{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T22:19:57Z","timestamp":1758925197799},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"S14","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,10]]},"DOI":"10.1186\/1471-2105-14-s14-s11","type":"journal-article","created":{"date-parts":[[2013,10,9]],"date-time":"2013-10-09T09:20:47Z","timestamp":1381310447000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["A systems approach for analysis of high content screening assay data with topic modeling"],"prefix":"10.1186","volume":"14","author":[{"given":"Halil","family":"Bisgin","sequence":"first","affiliation":[]},{"given":"Minjun","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Yuping","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Reagan","family":"Kelly","sequence":"additional","affiliation":[]},{"given":"Hong","family":"Fang","sequence":"additional","affiliation":[]},{"given":"Xiaowei","family":"Xu","sequence":"additional","affiliation":[]},{"given":"Weida","family":"Tong","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,10,9]]},"reference":[{"issue":"6","key":"6089_CR1","doi-asserted-by":"publisher","first-page":"788","DOI":"10.1038\/clpt.2011.63","volume":"89","author":"PB Watkins","year":"2011","unstructured":"Watkins PB: Drug safety sciences and the bottleneck in drug development. Clin Pharmacol Ther. 2011, 89 (6): 788-790. 10.1038\/clpt.2011.63.","journal-title":"Clin Pharmacol Ther"},{"issue":"15-16","key":"6089_CR2","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1016\/j.drudis.2011.05.007","volume":"16","author":"M Chen","year":"2011","unstructured":"Chen M, Vijay V, Shi Q, Liu Z, Fang H, Tong W: FDA-approved drug labeling for the study of drug-induced liver injury. Drug discovery today. 2011, 16 (15-16): 697-703. 10.1016\/j.drudis.2011.05.007.","journal-title":"Drug discovery today"},{"issue":"9","key":"6089_CR3","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1007\/s00204-006-0091-3","volume":"80","author":"PJ O'Brien","year":"2006","unstructured":"O'Brien PJ, Irwin W, Diaz D, Howard-Cofield E, Krejsa CM, Slaughter MR, Gao B, Kaludercic N, Angeline A, Bernardi P: High concordance of drug-induced human hepatotoxicity with in vitro cytotoxicity measured in a novel cell-based model using high content screening. Arch Toxicol. 2006, 80 (9): 580-604. 10.1007\/s00204-006-0091-3.","journal-title":"Arch Toxicol"},{"issue":"7","key":"6089_CR4","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1177\/1087057104265387","volume":"9","author":"KA Giuliano","year":"2004","unstructured":"Giuliano KA, Chen YT, Taylor DL: High-content screening with siRNA optimizes a cell biological approach to drug discovery: defining the role of P53 activation in the cellular response to anticancer drugs. J Biomol Screen. 2004, 9 (7): 557-568. 10.1177\/1087057104265387.","journal-title":"J Biomol Screen"},{"issue":"19","key":"6089_CR5","doi-asserted-by":"publisher","first-page":"19078","DOI":"10.1074\/jbc.M501467200","volume":"280","author":"A Vogt","year":"2005","unstructured":"Vogt A, Tamewitz A, Skoko J, Sikorski RP, Giuliano KA, Lazo JS: The benzo[c]phenanthridine alkaloid, sanguinarine, is a selective, cell-active inhibitor of mitogen-activated protein kinase phosphatase-1. J Biol Chem. 2005, 280 (19): 19078-19086. 10.1074\/jbc.M501467200.","journal-title":"J Biol Chem"},{"issue":"5699","key":"6089_CR6","doi-asserted-by":"publisher","first-page":"1194","DOI":"10.1126\/science.1100709","volume":"306","author":"ZE Perlman","year":"2004","unstructured":"Perlman ZE, Slack MD, Feng Y, Mitchison TJ, Wu LF, Altschuler SJ: Multidimensional drug profiling by automated microscopy. Science. 2004, 306 (5699): 1194-1198. 10.1126\/science.1100709.","journal-title":"Science"},{"issue":"5","key":"6089_CR7","doi-asserted-by":"publisher","first-page":"e128","DOI":"10.1371\/journal.pbio.0030128","volume":"3","author":"M Tanaka","year":"2005","unstructured":"Tanaka M, Bateman R, Rauh D, Vaisberg E, Ramachandani S, Zhang C, Hansen KC, Burlingame AL, Trautman JK, Shokat KM: An unbiased cell morphology-based screen for new, biologically active small molecules. PLoS Biol. 2005, 3 (5): e128-10.1371\/journal.pbio.0030128.","journal-title":"PLoS Biol"},{"issue":"5","key":"6089_CR8","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1158\/1535-7163.521.3.5","volume":"3","author":"H Lovborg","year":"2004","unstructured":"Lovborg H, Nygren P, Larsson R: Multiparametric evaluation of apoptosis: effects of standard cytotoxic agents and the cyanoguanidine CHS 828. Mol Cancer Ther. 2004, 3 (5): 521-526.","journal-title":"Mol Cancer Ther"},{"issue":"5","key":"6089_CR9","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1089\/adt.2004.2.473","volume":"2","author":"RN Ghosh","year":"2004","unstructured":"Ghosh RN, Grove L, Lapets O: A Quantitative Cell-Based High-Content Screening Assay for the Epidermal Growth Factor Receptor-Specific Activation of Mitogen-Activated Protein Kinase. Assay and Drug Development Technologies. 2004, 2 (5): 473-481. 10.1089\/adt.2004.2.473.","journal-title":"Assay and Drug Development Technologies"},{"issue":"13","key":"6089_CR10","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1016\/S1359-6446(03)02738-7","volume":"8","author":"G Milligan","year":"2003","unstructured":"Milligan G: High-content assays for ligand regulation of G-protein-coupled receptors. Drug discovery today. 2003, 8 (13): 579-585. 10.1016\/S1359-6446(03)02738-7.","journal-title":"Drug discovery today"},{"key":"6089_CR11","first-page":"349","volume":"2","author":"VC Abraham","year":"2004","unstructured":"Abraham VC, B Samson OL, Haskins JR: Automated Classification of Individual Cellular Responses Across Multiple Targets. Preclinica. 2004, 2: 349-355.","journal-title":"Preclinica"},{"issue":"2","key":"6089_CR12","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1016\/j.ddtec.2005.05.023","volume":"2","author":"DL Taylor","year":"2005","unstructured":"Taylor DL, Giuliano KA: Multiplexed high content screening assays create a systems cell biology approach to drug discovery. Drug Discovery Today: Technologies. 2005, 2 (2): 149-154. 10.1016\/j.ddtec.2005.05.023.","journal-title":"Drug Discovery Today: Technologies"},{"issue":"1","key":"6089_CR13","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1016\/j.tibtech.2003.10.012","volume":"22","author":"VC Abraham","year":"2004","unstructured":"Abraham VC, Taylor DL, Haskins JR: High content screening applied to large-scale cell biology. Trends in Biotechnology. 2004, 22 (1): 15-22. 10.1016\/j.tibtech.2003.10.012.","journal-title":"Trends in Biotechnology"},{"issue":"1","key":"6089_CR14","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1093\/toxsci\/kfn109","volume":"105","author":"JJ Xu","year":"2008","unstructured":"Xu JJ, Henstock PV, Dunn MC, Smith AR, Chabot JR, de Graaf D: Cellular Imaging Predictions of Clinical Drug-Induced Liver Injury. Toxicological Sciences. 2008, 105 (1): 97-105. 10.1093\/toxsci\/kfn109.","journal-title":"Toxicological Sciences"},{"issue":"5","key":"6089_CR15","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1038\/clpt.2013.16","volume":"95","author":"M Chen","year":"2013","unstructured":"Chen M, Zhang J, Wang Y, Liu Z, Kelly R, Zhou G, Fang H, Borlak J, Tong W: Liver Toxicity Knowledge Base (LTKB) - A Systems Approach to a Complex Endpoint. Clinical Pharmacology & Therapeutics. 2013, 95 (5): 409-412.","journal-title":"Clinical Pharmacology & Therapeutics"},{"issue":"4-5","key":"6089_CR16","first-page":"993","volume":"3","author":"DM Blei","year":"2003","unstructured":"Blei DM, Ng AY, Jordan MI: Latent Dirichlet allocation. Journal of Machine Learning Research. 2003, 3 (4-5): 993-1022.","journal-title":"Journal of Machine Learning Research"},{"issue":"Suppl 10","key":"6089_CR17","doi-asserted-by":"publisher","first-page":"S11","DOI":"10.1186\/1471-2105-12-S10-S11","volume":"12","author":"H Bisgin","year":"2011","unstructured":"Bisgin H, Liu Z, Fang H, Xu X, Tong W: Mining FDA drug labels using an unsupervised learning technique--topic modeling. BMC Bioinformatics. 2011, 12 (Suppl 10): S11-10.1186\/1471-2105-12-S10-S11.","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 3","key":"6089_CR18","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1186\/1755-8794-5-2","volume":"13","author":"Y Chen","year":"2012","unstructured":"Chen Y, Yin X, Li Z, Hu X, Huang JX: A LDA-based approach to promoting ranking diversity for genomics information retrieval. BMC genomics. 2012, 13 (Suppl 3): S2-","journal-title":"BMC genomics"},{"key":"6089_CR19","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1186\/1471-2105-7-58","volume":"7","author":"B Zheng","year":"2006","unstructured":"Zheng B, McLean DC, Lu X: Identifying biological concepts from a protein-related corpus with a probabilistic topic model. BMC Bioinformatics. 2006, 7: 58-10.1186\/1471-2105-7-58.","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 15","key":"6089_CR20","doi-asserted-by":"publisher","first-page":"S6","DOI":"10.1186\/1471-2105-13-S15-S6","volume":"13","author":"H Bisgin","year":"2012","unstructured":"Bisgin H, Liu Z, Kelly R, Fang H, Xu X, Tong W: Investigating drug repositioning opportunities in FDA drug labels through topic modeling. BMC Bioinformatics. 2012, 13 (Suppl 15): S6-10.1186\/1471-2105-13-S15-S6.","journal-title":"BMC Bioinformatics"},{"issue":"12","key":"6089_CR21","doi-asserted-by":"publisher","first-page":"e27506","DOI":"10.1371\/journal.pone.0027506","volume":"6","author":"B He","year":"2011","unstructured":"He B, Tang J, Ding Y, Wang H, Sun Y, Shin JH, Chen B, Moorthy G, Qiu J, Desai P: Mining Relational Paths in Integrated Biomedical Data. PLoS ONE. 2011, 6 (12): e27506-10.1371\/journal.pone.0027506.","journal-title":"PLoS ONE"},{"issue":"3","key":"6089_CR22","doi-asserted-by":"publisher","first-page":"e17243","DOI":"10.1371\/journal.pone.0017243","volume":"6","author":"H Wang","year":"2011","unstructured":"Wang H, Ding Y, Tang J, Dong X, He B, Qiu J, Wild DJ: Finding Complex Biological Relationships in Recent PubMed Articles Using Bio-LDA. PLoS ONE. 2011, 6 (3): e17243-10.1371\/journal.pone.0017243.","journal-title":"PLoS ONE"},{"issue":"7","key":"6089_CR23","doi-asserted-by":"publisher","first-page":"783","DOI":"10.1177\/1087057110376413","volume":"15","author":"KA Giuliano","year":"2010","unstructured":"Giuliano KA, Gough AH, Taylor DL, Vernetti LA, Johnston PA: Early safety assessment using cellular systems biology yields insights into mechanisms of action. J Biomol Screen. 2010, 15 (7): 783-797. 10.1177\/1087057110376413.","journal-title":"J Biomol Screen"},{"key":"6089_CR24","volume-title":"Elsevier Science","author":"N Berry","year":"1991","unstructured":"Berry N, Barritt GJ, Edwards AM: Isolated Hepatocytes: Preparation, Properties and Applications. Elsevier Science. 1991"},{"issue":"2","key":"6089_CR25","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1002\/mnfr.200900169","volume":"54","author":"T Uehara","year":"2010","unstructured":"Uehara T, Ono A, Maruyama T, Kato I, Yamada H, Ohno Y, Urushidani T: The Japanese toxicogenomics project: application of toxicogenomics. Mol Nutr Food Res. 2010, 54 (2): 218-227. 10.1002\/mnfr.200900169.","journal-title":"Mol Nutr Food Res"},{"issue":"2","key":"6089_CR26","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1093\/toxsci\/kfs223","volume":"130","author":"M Chen","year":"2012","unstructured":"Chen M, Zhang M, Borlak J, Tong W: A Decade of Toxicogenomic Research and Its Contribution to Toxicological Science. Toxicol Sci. 2012, 130 (2): 217-228. 10.1093\/toxsci\/kfs223.","journal-title":"Toxicol Sci"},{"key":"6089_CR27","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1007\/BFb0017012","volume-title":"Machine Learning \u00e2\u20ac\" EWSL-91","author":"Y Kodratoff","year":"1991","unstructured":"Kodratoff Y, Catlett J: On changing continuous attributes into ordered discrete attributes. Machine Learning \u00e2\u20ac\" EWSL-91. 1991, Springer Berlin Heidelberg, 482: 164-178. 10.1007\/BFb0017012."},{"key":"6089_CR28","first-page":"50","volume-title":"Proceedings of the Twenty-Second Annual International SIGIR Conference on Research and Development in Information Retrieval (SIGIR-99) 1999","author":"T Hofmann","year":"1999","unstructured":"Hofmann T: Probabilistic Latent Semantic Indexing. Proceedings of the Twenty-Second Annual International SIGIR Conference on Research and Development in Information Retrieval (SIGIR-99) 1999. 1999, Berkley, CA USA, 50-57."},{"key":"6089_CR29","first-page":"391","volume-title":"Journal of the American Society for Information Science: 1990","author":"S Deerwester","year":"1990","unstructured":"Deerwester S, Dumais S, Furnas G, Landauer T, Harshman R: Indexing by latent semantic analysis. Journal of the American Society for Information Science: 1990. 1990, 391-407."},{"issue":"Suppl 1","key":"6089_CR30","doi-asserted-by":"publisher","first-page":"5228","DOI":"10.1073\/pnas.0307752101","volume":"101","author":"TL Griffiths","year":"2004","unstructured":"Griffiths TL, Steyvers M: Finding scientific topics. Proc Natl Acad Sci USA. 2004, 101 (Suppl 1): 5228-5235.","journal-title":"Proc Natl Acad Sci USA"},{"key":"6089_CR31","unstructured":"[http:\/\/www.cs.princeton.edu\/~blei\/lda-c\/index.html]"},{"issue":"15","key":"6089_CR32","doi-asserted-by":"publisher","first-page":"3286","DOI":"10.1093\/bioinformatics\/bti515","volume":"21","author":"P Flaherty","year":"2005","unstructured":"Flaherty P, Giaever G, Kumm J, Jordan MI, Arkin AP: A latent variable model for chemogenomic profiling. Bioinformatics. 2005, 21 (15): 3286-3293. 10.1093\/bioinformatics\/bti515.","journal-title":"Bioinformatics"},{"issue":"24","key":"6089_CR33","doi-asserted-by":"publisher","first-page":"3105","DOI":"10.1093\/bioinformatics\/btq576","volume":"26","author":"B Liu","year":"2010","unstructured":"Liu B, Liu L, Tsykin A, Goodall GJ, Green JE, Zhu M, Kim CH, Li J: Identifying functional miRNA-mRNA regulatory modules with correspondence latent dirichlet allocation. Bioinformatics. 2010, 26 (24): 3105-3111. 10.1093\/bioinformatics\/btq576.","journal-title":"Bioinformatics"},{"issue":"5","key":"6089_CR34","doi-asserted-by":"publisher","first-page":"1571","DOI":"10.1016\/S0002-9440(10)64291-5","volume":"162","author":"VV Didenko","year":"2003","unstructured":"Didenko VV, Ngo H, Baskin DS: Early necrotic DNA degradation: presence of blunt-ended DNA breaks, 3' and 5' overhangs in apoptosis, but only 5' overhangs in early necrosis. Am J Pathol. 2003, 162 (5): 1571-1578. 10.1016\/S0002-9440(10)64291-5.","journal-title":"Am J Pathol"},{"issue":"1","key":"6089_CR35","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1101\/gad.1376506","volume":"20","author":"WX Zong","year":"2006","unstructured":"Zong WX, Thompson CB: Necrotic death as a cell fate. Genes Dev. 2006, 20 (1): 1-15. 10.1101\/gad.1376506.","journal-title":"Genes Dev"},{"issue":"1-2","key":"6089_CR36","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1016\/S0005-2728(98)00112-1","volume":"1366","author":"JJ Lemasters","year":"1998","unstructured":"Lemasters JJ, Nieminen AL, Qian T, Trost LC, Elmore SP, Nishimura Y, Crowe RA, Cascio WE, Bradham CA, Brenner DA: The mitochondrial permeability transition in cell death: a common mechanism in necrosis, apoptosis and autophagy. Biochim Biophys Acta. 1998, 1366 (1-2): 177-196. 10.1016\/S0005-2728(98)00112-1.","journal-title":"Biochim Biophys Acta"},{"issue":"6","key":"6089_CR37","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1016\/j.ceb.2004.09.011","volume":"16","author":"AL Edinger","year":"2004","unstructured":"Edinger AL, Thompson CB: Death by design: apoptosis, necrosis and autophagy. Curr Opin Cell Biol. 2004, 16 (6): 663-669. 10.1016\/j.ceb.2004.09.011.","journal-title":"Curr Opin Cell Biol"},{"issue":"11","key":"6089_CR38","first-page":"4673","volume":"42","author":"G Michalopoulos","year":"1982","unstructured":"Michalopoulos G, Cianciulli HD, Novotny AR, Kligerman AD, Strom SC, Jirtle RL: Liver regeneration studies with rat hepatocytes in primary culture. Cancer Res. 1982, 42 (11): 4673-4682.","journal-title":"Cancer Res"},{"issue":"7323","key":"6089_CR39","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1038\/468513a","volume":"468","author":"O Cohen-Fix","year":"2010","unstructured":"Cohen-Fix O: Cell biology: Import and nuclear size. Nature. 2010, 468 (7323): 513-516. 10.1038\/468513a.","journal-title":"Nature"},{"key":"6089_CR40","volume-title":"Genome Size Evolution in Animals","author":"T Gregory","year":"2005","unstructured":"Gregory T: Genome Size Evolution in Animals. 2005, London: Elsevier Academic Press, 1:"},{"issue":"13","key":"6089_CR41","doi-asserted-by":"publisher","first-page":"1166","DOI":"10.1016\/j.cub.2012.05.016","volume":"22","author":"Y Miyaoka","year":"2012","unstructured":"Miyaoka Y, Ebato K, Kato H, Arakawa S, Shimizu S, Miyajima A: Hypertrophy and Unconventional Cell Division of Hepatocytes Underlie Liver Regeneration. Current Biology. 2012, 22 (13): 1166-1175. 10.1016\/j.cub.2012.05.016.","journal-title":"Current Biology"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S14-S11.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,5]],"date-time":"2023-07-05T06:31:29Z","timestamp":1688538689000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-S14-S11"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,10]]},"references-count":41,"journal-issue":{"issue":"S14","published-print":{"date-parts":[[2013,10]]}},"alternative-id":["6089"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-s14-s11","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,10]]},"assertion":[{"value":"9 October 2013","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S11"}}