{"id":"https://openalex.org/W4226229254","doi":"https://doi.org/10.1093/bib/bbac170","title":"Decoding multilevel relationships with the human tissue-cell-molecule network","display_name":"Decoding multilevel relationships with the human tissue-cell-molecule network","publication_year":2022,"publication_date":"2022-04-19","ids":{"openalex":"https://openalex.org/W4226229254","doi":"https://doi.org/10.1093/bib/bbac170","pmid":"https://pubmed.ncbi.nlm.nih.gov/35551347"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac170","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac170","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033870400","display_name":"Siyu Hou","orcid":"https://orcid.org/0000-0002-5300-6495"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Siyu Hou","raw_affiliation_strings":["Institute for TCM-X, MOE Key Laboratory of Bioinformatics , Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, 100084 Beijing , China"],"raw_orcid":"https://orcid.org/0000-0002-5300-6495","affiliations":[{"raw_affiliation_string":"Institute for TCM-X, MOE Key Laboratory of Bioinformatics , Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, 100084 Beijing , China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100364149","display_name":"Peng Zhang","orcid":"https://orcid.org/0000-0002-5858-207X"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peng Zhang","raw_affiliation_strings":["Institute for TCM-X, MOE Key Laboratory of Bioinformatics , Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, 100084 Beijing , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for TCM-X, MOE Key Laboratory of Bioinformatics , Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, 100084 Beijing , China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051184139","display_name":"Kuo Yang","orcid":"https://orcid.org/0000-0003-0736-4512"},"institutions":[{"id":"https://openalex.org/I21193070","display_name":"Beijing Jiaotong University","ror":"https://ror.org/01yj56c84","country_code":"CN","type":"education","lineage":["https://openalex.org/I21193070"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kuo Yang","raw_affiliation_strings":["Institute for TCM-X, MOE Key Laboratory of Bioinformatics , Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, 100084 Beijing , China","School of Computer and Information Technology , Beijing Jiaotong University, Beijing, 100044 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for TCM-X, MOE Key Laboratory of Bioinformatics , Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, 100084 Beijing , China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"School of Computer and Information Technology , Beijing Jiaotong University, Beijing, 100044 , China","institution_ids":["https://openalex.org/I21193070"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040850850","display_name":"Lan Wang","orcid":"https://orcid.org/0000-0002-8931-7201"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lan Wang","raw_affiliation_strings":["Institute for TCM-X, MOE Key Laboratory of Bioinformatics , Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, 100084 Beijing , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for TCM-X, MOE Key Laboratory of Bioinformatics , Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, 100084 Beijing , China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043149501","display_name":"Changzheng Ma","orcid":"https://orcid.org/0000-0002-8818-7046"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Changzheng Ma","raw_affiliation_strings":["Institute for TCM-X, MOE Key Laboratory of Bioinformatics , Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, 100084 Beijing , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for TCM-X, MOE Key Laboratory of Bioinformatics , Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, 100084 Beijing , China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033512723","display_name":"Yanda Li","orcid":"https://orcid.org/0000-0002-9439-202X"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanda Li","raw_affiliation_strings":["Institute for TCM-X, MOE Key Laboratory of Bioinformatics , Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, 100084 Beijing , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for TCM-X, MOE Key Laboratory of Bioinformatics , Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, 100084 Beijing , China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076576399","display_name":"Shao Li","orcid":"https://orcid.org/0000-0002-8709-9167"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shao Li","raw_affiliation_strings":["Institute for TCM-X, MOE Key Laboratory of Bioinformatics , Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, 100084 Beijing , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for TCM-X, MOE Key Laboratory of Bioinformatics , Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, 100084 Beijing , China","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5076576399"],"corresponding_institution_ids":["https://openalex.org/I99065089"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.2993,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.79067409,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"23","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9977999925613403,"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":0.9977999925613403,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9948999881744385,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9819999933242798,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/decoding-methods","display_name":"Decoding methods","score":0.7527312636375427},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4864063262939453},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3937947452068329},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23646560311317444},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.11535295844078064}],"concepts":[{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.7527312636375427},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4864063262939453},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3937947452068329},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23646560311317444},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.11535295844078064}],"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013274","descriptor_name":"Stomach Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013274","descriptor_name":"Stomach Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac170","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac170","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35551347","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35551347","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6370538713","display_name":null,"funder_award_id":"62061160369","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6429079033","display_name":"\u57fa\u4e8e\u751f\u7269\u7f51\u7edc\u7684\u75c5\u8bc1\u7ed3\u5408\u7814\u7a76\u65b9\u6cd5","funder_award_id":"81630103","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":61,"referenced_works":["https://openalex.org/W978308701","https://openalex.org/W1505893511","https://openalex.org/W1533942137","https://openalex.org/W1975449945","https://openalex.org/W1980568044","https://openalex.org/W1981409633","https://openalex.org/W1982330633","https://openalex.org/W2001939488","https://openalex.org/W2009405916","https://openalex.org/W2018570668","https://openalex.org/W2024038403","https://openalex.org/W2035506626","https://openalex.org/W2038122249","https://openalex.org/W2056782561","https://openalex.org/W2060177339","https://openalex.org/W2062533676","https://openalex.org/W2068714945","https://openalex.org/W2077997913","https://openalex.org/W2079673140","https://openalex.org/W2080240378","https://openalex.org/W2083045667","https://openalex.org/W2097498614","https://openalex.org/W2118607021","https://openalex.org/W2119943416","https://openalex.org/W2126249571","https://openalex.org/W2133696655","https://openalex.org/W2144086069","https://openalex.org/W2154851992","https://openalex.org/W2156443053","https://openalex.org/W2163480486","https://openalex.org/W2347110697","https://openalex.org/W2493614923","https://openalex.org/W2567841939","https://openalex.org/W2624021832","https://openalex.org/W2735272571","https://openalex.org/W2757254843","https://openalex.org/W2807869290","https://openalex.org/W2895456557","https://openalex.org/W2899291554","https://openalex.org/W2911932738","https://openalex.org/W2937762029","https://openalex.org/W2944311410","https://openalex.org/W2949475756","https://openalex.org/W2962756421","https://openalex.org/W2977707586","https://openalex.org/W3006650868","https://openalex.org/W3013151148","https://openalex.org/W3021838782","https://openalex.org/W3034402905","https://openalex.org/W3036981277","https://openalex.org/W3089299640","https://openalex.org/W3102189550","https://openalex.org/W3104097132","https://openalex.org/W3107527779","https://openalex.org/W3133960398","https://openalex.org/W3167882125","https://openalex.org/W3184729641","https://openalex.org/W3189676628","https://openalex.org/W3210147532","https://openalex.org/W4297808394","https://openalex.org/W6844194202"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Understanding":[0],"the":[1,98,106,109,146,157,174,177,190],"biological":[2],"functions":[3],"of":[4,38,52,91,108,148,181],"molecules":[5],"in":[6,125,145],"specific":[7,149],"human":[8,19,75],"tissues":[9,85,150],"or":[10,151],"cell":[11,42,87,137],"types":[12,43,88],"is":[13,28],"crucial":[14],"for":[15],"gaining":[16],"insights":[17,172],"into":[18,173],"physiology":[20],"and":[21,44,55,86,139,142,162,179,198,206],"disease.":[22],"To":[23,57],"address":[24,58],"this":[25,59],"issue,":[26],"it":[27],"essential":[29],"to":[30,135,192],"systematically":[31,96,193],"uncover":[32,194],"associations":[33],"among":[34,202],"multilevel":[35,76,102],"elements":[36,103],"consisting":[37],"disease":[39,126,196],"phenotypes,":[40],"tissues,":[41],"molecules,":[45],"which":[46],"could":[47],"pose":[48],"a":[49,63,74,154],"challenge":[50],"because":[51],"their":[53],"heterogeneity":[54],"incompleteness.":[56],"challenge,":[60],"we":[61,80],"describe":[62],"new":[64],"methodological":[65,187],"framework,":[66],"called":[67],"Graph":[68],"Local":[69],"InfoMax":[70],"(GLIM),":[71],"based":[72],"on":[73,89],"network":[77,159],"(HMLN)":[78],"that":[79,118],"established":[81],"by":[82,104,168],"introducing":[83],"multiple":[84],"top":[90],"molecular":[92,143,207],"networks.":[93],"GLIM":[94,119,130],"can":[95],"mine":[97,199],"potential":[99,191],"relationships":[100,201],"between":[101],"embedding":[105],"features":[107],"HMLN":[110],"through":[111],"contrastive":[112],"learning.":[113],"Our":[114],"simulation":[115],"results":[116],"demonstrated":[117],"consistently":[120],"outperforms":[121],"other":[122],"state-of-the-art":[123],"algorithms":[124],"gene":[127],"prediction.":[128],"Moreover,":[129],"was":[131,165],"also":[132],"successfully":[133],"used":[134],"infer":[136],"markers":[138],"rewire":[140],"intercellular":[141],"interactions":[144],"context":[147],"diseases.":[152],"As":[153],"typical":[155],"case,":[156],"tissue-cell-molecule":[158],"underlying":[160,176],"gastritis":[161],"gastric":[163,182],"cancer":[164],"first":[166],"uncovered":[167],"GLIM,":[169],"providing":[170],"systematic":[171],"mechanism":[175],"occurrence":[178],"development":[180],"cancer.":[183],"Overall,":[184],"our":[185],"constructed":[186],"framework":[188],"has":[189],"complex":[195],"mechanisms":[197],"high-quality":[200],"phenotypical,":[203],"tissue,":[204],"cellular":[205],"elements.":[208]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":6}],"updated_date":"2026-06-06T09:05:17.133730","created_date":"2025-10-10T00:00:00"}
