{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T01:11:16Z","timestamp":1776733876083,"version":"3.51.2"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2019,7,8]],"date-time":"2019-07-08T00:00:00Z","timestamp":1562544000000},"content-version":"vor","delay-in-days":7,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"JST PRESTO","award":["JPMJPR15D8"],"award-info":[{"award-number":["JPMJPR15D8"]}]},{"name":"JST AIP-PRISM","award":["JPMJCR18Y5"],"award-info":[{"award-number":["JPMJCR18Y5"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Genome-wide identification of the transcriptomic responses of human cell lines to drug treatments is a challenging issue in medical and pharmaceutical research. However, drug-induced gene expression profiles are largely unknown and unobserved for all combinations of drugs and human cell lines, which is a serious obstacle in practical applications.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we developed a novel computational method to predict unknown parts of drug-induced gene expression profiles for various human cell lines and predict new drug therapeutic indications for a wide range of diseases. We proposed a tensor-train weighted optimization (TT-WOPT) algorithm to predict the potential values for unknown parts in tensor-structured gene expression data. Our results revealed that the proposed TT-WOPT algorithm can accurately reconstruct drug-induced gene expression data for a range of human cell lines in the Library of Integrated Network-based Cellular Signatures. The results also revealed that in comparison with the use of original gene expression profiles, the use of imputed gene expression profiles improved the accuracy of drug repositioning. We also performed a comprehensive prediction of drug indications for diseases with gene expression profiles, which suggested many potential drug indications that were not predicted by previous approaches.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz313","type":"journal-article","created":{"date-parts":[[2019,5,9]],"date-time":"2019-05-09T11:20:03Z","timestamp":1557400803000},"page":"i191-i199","source":"Crossref","is-referenced-by-count":32,"title":["Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm"],"prefix":"10.1093","volume":"35","author":[{"given":"Michio","family":"Iwata","sequence":"first","affiliation":[{"name":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Longhao","family":"Yuan","sequence":"additional","affiliation":[{"name":"Graduate School of Engineering, Saitama Institute of Technology, Fukaya, Saitama, Japan"},{"name":"RIKEN Center for Advanced Intelligence Project, Chuo-ku, Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qibin","family":"Zhao","sequence":"additional","affiliation":[{"name":"RIKEN Center for Advanced Intelligence Project, Chuo-ku, Tokyo, Japan"},{"name":"School of Automation, Guangdong University of Technology, Guangzhou, Guangdong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yasuo","family":"Tabei","sequence":"additional","affiliation":[{"name":"RIKEN Center for Advanced Intelligence Project, Chuo-ku, Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francois","family":"Berenger","sequence":"additional","affiliation":[{"name":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ryusuke","family":"Sawada","sequence":"additional","affiliation":[{"name":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sayaka","family":"Akiyoshi","sequence":"additional","affiliation":[{"name":"Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Momoko","family":"Hamano","sequence":"additional","affiliation":[{"name":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yoshihiro","family":"Yamanishi","sequence":"additional","affiliation":[{"name":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan"},{"name":"PRESTO Japan Science and Technology Agency, Kawaguchi, Saitama, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,7,5]]},"reference":[{"key":"2023062712341063700_btz313-B1","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.chemolab.2010.08.004","article-title":"Scalable tensor factorizations for incomplete data","volume":"106","author":"Acar","year":"2011","journal-title":"Chemometr. 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