{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,14]],"date-time":"2025-11-14T17:12:42Z","timestamp":1763140362666,"version":"3.37.0"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2009,4,22]],"date-time":"2009-04-22T00:00:00Z","timestamp":1240358400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2009,12]]},"DOI":"10.1186\/1752-0509-3-41","type":"journal-article","created":{"date-parts":[[2009,4,22]],"date-time":"2009-04-22T18:13:51Z","timestamp":1240424031000},"source":"Crossref","is-referenced-by-count":47,"title":["Recursive regularization for inferring gene networks from time-course gene expression profiles"],"prefix":"10.1186","volume":"3","author":[{"given":"Teppei","family":"Shimamura","sequence":"first","affiliation":[]},{"given":"Seiya","family":"Imoto","sequence":"additional","affiliation":[]},{"given":"Rui","family":"Yamaguchi","sequence":"additional","affiliation":[]},{"given":"Andr\u00e9","family":"Fujita","sequence":"additional","affiliation":[]},{"given":"Masao","family":"Nagasaki","sequence":"additional","affiliation":[]},{"given":"Satoru","family":"Miyano","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,4,22]]},"reference":[{"key":"309_CR1","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1038\/nbt1075","volume":"23","author":"D Di Bernardo","year":"2005","unstructured":"Di Bernardo D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, Elliott SJ, Schaus SE, Collins JJ: Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat Biotechnol. 2005, 23: 377-383.","journal-title":"Nat Biotechnol"},{"key":"309_CR2","doi-asserted-by":"publisher","first-page":"e8","DOI":"10.1371\/journal.pbio.0050008","volume":"5","author":"JJ Faith","year":"2007","unstructured":"Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS: Large-scale mapping and validation of Escherichia coli transcriptional regulation from a Compedium of expression profiles. PLoS Biol. 2007, 5: e8.","journal-title":"PLoS Biol"},{"key":"309_CR3","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1126\/science.1081900","volume":"301","author":"TS Gardner","year":"2003","unstructured":"Gardner TS, di Bernardo D, Lorenz D, Collins JJ: Inferring genetic networks and identifying compound mode of action via expression profiling. Science. 2003, 301: 102-105.","journal-title":"Science"},{"key":"309_CR4","first-page":"559","volume-title":"Pac Symp Biocomput","author":"S Imoto","year":"2006","unstructured":"Imoto S, Tamada Y, Araki H, Yasuda K, Print CG, Charnock-Jones SD, Sanders D, Savoie CJ, Tashiro K, Kuhara S, Miyano S: Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles. Pac Symp Biocomput. 2006, 559-571."},{"key":"309_CR5","first-page":"182","volume":"16","author":"Y Tamada","year":"2005","unstructured":"Tamada Y, Imoto S, Tashiro K, Kuhara S, Miyano S: Identifying drug active pathways from gene networks estimated by gene expression data. Genome Informatics. 2005, 16: 182-191.","journal-title":"Genome Informatics"},{"key":"309_CR6","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1186\/1752-0509-1-39","volume":"1","author":"A Fujita","year":"2007","unstructured":"Fujita A, Sato JR, Garay-Malpartida HM, Yamaguchi R, Miyano S, Sogayar MC, Ferreira CE: Modeling gene expression regulatory networks with the sparse vector autoregressive model. BMC Syst Biol. 2007, 1: 39.","journal-title":"BMC Syst Biol"},{"issue":"Suppl 2","key":"309_CR7","doi-asserted-by":"publisher","first-page":"S3","DOI":"10.1186\/1471-2105-8-S2-S3","volume":"8","author":"R Opgen-Rhein","year":"2007","unstructured":"Opgen-Rhein R, Strimmer K: Learning causal networks from systems biology time course data: an effective model selection procedure for the vector autoregressive process. BMC Bioinformatics. 2007, 8 (Suppl 2): S3.","journal-title":"BMC Bioinformatics"},{"key":"309_CR8","doi-asserted-by":"publisher","first-page":"1304","DOI":"10.1080\/01621459.2000.10474336","volume":"95","author":"EI George","year":"2000","unstructured":"George EI: The variable selection problem. J Am Statist Assoc. 2000, 95: 1304-1308.","journal-title":"J Am Statist Assoc"},{"key":"309_CR9","doi-asserted-by":"publisher","DOI":"10.1201\/9781420035933","volume-title":"Subset Selection in Regression","author":"A Miller","year":"2002","unstructured":"Miller A: Subset Selection in Regression. 2002, Chapman & Hall\/CRC, Second.","edition":"Second"},{"key":"309_CR10","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1111\/j.2517-6161.1996.tb02080.x","volume":"58","author":"R Tibshirani","year":"1996","unstructured":"Tibshirani R: Regression shrinkage and selection via the lasso. J R Statist Soc B. 1996, 58: 267-288.","journal-title":"J R Statist Soc B"},{"key":"309_CR11","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1111\/j.1467-9868.2008.00674.x","volume":"70","author":"J Fan","year":"2008","unstructured":"Fan J, Lv J: Sure independence screening for ultrahigh dimensional feature space. J R Statist Soc B. 2008, 70: 849-911.","journal-title":"J R Statist Soc B"},{"key":"309_CR12","doi-asserted-by":"publisher","first-page":"2350","DOI":"10.1214\/aos\/1032181158","volume":"24","author":"L Breiman","year":"1996","unstructured":"Breiman L: Heuristics of instability and stabilization in model selection. The Annals of Statistics. 1996, 24: 2350-2383.","journal-title":"The Annals of Statistics"},{"key":"309_CR13","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1111\/j.1467-9868.2005.00503.x","volume":"67","author":"H Zou","year":"2005","unstructured":"Zou H, Hastie T: Regularization and variable selection via the elastic net. J R Statist Soc B. 2005, 67: 301-320.","journal-title":"J R Statist Soc B"},{"key":"309_CR14","doi-asserted-by":"publisher","first-page":"424","DOI":"10.2307\/1912791","volume":"37","author":"CWJ Granger","year":"1969","unstructured":"Granger CWJ: Investigating causal relation by econometric and cross-sectional method. Econometrica. 1969, 37: 424-438.","journal-title":"Econometrica"},{"key":"309_CR15","first-page":"1273","volume":"16","author":"C Leng","year":"2006","unstructured":"Leng C, Lin Y, Wahba G: A note on lasso and related procedures in model selection. Statistica Sinica. 2006, 16: 1273-1284.","journal-title":"Statistica Sinica"},{"key":"309_CR16","doi-asserted-by":"publisher","first-page":"5277","DOI":"10.1016\/j.csda.2008.05.006","volume":"52","author":"H Wang","year":"2008","unstructured":"Wang H, Leng C: A note on adaptive group lasso. Comput Statist Data Anal. 2008, 52: 5277-5286.","journal-title":"Comput Statist Data Anal"},{"key":"309_CR17","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1111\/j.1467-9868.2007.00581.x","volume":"69","author":"M Yuan","year":"2007","unstructured":"Yuan M, Lin Y: On the nonnegative garrote estimator. J R Statist Soc B. 2007, 69: 143-161.","journal-title":"J R Statist Soc B"},{"key":"309_CR18","doi-asserted-by":"publisher","first-page":"1418","DOI":"10.1198\/016214506000000735","volume":"101","author":"H Zou","year":"2006","unstructured":"Zou H: The adaptive lasso and its oracle properties. J Am Statist Assoc. 2006, 101: 1418-1429.","journal-title":"J Am Statist Assoc"},{"key":"309_CR19","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1093\/biomet\/asm037","volume":"94","author":"HH Zhang","year":"2006","unstructured":"Zhang HH, Lu W: Adaptive lasso for Cox's proportional hazards model. Biometrika. 2006, 94: 691-703.","journal-title":"Biometrika"},{"key":"309_CR20","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1198\/073500106000000251","volume":"25","author":"H Wang","year":"2007","unstructured":"Wang H, Guodong L, Guohua J: Robust regression shrinkage and consistent variable selection through LAD-lasso. J Bus Econ Statist. 2007, 25: 347-355.","journal-title":"J Bus Econ Statist"},{"key":"309_CR21","first-page":"142","volume":"19","author":"T Shimamura","year":"2007","unstructured":"Shimamura T, Imoto S, Yamaguchi R, Miyano S: Weighted lasso in graphical Gaussian modeling for large gene network estimation based on microarray data. Genome Informatics. 2007, 19: 142-153.","journal-title":"Genome Informatics"},{"key":"309_CR22","doi-asserted-by":"publisher","first-page":"2173","DOI":"10.1214\/009053607000000127","volume":"35","author":"H Zou","year":"2007","unstructured":"Zou H, Hastie T, Tibshirani R: On the \"degrees of freedom\" of the lasso. Ann Statist. 2007, 35: 2173-2192.","journal-title":"Ann Statist"},{"key":"309_CR23","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1214\/aos\/1176344136","volume":"6","author":"G Schwarz","year":"1978","unstructured":"Schwarz G: Estimating the dimension of a model. Ann Statist. 1978, 6: 461-464.","journal-title":"Ann Statist"},{"key":"309_CR24","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1093\/biomet\/78.3.521","volume":"78","author":"CM Hurvich","year":"1991","unstructured":"Hurvich CM, Tsai CL: Bias of the corrected AIC criterion for underfitted regression and time series models. Biometrika. 1991, 78: 521-530.","journal-title":"Biometrika"},{"key":"309_CR25","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1080\/03610927808827599","volume":"7","author":"N Sugiura","year":"1978","unstructured":"Sugiura N: Further analysis of the data by Akaike's information criterion and the finite corrections. Comm Statist A. 1978, 7: 13-26.","journal-title":"Comm Statist A"},{"key":"309_CR26","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1126\/science.286.5439.509","volume":"286","author":"AL Barab\u00e1si","year":"1999","unstructured":"Barab\u00e1si AL, Albert R: Emergence of scaling in random networks. Science. 1999, 286: 509-512.","journal-title":"Science"},{"key":"309_CR27","unstructured":"Cs\u00e1rdi G, Nepusz T: igraph Reference Manual. http:\/\/cneurocvs.rmki.kfki.hu\/igraph\/"},{"key":"309_CR28","unstructured":"NCBI Gene expression omnibus Accession Number GSE6462. http:\/\/www.ncbi.nlm.nih.gov\/geo\/"},{"key":"309_CR29","doi-asserted-by":"publisher","first-page":"2778","DOI":"10.1093\/bioinformatics\/bth327","volume":"20","author":"KV Ballman","year":"2004","unstructured":"Ballman KV, Grill DE, Oberg AL, Therneau TM: Faster cyclic loess: normalizing RNA arrays via linear models. Bioinformatics. 2004, 20: 2778-2786.","journal-title":"Bioinformatics"},{"key":"309_CR30","doi-asserted-by":"publisher","first-page":"79879","DOI":"10.1155\/2007\/79879","volume":"2007","author":"PE Meyer","year":"2007","unstructured":"Meyer PE, Kontos K, Lafitte F, Bontempi G: Information-theoretic inference of large transcriptional regulatory networks. EURASIP J Bioinform Syst Biol. 2007, 2007: 79879.","journal-title":"EURASIP J Bioinform Syst Biol"},{"key":"309_CR31","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1038\/ng1532","volume":"37","author":"K Basso","year":"2005","unstructured":"Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A: Reverse engineering of regulatory networks in human B cells. Nat Genet. 2005, 37: 382-390.","journal-title":"Nat Genet"},{"key":"309_CR32","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1186\/1471-2105-9-461","volume":"9","author":"PE Meyer","year":"2008","unstructured":"Meyer PE, Lafitte F, Bontempi G: minet: A R\/Bioconductor package for inferring large transcriptional networks using mutual information. BMC Bioinformatics. 2008, 9: 461.","journal-title":"BMC Bioinformatics"},{"key":"309_CR33","unstructured":"TRANSPATH: the pathway databases. http:\/\/www.biobase.de\/pages\/index.php?sid=transpathdatabases"},{"key":"309_CR34","doi-asserted-by":"publisher","first-page":"4045","DOI":"10.1074\/jbc.M608653200","volume":"282","author":"T Nagashima","year":"2007","unstructured":"Nagashima T, Shimodaira H, Ide K, Nakakuki T, Tani Y, Takahashi K, Yumoto N, Hatakeyama M: Quantitative transcriptional control of ErbB receptor signaling undergoes graded to biphasic response for cell differentiation. J Biol Chem. 2007, 282: 4045-4056.","journal-title":"J Biol Chem"},{"key":"309_CR35","unstructured":"Cell Illustrator. http:\/\/cionline.hgc.jp\/"},{"key":"309_CR36","first-page":"181","volume":"2","author":"M Nagasaki","year":"2003","unstructured":"Nagasaki M, Doi A, Matsuno H, Miyano S: Genomic Object Net: I. A platform for modeling and simulating biopathways. Applied Bioinformatics. 2003, 2: 181-184.","journal-title":"Applied Bioinformatics"},{"key":"309_CR37","doi-asserted-by":"publisher","first-page":"6163","DOI":"10.1073\/pnas.092576199","volume":"99","author":"MK Yeung","year":"2002","unstructured":"Yeung MK, Tegne'r J, Collins JJ: Reverse engineering gene networks using singular value decomposition and robust regression. Proc Natl Acad Sci USA. 2002, 99: 6163-6168.","journal-title":"Proc Natl Acad Sci USA"},{"key":"309_CR38","doi-asserted-by":"publisher","first-page":"2413","DOI":"10.1093\/bioinformatics\/btl396","volume":"22","author":"Y Wang","year":"2006","unstructured":"Wang Y, Joshi T, Zhang XS, Xu D, Chen L: Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics. 2006, 22: 2413-2420.","journal-title":"Bioinformatics"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-3-41.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1752-0509-3-41\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-3-41.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,9]],"date-time":"2025-02-09T03:56:43Z","timestamp":1739073403000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-3-41"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,4,22]]},"references-count":38,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["309"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-3-41","relation":{},"ISSN":["1752-0509"],"issn-type":[{"type":"electronic","value":"1752-0509"}],"subject":[],"published":{"date-parts":[[2009,4,22]]},"article-number":"41"}}