{"id":"https://openalex.org/W4309933640","doi":"https://doi.org/10.1038/s43588-022-00352-8","title":"Pathway trajectory analysis with tensor imputation reveals drug-induced single-cell transcriptomic landscape","display_name":"Pathway trajectory analysis with tensor imputation reveals drug-induced single-cell transcriptomic landscape","publication_year":2022,"publication_date":"2022-11-24","ids":{"openalex":"https://openalex.org/W4309933640","doi":"https://doi.org/10.1038/s43588-022-00352-8","pmid":"https://pubmed.ncbi.nlm.nih.gov/38177364"},"language":"en","primary_location":{"id":"doi:10.1038/s43588-022-00352-8","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s43588-022-00352-8","pdf_url":"https://www.nature.com/articles/s43588-022-00352-8.pdf","source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://www.nature.com/articles/s43588-022-00352-8.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088317641","display_name":"M Iwata","orcid":"https://orcid.org/0000-0001-6500-4692"},"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":"Michio Iwata","raw_affiliation_strings":["Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan"],"raw_orcid":"https://orcid.org/0000-0001-6500-4692","affiliations":[{"raw_affiliation_string":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan","institution_ids":["https://openalex.org/I207014233"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052219072","display_name":"Hiroaki Mutsumine","orcid":null},"institutions":[{"id":"https://openalex.org/I4210112155","display_name":"Ono Pharmaceutical (Japan)","ror":"https://ror.org/022jefx64","country_code":"JP","type":"company","lineage":["https://openalex.org/I4210112155"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroaki Mutsumine","raw_affiliation_strings":["Tsukuba Research Institute, Ono Pharmaceutical Co., Ltd, Tsukuba, Ibaraki, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tsukuba Research Institute, Ono Pharmaceutical Co., Ltd, Tsukuba, Ibaraki, Japan","institution_ids":["https://openalex.org/I4210112155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103083305","display_name":"Yusuke Nakayama","orcid":"https://orcid.org/0000-0002-5691-7964"},"institutions":[{"id":"https://openalex.org/I4210112155","display_name":"Ono Pharmaceutical (Japan)","ror":"https://ror.org/022jefx64","country_code":"JP","type":"company","lineage":["https://openalex.org/I4210112155"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yusuke Nakayama","raw_affiliation_strings":["Tsukuba Research Institute, Ono Pharmaceutical Co., Ltd, Tsukuba, Ibaraki, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tsukuba Research Institute, Ono Pharmaceutical Co., Ltd, Tsukuba, Ibaraki, Japan","institution_ids":["https://openalex.org/I4210112155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014882591","display_name":"Naomasa Suita","orcid":null},"institutions":[{"id":"https://openalex.org/I4210112155","display_name":"Ono Pharmaceutical (Japan)","ror":"https://ror.org/022jefx64","country_code":"JP","type":"company","lineage":["https://openalex.org/I4210112155"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Naomasa Suita","raw_affiliation_strings":["Tsukuba Research Institute, Ono Pharmaceutical Co., Ltd, Tsukuba, Ibaraki, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tsukuba Research Institute, Ono Pharmaceutical Co., Ltd, Tsukuba, Ibaraki, Japan","institution_ids":["https://openalex.org/I4210112155"]}]},{"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, Iizuka, Fukuoka, Japan. yamani@bio.kyutech.ac.jp","Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan"],"raw_orcid":"https://orcid.org/0000-0003-2279-8773","affiliations":[{"raw_affiliation_string":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan. yamani@bio.kyutech.ac.jp","institution_ids":["https://openalex.org/I207014233"]},{"raw_affiliation_string":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan","institution_ids":["https://openalex.org/I207014233"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5035394108"],"corresponding_institution_ids":["https://openalex.org/I207014233"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":{"value":9750,"currency":"EUR","value_usd":11690},"fwci":0.3465,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.56459884,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"2","issue":"11","first_page":"758","last_page":"770"},"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":0.9954000115394592,"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":0.993399977684021,"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/imputation","display_name":"Imputation (statistics)","score":0.7274266481399536},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.6838948726654053},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6626764535903931},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5038134455680847},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4637397527694702},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.45273250341415405},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4301607012748718},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.42707327008247375},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4224620461463928},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.302982896566391},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29300761222839355},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.2005690038204193},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.14296016097068787},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.12475234270095825}],"concepts":[{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.7274266481399536},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.6838948726654053},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6626764535903931},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5038134455680847},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4637397527694702},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.45273250341415405},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4301607012748718},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.42707327008247375},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4224620461463928},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.302982896566391},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29300761222839355},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.2005690038204193},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.14296016097068787},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.12475234270095825}],"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":"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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1038/s43588-022-00352-8","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s43588-022-00352-8","pdf_url":"https://www.nature.com/articles/s43588-022-00352-8.pdf","source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},{"id":"pmid:38177364","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38177364","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":"Nature computational science","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10768635","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10768635","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10768635/pdf/43588_2022_Article_352.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Nat Comput Sci","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1038/s43588-022-00352-8","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s43588-022-00352-8","pdf_url":"https://www.nature.com/articles/s43588-022-00352-8.pdf","source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.6100000143051147}],"awards":[{"id":"https://openalex.org/G789622214","display_name":null,"funder_award_id":"21H04915","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4309933640.pdf"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1814521481","https://openalex.org/W1998728654","https://openalex.org/W2019490156","https://openalex.org/W2024165284","https://openalex.org/W2110065044","https://openalex.org/W2121604817","https://openalex.org/W2152454589","https://openalex.org/W2154362705","https://openalex.org/W2248179576","https://openalex.org/W2516041031","https://openalex.org/W2557659496","https://openalex.org/W2612467560","https://openalex.org/W2747877289","https://openalex.org/W2792693509","https://openalex.org/W2805619986","https://openalex.org/W2889326414","https://openalex.org/W2916020270","https://openalex.org/W2939946042","https://openalex.org/W2951217100","https://openalex.org/W2970633838","https://openalex.org/W2990393937","https://openalex.org/W3005127469","https://openalex.org/W3021001036","https://openalex.org/W3022232494","https://openalex.org/W3025692045","https://openalex.org/W3080162757","https://openalex.org/W3080295962","https://openalex.org/W3087481014","https://openalex.org/W3150951911","https://openalex.org/W3164692211","https://openalex.org/W3205959358","https://openalex.org/W4294216483","https://openalex.org/W4394103793","https://openalex.org/W6784195601","https://openalex.org/W6964005666","https://openalex.org/W7074166678"],"related_works":["https://openalex.org/W1976510917","https://openalex.org/W2073305407","https://openalex.org/W2052655934","https://openalex.org/W104645380","https://openalex.org/W2027213253","https://openalex.org/W2017047508","https://openalex.org/W2165201120","https://openalex.org/W2023641020","https://openalex.org/W2188530857","https://openalex.org/W2133040682"],"abstract_inverted_index":{"Genome-wide":[0],"identification":[1],"of":[2,6,29,60,91,100,105,108,136,140],"single-cell":[3,34,41,51,138],"transcriptomic":[4,42,78],"responses":[5,79],"drugs":[7,109,141],"in":[8,16,124],"various":[9],"human":[10,111],"cells":[11,112],"is":[12,130],"a":[13,24],"challenging":[14],"issue":[15],"medical":[17],"and":[18,57,75,110,117],"pharmaceutical":[19],"research.":[20],"Here":[21],"we":[22,47],"present":[23],"computational":[25],"method,":[26],"tensor-based":[27],"imputation":[28,67,70],"gene-expression":[30,52,103],"data":[31,53,73],"at":[32,142],"the":[33,39,88,101,137,143],"level":[35],"(TIGERS),":[36],"which":[37],"reveals":[38],"drug-induced":[40,50,122],"landscape.":[43],"With":[44],"this":[45],"algorithm,":[46],"predict":[48],"missing":[49],"with":[54],"tensor":[55],"imputation,":[56],"identify":[58],"trajectories":[59,119],"regulated":[61],"pathways":[62],"considering":[63],"intercellular":[64],"heterogeneity.":[65],"Tensor":[66],"outperformed":[68],"existing":[69],"methods":[71],"for":[72,80,94],"completion,":[74],"provided":[76],"cell-type-specific":[77,89],"unobserved":[81],"drugs.":[82],"For":[83],"example,":[84],"TIGERS":[85],"correctly":[86],"predicted":[87],"expression":[90],"maker":[92],"genes":[93],"pancreatic":[95],"islets.":[96],"Pathway":[97],"trajectory":[98],"analysis":[99],"imputed":[102],"profiles":[104],"all":[106],"combinations":[107],"identified":[113],"single-cell-specific":[114],"drug":[115],"activities":[116],"pathway":[118,125,144],"that":[120],"reflect":[121],"changes":[123],"regulation.":[126],"The":[127],"proposed":[128],"method":[129],"expected":[131],"to":[132],"expand":[133],"our":[134],"understanding":[135],"mechanisms":[139],"level.":[145]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}