TX 77030, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Gynecologic Oncology and Reproductive Medicine , Division of Surgery, , 1155 Pressler St., Houston, TX 77030 ,","institution_ids":["https://openalex.org/I117693200"]},{"raw_affiliation_string":"The University of Texas MD Anderson Cancer Center , Division of Surgery, , 1155 Pressler St., Houston, TX 77030 ,","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"Department of Gynecologic Oncology and Reproductive Medicine, Division of Surgery, The University of Texas MD Anderson Cancer Center, 1155 Pressler St., Houston, TX 77030, United States","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100462647","display_name":"Pei Wang","orcid":"https://orcid.org/0000-0002-6890-6453"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pei Wang","raw_affiliation_strings":["Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , 1399 Park Ave, New York, NY 10029 ,","Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1399 Park Ave, New York, NY 10029, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , 1399 Park Ave, New York, NY 10029 ,","institution_ids":["https://openalex.org/I98704320"]},{"raw_affiliation_string":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1399 Park Ave, New York, NY 10029, United States","institution_ids":["https://openalex.org/I98704320"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.4528,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.79711105,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"26","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","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/T11289","display_name":"Single-cell and spatial transcriptomics","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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9984999895095825,"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":0.9983999729156494,"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/stromal-cell","display_name":"Stromal cell","score":0.7854069471359253},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.5738794207572937},{"id":"https://openalex.org/keywords/tumor-microenvironment","display_name":"Tumor microenvironment","score":0.5503026843070984},{"id":"https://openalex.org/keywords/serous-fluid","display_name":"Serous fluid","score":0.48625648021698},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4854603409767151},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4828825294971466},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.4493100643157959},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4197009205818176},{"id":"https://openalex.org/keywords/cancer-research","display_name":"Cancer research","score":0.3959890305995941},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.1995423436164856},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07613655924797058}],"concepts":[{"id":"https://openalex.org/C16930146","wikidata":"https://www.wikidata.org/wiki/Q4381253","display_name":"Stromal cell","level":2,"score":0.7854069471359253},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.5738794207572937},{"id":"https://openalex.org/C2776107976","wikidata":"https://www.wikidata.org/wiki/Q1786433","display_name":"Tumor microenvironment","level":3,"score":0.5503026843070984},{"id":"https://openalex.org/C150173356","wikidata":"https://www.wikidata.org/wiki/Q6144101","display_name":"Serous fluid","level":2,"score":0.48625648021698},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4854603409767151},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4828825294971466},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.4493100643157959},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4197009205818176},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.3959890305995941},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.1995423436164856},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07613655924797058},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011956","descriptor_name":"Receptors, Cell Surface","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","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":"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":"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":"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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"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":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1093/bib/bbaf085","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf085","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf085/62364411/bbaf085.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40062614","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40062614","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:ark:/13030/qt4zt1t57t","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:digitalcommons.library.tmc.edu:uthgsbs_docs-5987","is_oa":false,"landing_page_url":"https://digitalcommons.library.tmc.edu/uthgsbs_docs/5126","pdf_url":null,"source":{"id":"https://openalex.org/S4306401994","display_name":"DigtalCommons @ Texas Medical Center Library (Texas Medical Center)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I867280407","host_organization_name":"The University of Texas Southwestern Medical Center","host_organization_lineage":["https://openalex.org/I867280407"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty, Staff and Student Publications","raw_type":"text"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt4zt1t57t","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/4zt1t57t","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics, vol 26, iss 2","raw_type":"article"},{"id":"pmh:oai:europepmc.org:10702916","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11891659","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf085","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf085","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf085/62364411/bbaf085.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3771350101","display_name":null,"funder_award_id":"U24 CA271114","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G687683514","display_name":null,"funder_award_id":"R01 CA268380","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4408300361.pdf"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W156821250","https://openalex.org/W1016059894","https://openalex.org/W1781764024","https://openalex.org/W2006683252","https://openalex.org/W2044124287","https://openalex.org/W2073307618","https://openalex.org/W2100603120","https://openalex.org/W2123696077","https://openalex.org/W2127256767","https://openalex.org/W2128088446","https://openalex.org/W2131593373","https://openalex.org/W2152227081","https://openalex.org/W2225255384","https://openalex.org/W2322659453","https://openalex.org/W2464880876","https://openalex.org/W2471536144","https://openalex.org/W2611370172","https://openalex.org/W2756270022","https://openalex.org/W2767421465","https://openalex.org/W2777190022","https://openalex.org/W2940899024","https://openalex.org/W2992151131","https://openalex.org/W3007935255","https://openalex.org/W3012498554","https://openalex.org/W3021920958","https://openalex.org/W3045892125","https://openalex.org/W3114457750","https://openalex.org/W3119379269","https://openalex.org/W3130232612","https://openalex.org/W3132661792","https://openalex.org/W3134482219","https://openalex.org/W3155546248","https://openalex.org/W3163061470","https://openalex.org/W3187534341","https://openalex.org/W4200220118","https://openalex.org/W4220864906","https://openalex.org/W4285588297","https://openalex.org/W4287219340","https://openalex.org/W4289868596","https://openalex.org/W4299515571","https://openalex.org/W4312094047","https://openalex.org/W4320709643","https://openalex.org/W4321760721","https://openalex.org/W4385556257","https://openalex.org/W4388997570","https://openalex.org/W4393858351","https://openalex.org/W6858709717"],"related_works":["https://openalex.org/W2980421756","https://openalex.org/W2014221109","https://openalex.org/W183804059","https://openalex.org/W2314776203","https://openalex.org/W2607392433","https://openalex.org/W3118727544","https://openalex.org/W2406061890","https://openalex.org/W2025926545","https://openalex.org/W4322709813","https://openalex.org/W2023695613"],"abstract_inverted_index":{"To":[0],"unravel":[1],"the":[2,28,87,114,193],"mechanism":[3],"of":[4,117,142,147,164,179,207],"immune":[5],"activation":[6],"and":[7,24,40,94,130,156,174,197],"suppression":[8],"within":[9],"tumors,":[10],"a":[11,44,80,103,109,132,171,175],"critical":[12],"step":[13],"is":[14,209],"to":[15,32,65,85,112,136,144,192],"identify":[16],"transcriptional":[17],"signals":[18],"governing":[19],"cell-cell":[20,73],"communication":[21,34,194],"between":[22,37,91,195],"tumor":[23,29,93,151,182,196],"immune/stromal":[25,198],"cells":[26,96,199],"in":[27,53,54,200],"microenvironment.":[30],"Central":[31],"this":[33,76],"are":[35],"interactions":[36,166],"secreted":[38],"ligands":[39],"cell-surface":[41],"receptors,":[42],"creating":[43],"highly":[45],"connected":[46],"signaling":[47,69],"network":[48,139],"among":[49],"cells.":[50],"Recent":[51],"advancements":[52],"situ-omics":[55],"profiling,":[56],"particularly":[57],"spatial":[58],"transcriptomic":[59],"(ST)":[60],"technology,":[61],"provide":[62],"unique":[63],"opportunities":[64],"directly":[66],"characterize":[67,86],"ligand-receptor":[68,88,124,158],"networks":[70,90],"that":[71],"power":[72],"communication.":[74],"In":[75],"paper,":[77],"we":[78],"propose":[79],"novel":[81,110],"statistical":[82],"method,":[83],"LRnetST,":[84],"interaction":[89],"adjacent":[92],"immune/stroma":[95],"based":[97],"on":[98,188,211],"ST":[99,118,145],"data.":[100,119],"LRnetST":[101,143,208],"utilizes":[102],"directed":[104],"acyclic":[105],"graph":[106],"model":[107],"with":[108],"approach":[111],"handle":[113],"zero-inflated":[115],"distributions":[116],"It":[120],"also":[121],"leverages":[122],"existing":[123],"regulation":[125],"databases":[126],"as":[127],"prior":[128],"information,":[129],"employs":[131],"bootstrap":[133],"aggregation":[134],"strategy":[135],"achieve":[137],"robust":[138],"estimation.":[140],"Application":[141],"data":[146],"high-grade":[148],"serous":[149],"ovarian":[150,181,201],"samples":[152],"revealed":[153],"both":[154,170],"common":[155],"distinct":[157],"regulations":[159],"across":[160],"different":[161],"tumors.":[162,202],"Some":[163],"these":[165],"were":[167],"validated":[168],"through":[169],"MERFISH":[172],"dataset":[173,178],"CosMx":[176],"SMI":[177],"independent":[180],"samples.":[183],"These":[184],"results":[185],"cast":[186],"light":[187],"biological":[189],"processes":[190],"relating":[191],"An":[203],"open-source":[204],"R":[205],"package":[206],"available":[210],"GitHub":[212],"at":[213],"https://github.com/jie108/LRnetST.":[214]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-14T08:27:34.040176","created_date":"2025-10-10T00:00:00"}