{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,26]],"date-time":"2025-02-26T05:30:50Z","timestamp":1740547850881,"version":"3.38.0"},"publisher-location":"Berlin, Heidelberg","reference-count":26,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642150197"},{"type":"electronic","value":"9783642150203"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010]]},"DOI":"10.1007\/978-3-642-15020-3_15","type":"book-chapter","created":{"date-parts":[[2010,9,9]],"date-time":"2010-09-09T12:14:54Z","timestamp":1284034494000},"page":"158-171","source":"Crossref","is-referenced-by-count":0,"title":["A Self-organizing State Space Approach to Inferring Time-Varying Causalities between Regulatory Proteins"],"prefix":"10.1007","author":[{"given":"Osamu","family":"Hirose","sequence":"first","affiliation":[]},{"given":"Kentaro","family":"Shimizu","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"key":"15_CR1","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1089\/106652700750050961","volume":"7","author":"N. Friedman","year":"2000","unstructured":"Friedman, N., Linial, M., Nachman, I., Pe\u2019er, D.: Using ayesian networks to analyze expression data. J. Comput. Biol.\u00a07, 601\u2013620 (2000)","journal-title":"J. Comput. Biol."},{"key":"15_CR2","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1126\/science.1094068","volume":"303","author":"N. Friedman","year":"2004","unstructured":"Friedman, N.: Inferring cellular networks using probabilistic graphical models. Science\u00a0303, 799\u2013805 (2004)","journal-title":"Science"},{"key":"15_CR3","unstructured":"Imoto, S., Goto, T., Miyano, S.: Estimation of genetic networks and functional structures between genes by using bayesian networks and nonparametric regression. In: Proceedings of Pacific Symposium of Biocomputing, pp. 175\u2013186 (2002)"},{"key":"15_CR4","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 Inform.\u00a016, 182\u2013191 (2005)","journal-title":"Genome Inform."},{"key":"15_CR5","doi-asserted-by":"publisher","first-page":"1623","DOI":"10.1093\/bioinformatics\/btm151","volume":"23","author":"A. Fujita","year":"2007","unstructured":"Fujita, A., Sato, J.R., Garay-Malpartida, H.M., Morettin, P.A., Sogayar, M.C., Ferreira, C.E.: Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method. Bioinformatics\u00a023, 1623\u20131630 (2007)","journal-title":"Bioinformatics"},{"key":"15_CR6","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1186\/1752-0509-3-41","volume":"3","author":"T. Shimamura","year":"2009","unstructured":"Shimamura, T., Imoto, S., Yamaguchi, R., Fujita, A., Nagasaki, M., Miyano, S.: Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Syst. Biol.\u00a03, 41 (2009)","journal-title":"BMC Syst. Biol."},{"key":"15_CR7","first-page":"37","volume":"20","author":"K. Kojima","year":"2008","unstructured":"Kojima, K., Fujita, A., Shimamura, T., Imoto, S., Miyano, S.: Estimation of nonlinear gene regulatory networks via L1 regularized NVAR from time series gene expression data. Genome Inform.\u00a020, 37\u201351 (2008)","journal-title":"Genome Inform."},{"key":"15_CR8","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1093\/bioinformatics\/bti014","volume":"21","author":"M.J. Beal","year":"2005","unstructured":"Beal, M.J., Falciani, F., Ghahramani, Z., Rangel, C., Wild, D.L.: A Bayesian approach to reconstructing genetic regulatory networks with hidden factors. Bioinformatics\u00a021, 349\u2013356 (2005)","journal-title":"Bioinformatics"},{"key":"15_CR9","doi-asserted-by":"publisher","first-page":"1361","DOI":"10.1093\/bioinformatics\/bth093","volume":"20","author":"C. Rangel","year":"2004","unstructured":"Rangel, C., Angus, J., Ghahramani, Z., Lioumi, M., Sotheran, E., Gaiba, A., Wild, D.L., Falciani, F.: Modeling T-cell activation using gene expression profiling and state-space models. Bioinformatics\u00a020, 1361\u20131372 (2004)","journal-title":"Bioinformatics"},{"key":"15_CR10","doi-asserted-by":"crossref","unstructured":"Wu, F.X., Zhang, W.J., Kusalik, A.J.: Modeling gene expression from microarray expression data with state-space equations. In: Proceedings of Pacific Symposium on Biocomputing, pp. 581\u2013592 (2004)","DOI":"10.1142\/9789812704856_0054"},{"key":"15_CR11","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1109\/MSP.2007.273053","volume":"24","author":"R. Yamaguchi","year":"2007","unstructured":"Yamaguchi, R., Yoshida, R., Imoto, S., Higuchi, T., Miyano, S.: Finding module-based gene networks with state-space models. IEEE Signal Processing Magazine\u00a024, 37\u201346 (2007)","journal-title":"IEEE Signal Processing Magazine"},{"key":"15_CR12","doi-asserted-by":"crossref","unstructured":"Yoshida, R., Imoto, S., Higuchi, T.: Estimating time-dependent gene networks from time series microarray data by dynamic linear models with markov switching. In: Proceedings of Computational Systems Bioinformatics, pp. 289\u2013298 (2005)","DOI":"10.1109\/CSB.2005.32"},{"key":"15_CR13","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1093\/bioinformatics\/btk034","volume":"22","author":"Z. Li","year":"2006","unstructured":"Li, Z., Shaw, S.M., Yedwabnick, M.J., Chan, C.: Using a state-space model with hidden variables to infer transcription factor activities. Bioinformatics\u00a022, 747\u2013754 (2006)","journal-title":"Bioinformatics"},{"key":"15_CR14","doi-asserted-by":"crossref","unstructured":"Rao, A., Hero, A.O., States, D.J., Engel, J.D.: Using directed information to build biologically relevant influence networks. In: Comput. Syst. Bioinformatics Conf., vol.\u00a06, pp. 145\u2013156 (2007)","DOI":"10.1142\/9781860948732_0018"},{"key":"15_CR15","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1111\/j.1467-9892.1982.tb00349.x","volume":"3","author":"R.H. Shumway","year":"1982","unstructured":"Shumway, R.H., Stoffer, D.S.: An approach to time series smoothing and forecasting using the EM algorithm. Journal of Time Series Analysis\u00a03, 253\u2013264 (1982)","journal-title":"Journal of Time Series Analysis"},{"key":"15_CR16","first-page":"1203","volume":"93","author":"G. Kitagawa","year":"1998","unstructured":"Kitagawa, G.: A self-organizing state-space model. Journal of the American Statistical Association\u00a093, 1203\u20131215 (1998)","journal-title":"Journal of the American Statistical Association"},{"key":"15_CR17","first-page":"36","volume":"83","author":"T. Higuchi","year":"2000","unstructured":"Higuchi, T., Kitagawa, G.: Knowledge discovery and self-organizing state space model. IEICE Transactions on Information and Systems E Series D\u00a083, 36\u201343 (2000)","journal-title":"IEICE Transactions on Information and Systems E Series D"},{"key":"15_CR18","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1007\/s00180-007-0027-2","volume":"23","author":"K. Yano","year":"2008","unstructured":"Yano, K.: A self-organizing state space model and simplex initial distribution search. Computational Statistics\u00a023, 197\u2013216 (2008)","journal-title":"Computational Statistics"},{"key":"15_CR19","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1126\/science.1075090","volume":"298","author":"T.I. Lee","year":"2002","unstructured":"Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I., Zeitlinger, J., Jennings, E.G., Murray, H.L., Gordon, D.B., Ren, B., Wyrick, J.J., Tagne, J.B., Volkert, T.L., Fraenkel, E., Gifford, D.K., Young, R.A.: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science\u00a0298, 799\u2013804 (2002)","journal-title":"Science"},{"key":"15_CR20","doi-asserted-by":"publisher","first-page":"3273","DOI":"10.1091\/mbc.9.12.3273","volume":"9","author":"P.T. Spellman","year":"1998","unstructured":"Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D., Futcher, B.: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell.\u00a09, 3273\u20133297 (1998)","journal-title":"Mol. Biol. Cell."},{"key":"15_CR21","doi-asserted-by":"publisher","first-page":"5064","DOI":"10.1128\/MCB.23.14.5064-5077.2003","volume":"23","author":"M. Costanzo","year":"2003","unstructured":"Costanzo, M., Schub, O., Andrews, B.: G1 transcription factors are differentially regulated in Saccharomyces cerevisiae by the Swi6-binding protein Stb1. Mol. Cell. Biol.\u00a023, 5064\u20135077 (2003)","journal-title":"Mol. Cell. Biol."},{"key":"15_CR22","doi-asserted-by":"publisher","first-page":"6919","DOI":"10.1128\/MCB.00211-08","volume":"28","author":"R.A.M. Bruin de","year":"2008","unstructured":"de Bruin, R.A.M., Kalashnikova, T.I., Wittenberg, C.: Stb1 collaborates with other regulators to modulate the G1-specific transcriptional circuit. Mol. Cell. Biol.\u00a028, 6919\u20136928 (2008)","journal-title":"Mol. Cell. Biol."},{"key":"15_CR23","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1016\/S0092-8674(01)00494-9","volume":"106","author":"I. Simon","year":"2001","unstructured":"Simon, I., Barnett, J., Hannett, N., Harbison, C.T., Rinaldi, N.J., Volkert, T.L., Wyrick, J.J., Zeitlinger, J., Gifford, D.K., Jaakkola, T.S., Young, R.A.: Serial regulation of transcriptional regulators in the yeast cell cycle. Cell\u00a0106, 697\u2013708 (2001)","journal-title":"Cell"},{"key":"15_CR24","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1038\/35017589","volume":"406","author":"M. Koranda","year":"2000","unstructured":"Koranda, M., Schleiffer, A., Endler, L., Ammerer, G.: Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2\/M-specific promoters. Nature\u00a0406, 94\u201398 (2000)","journal-title":"Nature"},{"key":"15_CR25","doi-asserted-by":"publisher","first-page":"2087","DOI":"10.1128\/MCB.20.6.2087-2097.2000","volume":"20","author":"N. Amar","year":"2000","unstructured":"Amar, N., Messenguy, F., Bakkoury, M.E., Dubois, E.: ArgRII, a component of the argr-mcm1 complex involved in the control of arginine metabolism in saccharomyces cerevisiae, is the sensor of arginine. Mol. Cell. Biol.\u00a020, 2087\u20132097 (2000)","journal-title":"Mol. Cell. Biol."},{"key":"15_CR26","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1038\/415180a","volume":"415","author":"Y. Ho","year":"2002","unstructured":"Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L., Wolting, C., Donaldson, I., Schandorff, S., Shewnarane, J., Vo, M., Taggart, J., Goudreault, M., Muskat, B., Alfarano, C., Dewar, D., Lin, Z., Michalickova, K., Willems, A.R., Sassi, H., Nielsen, P.A., Rasmussen, K.J., Andersen, J.R., Johansen, L.E., Hansen, L.H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Srensen, B.D., Matthiesen, J., Hendrickson, R.C., Gleeson, F., Pawson, T., Moran, M.F., Durocher, D., Mann, M., Hogue, C.W.V., Figeys, D., Tyers, M.: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature\u00a0415, 180\u2013183 (2002)","journal-title":"Nature"}],"container-title":["Lecture Notes in Computer Science","Information Technology in Bio- and Medical Informatics, ITBAM 2010"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-15020-3_15","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,25]],"date-time":"2025-02-25T17:28:18Z","timestamp":1740504498000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-15020-3_15"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010]]},"ISBN":["9783642150197","9783642150203"],"references-count":26,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-15020-3_15","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2010]]}}}