{"id":"https://openalex.org/W3201411589","doi":"https://doi.org/10.1021/acs.jcim.1c00967","title":"TRIOMPHE: Transcriptome-Based Inference and Generation of Molecules with Desired Phenotypes by Machine Learning","display_name":"TRIOMPHE: Transcriptome-Based Inference and Generation of Molecules with Desired Phenotypes by Machine Learning","publication_year":2021,"publication_date":"2021-09-16","ids":{"openalex":"https://openalex.org/W3201411589","doi":"https://doi.org/10.1021/acs.jcim.1c00967","mag":"3201411589","pmid":"https://pubmed.ncbi.nlm.nih.gov/34528432"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c00967","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00967","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5007053776","display_name":"Kazuma Kaitoh","orcid":"https://orcid.org/0000-0003-4237-1822"},"institutions":[{"id":"https://openalex.org/I207014233","display_name":"Kyushu Institute of Technology","ror":"https://ror.org/02278tr80","country_code":"JP","type":"education","lineage":["https://openalex.org/I207014233"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kazuma Kaitoh","raw_affiliation_strings":["Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan","institution_ids":["https://openalex.org/I207014233"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035394108","display_name":"Yoshihiro Yamanishi","orcid":"https://orcid.org/0000-0003-2279-8773"},"institutions":[{"id":"https://openalex.org/I207014233","display_name":"Kyushu Institute of Technology","ror":"https://ror.org/02278tr80","country_code":"JP","type":"education","lineage":["https://openalex.org/I207014233"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yoshihiro Yamanishi","raw_affiliation_strings":["Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan","institution_ids":["https://openalex.org/I207014233"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5035394108"],"corresponding_institution_ids":["https://openalex.org/I207014233"],"apc_list":null,"apc_paid":null,"fwci":2.0716,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.88777369,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"61","issue":"9","first_page":"4303","last_page":"4320"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9937999844551086,"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/transcriptome","display_name":"Transcriptome","score":0.8247154951095581},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6995232701301575},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.5849363207817078},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5532441139221191},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5371473431587219},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.5318467617034912},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5262188911437988},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.46078813076019287},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4457399249076843},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.42342519760131836},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3765942454338074},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2728514075279236},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2722429037094116},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.19525504112243652},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.15578767657279968},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13453376293182373}],"concepts":[{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.8247154951095581},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6995232701301575},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.5849363207817078},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5532441139221191},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5371473431587219},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.5318467617034912},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5262188911437988},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.46078813076019287},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4457399249076843},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.42342519760131836},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3765942454338074},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2728514075279236},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2722429037094116},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.19525504112243652},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.15578767657279968},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13453376293182373},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.1c00967","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00967","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:34528432","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34528432","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.6200000047683716,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G3516496435","display_name":null,"funder_award_id":"20H05797","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4793641312","display_name":null,"funder_award_id":"JP21nk0101111","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"}],"funders":[{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":87,"referenced_works":["https://openalex.org/W1710476689","https://openalex.org/W1959608418","https://openalex.org/W1971375063","https://openalex.org/W1975147762","https://openalex.org/W1979142801","https://openalex.org/W1979453000","https://openalex.org/W1981276685","https://openalex.org/W1988037271","https://openalex.org/W1988377311","https://openalex.org/W1999638776","https://openalex.org/W2007667104","https://openalex.org/W2017254234","https://openalex.org/W2027482274","https://openalex.org/W2027844138","https://openalex.org/W2033882981","https://openalex.org/W2038702914","https://openalex.org/W2046588282","https://openalex.org/W2086141419","https://openalex.org/W2088320215","https://openalex.org/W2094791588","https://openalex.org/W2096729078","https://openalex.org/W2098967508","https://openalex.org/W2100495367","https://openalex.org/W2108559088","https://openalex.org/W2121604817","https://openalex.org/W2123774442","https://openalex.org/W2126595303","https://openalex.org/W2134427192","https://openalex.org/W2139516171","https://openalex.org/W2152195021","https://openalex.org/W2154777073","https://openalex.org/W2154896031","https://openalex.org/W2156345326","https://openalex.org/W2166478947","https://openalex.org/W2171437346","https://openalex.org/W2267384021","https://openalex.org/W2273267066","https://openalex.org/W2318311899","https://openalex.org/W2394642790","https://openalex.org/W2529996553","https://openalex.org/W2568475068","https://openalex.org/W2592725663","https://openalex.org/W2593632281","https://openalex.org/W2610148085","https://openalex.org/W2736137960","https://openalex.org/W2782083554","https://openalex.org/W2788776141","https://openalex.org/W2803098868","https://openalex.org/W2806351858","https://openalex.org/W2896822135","https://openalex.org/W2898868646","https://openalex.org/W2901476322","https://openalex.org/W2911495555","https://openalex.org/W2912328818","https://openalex.org/W2913668833","https://openalex.org/W2917650400","https://openalex.org/W2921262115","https://openalex.org/W2948831670","https://openalex.org/W2952181316","https://openalex.org/W2960106955","https://openalex.org/W2986642182","https://openalex.org/W2990776556","https://openalex.org/W2992586577","https://openalex.org/W2998571806","https://openalex.org/W3001549920","https://openalex.org/W3003192283","https://openalex.org/W3004359474","https://openalex.org/W3004974539","https://openalex.org/W3005417975","https://openalex.org/W3007683801","https://openalex.org/W3009321976","https://openalex.org/W3010510082","https://openalex.org/W3010761615","https://openalex.org/W3037523055","https://openalex.org/W3043278204","https://openalex.org/W3043969542","https://openalex.org/W3045928028","https://openalex.org/W3090915092","https://openalex.org/W3096214162","https://openalex.org/W3098269892","https://openalex.org/W3113961789","https://openalex.org/W3116589398","https://openalex.org/W3130120676","https://openalex.org/W4214717370","https://openalex.org/W4230274588","https://openalex.org/W4232643761","https://openalex.org/W4289436753"],"related_works":["https://openalex.org/W3013693939","https://openalex.org/W2159052453","https://openalex.org/W2566616303","https://openalex.org/W3131327266","https://openalex.org/W2734887215","https://openalex.org/W2043558654","https://openalex.org/W4225792090","https://openalex.org/W2090863707","https://openalex.org/W4385741417","https://openalex.org/W4285201319"],"abstract_inverted_index":{"One":[0],"of":[1,14,43,77,82,97,107,113,121,132,180,185],"the":[2,7,11,50,94,105,118,163,176],"most":[3],"challenging":[4],"tasks":[5],"in":[6,80,104],"drug-discovery":[8],"process":[9],"is":[10,170],"efficient":[12],"identification":[13],"small":[15],"molecules":[16,44,99,122,143],"with":[17,45,100],"desired":[18,46,101,114],"phenotypes.":[19],"In":[20],"this":[21],"study,":[22],"we":[23,36,86],"propose":[24],"a":[25,108,183],"novel":[26,88],"computational":[27],"method":[28],"for":[29,129,175,182],"omics-based":[30,167],"<i>de":[31,177],"novo</i>":[32,178],"drug":[33],"design,":[34],"which":[35],"call":[37],"TRIOMPHE":[38],"(transcriptome-based":[39],"inference":[40],"and":[41,63],"generation":[42],"phenotypes).":[47],"We":[48,134],"investigated":[49],"correlation":[51],"between":[52],"chemically":[53,141],"induced":[54],"transcriptome":[55,66,102,115],"profiles":[56,67,103,116],"(reflecting":[57,68],"cellular":[58,69],"responses":[59,70],"to":[60,71,92,126,147,172],"compound":[61],"treatment)":[62],"genetically":[64],"perturbed":[65],"gene":[72,75],"knock-down":[73],"or":[74],"overexpression":[76],"target":[78,130,153,186],"proteins)":[79],"terms":[81],"ligand-target":[83],"interactions.":[84],"Subsequently,":[85],"developed":[87],"machine":[89],"learning":[90],"methods":[91,138,160],"generate":[93,140],"chemical":[95],"structures":[96],"new":[98],"framework":[106],"variational":[109],"autoencoder.":[110],"The":[111],"use":[112],"enables":[117],"automatic":[119],"design":[120,179],"that":[123,136,144,161],"are":[124,145],"likely":[125,146],"have":[127,148],"bioactivities":[128],"proteins":[131],"interest.":[133],"showed":[135],"our":[137],"can":[139,157],"valid":[142],"biological":[149],"activities":[150],"on":[151],"10":[152],"proteins;":[154],"moreover,":[155],"they":[156],"outperform":[158],"previous":[159],"had":[162],"same":[164],"objective.":[165],"Our":[166],"structure":[168],"generator":[169],"expected":[171],"be":[173],"useful":[174],"drugs":[181],"variety":[184],"proteins.":[187]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
