{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,5,5]],"date-time":"2023-05-05T09:08:53Z","timestamp":1683277733264},"reference-count":30,"publisher":"Springer Science and Business Media LLC","issue":"S6","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2013,12]]},"DOI":"10.1186\/1752-0509-7-s6-s11","type":"journal-article","created":{"date-parts":[[2013,12,13]],"date-time":"2013-12-13T12:07:50Z","timestamp":1386936470000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Shrinkage regression-based methods for microarray missing value imputation"],"prefix":"10.1186","volume":"7","author":[{"given":"Hsiuying","family":"Wang","sequence":"first","affiliation":[]},{"given":"Chia-Chun","family":"Chiu","sequence":"additional","affiliation":[]},{"given":"Yi-Ching","family":"Wu","sequence":"additional","affiliation":[]},{"given":"Wei-Sheng","family":"Wu","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,12,13]]},"reference":[{"key":"1234_CR1","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1126\/science.270.5235.467","volume":"270","author":"M Schena","year":"1995","unstructured":"Schena M, Shalon D, Davis R, Brown P: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995, 270: 467-470. 10.1126\/science.270.5235.467.","journal-title":"Science"},{"key":"1234_CR2","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-7-421","volume":"7","author":"W Wu","year":"2006","unstructured":"Wu W, Li W, Chen B: Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics. 2006, 7: 421-10.1186\/1471-2105-7-421.","journal-title":"BMC Bioinformatics"},{"key":"1234_CR3","doi-asserted-by":"publisher","first-page":"16892","DOI":"10.1073\/pnas.0706022104","volume":"104","author":"M Rowicka","year":"2007","unstructured":"Rowicka M, Kudlicki A, Tu B, Otwinowski Z: High-resolution timing of cell cycle-regulated gene expression. Proc Natl Acad Sci USA. 2007, 104: 16892-16897. 10.1073\/pnas.0706022104.","journal-title":"Proc Natl Acad Sci USA"},{"key":"1234_CR4","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1186\/1471-2105-8-188","volume":"8","author":"W Wu","year":"2007","unstructured":"Wu W, Li W, Chen B: Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC Bioinformatics. 2007, 8: 188-10.1186\/1471-2105-8-188.","journal-title":"BMC Bioinformatics"},{"key":"1234_CR5","doi-asserted-by":"publisher","first-page":"1063","DOI":"10.1093\/bioinformatics\/btn072","volume":"24","author":"M Futschik","year":"2008","unstructured":"Futschik M, Herzel H: Are we overestimating the number of cell-cycling genes? The impact of background models on time-series analysis. Bioinformatics. 2008, 24: 1063-1069. 10.1093\/bioinformatics\/btn072.","journal-title":"Bioinformatics"},{"key":"1234_CR6","doi-asserted-by":"publisher","first-page":"522","DOI":"10.1186\/1471-2105-9-522","volume":"9","author":"W Wu","year":"2008","unstructured":"Wu W, Li W: Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics. 2008, 9: 522-10.1186\/1471-2105-9-522.","journal-title":"BMC Bioinformatics"},{"key":"1234_CR7","doi-asserted-by":"publisher","first-page":"e1000460","DOI":"10.1371\/journal.pcbi.1000460","volume":"5","author":"D Siegal-Gaskins","year":"2009","unstructured":"Siegal-Gaskins D, Ash J, Crosson S: Model-based deconvolution of cell cycle time-series data reveals gene expression details at high resolution. PLoS Comput Biol. 2009, 5: e1000460-10.1371\/journal.pcbi.1000460.","journal-title":"PLoS Comput Biol"},{"key":"1234_CR8","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1016\/j.gene.2011.06.001","volume":"485","author":"H Wang","year":"2011","unstructured":"Wang H, Wang Y, Wu W: Yeast cell cycle transcription factors identification by variable selection criteria. Gene. 2011, 485: 172-176. 10.1016\/j.gene.2011.06.001.","journal-title":"Gene"},{"key":"1234_CR9","doi-asserted-by":"publisher","first-page":"4241","DOI":"10.1091\/mbc.11.12.4241","volume":"11","author":"A Gasch","year":"2000","unstructured":"Gasch A, Spellman P, Kao C, Carmel-Harel O, Eisen M, Storz G, Botstein D, Brown P: Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000, 11: 4241-4257. 10.1091\/mbc.11.12.4241.","journal-title":"Mol Biol Cell"},{"key":"1234_CR10","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1186\/1471-2164-9-439","volume":"9","author":"W Wu","year":"2008","unstructured":"Wu W, Li W: Identifying gene regulatory modules of heat shock response in yeast. BMC Genomics. 2008, 9: 439-10.1186\/1471-2164-9-439.","journal-title":"BMC Genomics"},{"key":"1234_CR11","doi-asserted-by":"publisher","first-page":"917","DOI":"10.1093\/bioinformatics\/bth007","volume":"20","author":"M Ouyang","year":"2004","unstructured":"Ouyang M, Welsh W, Georgopoulos P: Gaussian mixture clustering and imputation of microarray data. Bioinformatics. 2004, 20: 917-923. 10.1093\/bioinformatics\/bth007.","journal-title":"Bioinformatics"},{"key":"1234_CR12","doi-asserted-by":"publisher","first-page":"520","DOI":"10.1093\/bioinformatics\/17.6.520","volume":"17","author":"O Troyanskaya","year":"2001","unstructured":"Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman R: Missing value estimation methods for DNA microarrays. Bioinformatics. 2001, 17: 520-525. 10.1093\/bioinformatics\/17.6.520.","journal-title":"Bioinformatics"},{"key":"1234_CR13","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1142\/S0219720006002302","volume":"4","author":"Z Cai","year":"2006","unstructured":"Cai Z, Heydari M, Lin G: Iterated local least squares microarray missing value imputation. J Bioinform Comput Biol. 2006, 4: 935-957. 10.1142\/S0219720006002302.","journal-title":"J Bioinform Comput Biol"},{"key":"1234_CR14","doi-asserted-by":"publisher","first-page":"2088","DOI":"10.1093\/bioinformatics\/btg287","volume":"19","author":"S Oba","year":"2003","unstructured":"Oba S, Sato M, Takemasa I, Monden M, Matsubara K, Ishii S: A Bayesian missing value estimation method for gene expression profile data. Bioinformatics. 2003, 19: 2088-2096. 10.1093\/bioinformatics\/btg287.","journal-title":"Bioinformatics"},{"key":"1234_CR15","doi-asserted-by":"publisher","first-page":"723","DOI":"10.1109\/TCBB.2010.73","volume":"8","author":"T Yu","year":"2011","unstructured":"Yu T, Peng H, Sun W: Incorporating nonlinear relationships in microarray missing value imputation. IEEE\/ACM Trans Comput Biol Bioinform. 2011, 8: 723-731.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"1234_CR16","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1093\/bioinformatics\/btr597","volume":"28","author":"D Stekhoven","year":"2012","unstructured":"Stekhoven D, B\u00fchlmann P: MissForest-non-parametric missing value imputation for mixed-type data. Bioinformatics. 2012, 28: 112-118. 10.1093\/bioinformatics\/btr597.","journal-title":"Bioinformatics"},{"key":"1234_CR17","doi-asserted-by":"publisher","first-page":"e34","DOI":"10.1093\/nar\/gnh026","volume":"32","author":"T B\u00f8","year":"2004","unstructured":"B\u00f8 T, Dysvik B, Jonassen I: LSimpute: accurate estimation of missing values in microarray data with least squares methods. Nucleic Acids Res. 2004, 32: e34-10.1093\/nar\/gnh026.","journal-title":"Nucleic Acids Res"},{"key":"1234_CR18","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1093\/bioinformatics\/bth499","volume":"21","author":"H Kim","year":"2005","unstructured":"Kim H, Golub G, Park H: Missing value estimation for DNA microarray gene expression data: local least squares imputation. Bioinformatics. 2005, 21: 187-198. 10.1093\/bioinformatics\/bth499.","journal-title":"Bioinformatics"},{"key":"1234_CR19","doi-asserted-by":"publisher","first-page":"1112","DOI":"10.1016\/j.compbiomed.2008.08.006","volume":"38","author":"X Zhang","year":"2008","unstructured":"Zhang X, Song X, Wang H, Zhang H: Sequential local least squares imputation estimating missing value of microarray data. Comput Biol Med. 2008, 38: 1112-1120. 10.1016\/j.compbiomed.2008.08.006.","journal-title":"Comput Biol Med"},{"key":"1234_CR20","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/1471-2164-11-15","volume":"11","author":"M Celton","year":"2010","unstructured":"Celton M, Malpertuy A, Lelandais G, de Brevern A: Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments. BMC Genomics. 2010, 11: 15-10.1186\/1471-2164-11-15.","journal-title":"BMC Genomics"},{"key":"1234_CR21","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/1471-2105-9-12","volume":"9","author":"G Brock","year":"2008","unstructured":"Brock G, Shaffer J, Blakesley R, Lotz M, Tseng G: Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes. BMC Bioinformatics. 2008, 9: 12-10.1186\/1471-2105-9-12.","journal-title":"BMC Bioinformatics"},{"key":"1234_CR22","first-page":"197","volume":"1","author":"C Stein","year":"1956","unstructured":"Stein C: Inadmissibility of the usual estimator for the mean of a multivariate normal distribution. Proceedings of the Third Berkeley Symposium on Mathematical Statistics and Probability. 1956, 1: 197-206.","journal-title":"Proceedings of the Third Berkeley Symposium on Mathematical Statistics and Probability"},{"key":"1234_CR23","first-page":"361","volume":"1","author":"W James","year":"1961","unstructured":"James W, Stein C: Estimation with quadratic loss. Proceedings of the Fourth Berkeley Symposium on Mathematical Statistics and Probability. 1961, 1: 361-379.","journal-title":"Proceedings of the Fourth Berkeley Symposium on Mathematical Statistics and Probability"},{"key":"1234_CR24","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1214\/aos\/1018031210","volume":"27","author":"H Wang","year":"1999","unstructured":"Wang H: Brown's paradox in the estimated confidence approach. The Annals of Statistics. 1999, 27: 610-626. 10.1214\/aos\/1018031210.","journal-title":"The Annals of Statistics"},{"key":"1234_CR25","first-page":"659","volume":"10","author":"H Wang","year":"2000","unstructured":"Wang H: Improved confidence estimators for the multivariate normal confidence set. Statistica Sinica. 2000, 10: 659-664.","journal-title":"Statistica Sinica"},{"key":"1234_CR26","doi-asserted-by":"publisher","first-page":"4309","DOI":"10.1091\/mbc.11.12.4309","volume":"11","author":"N Ogawa","year":"2000","unstructured":"Ogawa N, DeRisi J, Brown P: New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Molecular Biology of the Cell. 2000, 11: 4309-4321. 10.1091\/mbc.11.12.4309.","journal-title":"Molecular Biology of the Cell"},{"key":"1234_CR27","doi-asserted-by":"publisher","first-page":"1926","DOI":"10.1073\/pnas.0437875100","volume":"100","author":"S Bohen","year":"2003","unstructured":"Bohen S, Troyanskaya O, Alter O, Warnke R, Botstein D, Brown P, Levy R: Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Proc Natl Acad Sci USA. 2003, 100: 1926-1930. 10.1073\/pnas.0437875100.","journal-title":"Proc Natl Acad Sci USA"},{"key":"1234_CR28","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1038\/35000501","volume":"403","author":"A Alizadeh","year":"2000","unstructured":"Alizadeh A, Eisen M, Davis R, Ma C, Lossos I, Rosenwald A, Boldrick J, Sabet H, Tran T, Yu X, Powell J, Yang L, Marti G, Moore T, Hudson J, Lu L, Lewis D, Tibshirani R, Sherlock G, Chan W, Greiner T, Weisenburger D, Armitage J, Warnke R, Levy R, Wilson W, Grever M, Byrd J, Botstein D, Brown P, Staudt L: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000, 403: 503-511. 10.1038\/35000501.","journal-title":"Nature"},{"key":"1234_CR29","doi-asserted-by":"publisher","first-page":"2503","DOI":"10.1091\/mbc.E04-11-0968","volume":"16","author":"M Brauer","year":"2005","unstructured":"Brauer M, Saldanha A, Dolinski K, Botstein D: Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures. Mol Biol Cell. 2005, 16: 2503-2517. 10.1091\/mbc.E04-11-0968.","journal-title":"Mol Biol Cell"},{"key":"1234_CR30","doi-asserted-by":"publisher","first-page":"5659","DOI":"10.1091\/mbc.E04-04-0340","volume":"15","author":"M Shapira","year":"2004","unstructured":"Shapira M, Segal E, Botstein D: Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress. Mol Biol Cell. 2004, 15: 5659-5669. 10.1091\/mbc.E04-04-0340.","journal-title":"Mol Biol Cell"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-7-S6-S11.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T19:41:48Z","timestamp":1630611708000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-7-S6-S11"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,12]]},"references-count":30,"journal-issue":{"issue":"S6","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["1234"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-7-s6-s11","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,12]]},"assertion":[{"value":"13 December 2013","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S11"}}