{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T14:24:05Z","timestamp":1743085445443,"version":"3.40.3"},"publisher-location":"Berlin, Heidelberg","reference-count":25,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642011832"},{"type":"electronic","value":"9783642011849"}],"license":[{"start":{"date-parts":[[2009,1,1]],"date-time":"2009-01-01T00:00:00Z","timestamp":1230768000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009]]},"DOI":"10.1007\/978-3-642-01184-9_2","type":"book-chapter","created":{"date-parts":[[2009,4,9]],"date-time":"2009-04-09T13:41:49Z","timestamp":1239284509000},"page":"13-24","source":"Crossref","is-referenced-by-count":0,"title":["Gaussian Graphical Models to Infer Putative Genes Involved in Nitrogen Catabolite Repression in S. cerevisiae"],"prefix":"10.1007","author":[{"given":"Kevin","family":"Kontos","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bruno","family":"Andr\u00e9","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacques","family":"van Helden","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gianluca","family":"Bontempi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"2_CR1","doi-asserted-by":"publisher","first-page":"3065","DOI":"10.1128\/MCB.01084-06","volume":"27","author":"P. Godard","year":"2007","unstructured":"Godard, P., Urrestarazu, A., Vissers, S., Kontos, K., Bontempi, G., van Helden, J., Andr\u00e9, B.: Effect of 21 different nitrogen sources on global gene expression in the yeast Saccharomyces cerevisiae. Molecular and Cellular Biology\u00a027, 3065\u20133086 (2007)","journal-title":"Molecular and Cellular Biology"},{"key":"2_CR2","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1111\/j.1567-1364.2006.00060.x","volume":"6","author":"B. Scherens","year":"2006","unstructured":"Scherens, B., Feller, A., Vierendeels, F., Messenguy, F., Dubois, E.: Identification of direct and indirect targets of the Gln3 and Gat1 activators by transcriptional profiling in response to nitrogen availability in the short and long term. FEMS Yeast Research\u00a06, 777\u2013791 (2006)","journal-title":"FEMS Yeast Research"},{"key":"2_CR3","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/1753-6561-2-s4-s5","volume":"2","author":"K. Kontos","year":"2008","unstructured":"Kontos, K., Godard, P., Andr\u00e9, B., van Helden, J., Bontempi, G.: Machine learning techniques to identify putative genes involved in nitrogen catabolite repression in the yeast Saccharomyces cerevisiae. BMC Proceedings\u00a02, S5 (2008)","journal-title":"BMC Proceedings"},{"key":"2_CR4","series-title":"Oxford Statistical Science Series","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780198522195.001.0001","volume-title":"Graphical Models","author":"S.L. Lauritzen","year":"1996","unstructured":"Lauritzen, S.L.: Graphical Models. Oxford Statistical Science Series. Clarendon Press, Oxford (1996)"},{"key":"2_CR5","doi-asserted-by":"publisher","first-page":"2370","DOI":"10.1093\/bioinformatics\/bth252","volume":"20","author":"N. Simonis","year":"2004","unstructured":"Simonis, N., Wodak, S.J., Cohen, G.N., van Helden, J.: Combining pattern discovery and discriminant analysis to predict gene co-regulation. Bioinformatics\u00a020, 2370\u20132379 (2004)","journal-title":"Bioinformatics"},{"key":"2_CR6","doi-asserted-by":"publisher","first-page":"32","DOI":"10.2202\/1544-6115.1175","volume":"4","author":"J. Sch\u00e4fer","year":"2005","unstructured":"Sch\u00e4fer, J., Strimmer, K.: A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Statistical Applications in Genetics and Molecular Biology\u00a04, 32 (2005)","journal-title":"Statistical Applications in Genetics and Molecular Biology"},{"key":"2_CR7","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1016\/j.jmva.2004.02.009","volume":"90","author":"A. Dobra","year":"2004","unstructured":"Dobra, A., Hans, C., Jones, B., Nevins, J., Yao, G., West, M.: Sparse graphical models for exploring gene expression data. Journal of Multivariate Analysis\u00a090, 196\u2013212 (2004)","journal-title":"Journal of Multivariate Analysis"},{"key":"2_CR8","first-page":"2621","volume":"7","author":"R. Castelo","year":"2006","unstructured":"Castelo, R., Roverato, A.: A robust procedure for Gaussian graphical model search from microarray data with p larger than n. Journal of Machine Learning Research\u00a07, 2621\u20132650 (2006)","journal-title":"Journal of Machine Learning Research"},{"key":"2_CR9","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1186\/gb-2004-5-12-r100","volume":"5","author":"P. Magwene","year":"2004","unstructured":"Magwene, P., Kim, J.: Estimating genomic coexpression networks using first-order conditional independence. Genome Biology\u00a05, R100 (2004)","journal-title":"Genome Biology"},{"key":"2_CR10","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1186\/gb-2004-5-11-r92","volume":"5","author":"A. Wille","year":"2004","unstructured":"Wille, A., Zimmermann, P., Vranov\u00e1, E., F\u00fcrholz, A., Laule, O., Bleuler, S., Hennig, L., Preli\u0107, A., von Rohr, P., Thiele, L., Zitzler, E., Gruissem, W., B\u00fchlmann, P.: Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana. Genome Biology\u00a05, R92 (2004)","journal-title":"Genome Biology"},{"key":"2_CR11","series-title":"CCIS 13","first-page":"273","volume-title":"BIRD 2008","author":"K. Kontos","year":"2008","unstructured":"Kontos, K., Bontempi, G.: Nested q-partial graphs for genetic network inference from \u201csmall n, large p\u201d microarray data. In: Elloumi, M., K\u00fcng, J., Linial, M., Murphy, R., Schneider, K., Toma, C. (eds.) BIRD 2008. CCIS 13, pp. 273\u2013287. Springer, Heidelberg (2008)"},{"key":"2_CR12","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1016\/S0047-259X(03)00096-4","volume":"88","author":"O. Ledoit","year":"2004","unstructured":"Ledoit, O., Wolf, M.: A well-conditioned estimator for large-dimensional covariance matrices. Journal of Multivariate Analysis\u00a088, 365\u2013411 (2004)","journal-title":"Journal of Multivariate Analysis"},{"key":"2_CR13","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1111\/j.1574-6976.2002.tb00612.x","volume":"26","author":"T.G. Cooper","year":"2002","unstructured":"Cooper, T.G.: Transmitting the signal of excess nitrogen in Saccharomyces cerevisiae from the Tor proteins to the GATA factors: connecting the dots. FEMS Microbiology Reviews\u00a026, 223\u2013238 (2002)","journal-title":"FEMS Microbiology Reviews"},{"key":"2_CR14","doi-asserted-by":"publisher","first-page":"1337","DOI":"10.1038\/nbt890","volume":"21","author":"Z. Bar-Joseph","year":"2003","unstructured":"Bar-Joseph, Z., Gerber, G., Lee, T., Rinaldi, N., Yoo, J., Robert, F., Gordon, D., Fraenkel, E., Jaakkola, T., Young, R., et al.: Computational discovery of gene modules and regulatory networks. Nature Biotechnology\u00a021, 1337\u20131342 (2003)","journal-title":"Nature Biotechnology"},{"key":"2_CR15","doi-asserted-by":"publisher","first-page":"12182","DOI":"10.1073\/pnas.220392197","volume":"97","author":"A. Butte","year":"2000","unstructured":"Butte, A., Tamayo, P., Slonim, D., Golub, T., Kohane, I.: Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proceedings of the National Academy of Sciences\u00a097, 12182\u201312186 (2000)","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"2_CR16","volume-title":"Graphical Models in Applied Multivariate Statistics","author":"J. Whittaker","year":"1990","unstructured":"Whittaker, J.: Graphical Models in Applied Multivariate Statistics. John Wiley and Sons, Inc., Chichester (1990)"},{"key":"2_CR17","series-title":"Springer Texts in Statistics","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4612-0493-0","volume-title":"Introduction to Graphical Modelling","author":"D. Edwards","year":"2000","unstructured":"Edwards, D.: Introduction to Graphical Modelling, 2nd edn. Springer Texts in Statistics. Springer, Heidelberg (2000)","edition":"2"},{"key":"2_CR18","doi-asserted-by":"publisher","first-page":"754","DOI":"10.1093\/bioinformatics\/bti062","volume":"21","author":"J. Sch\u00e4fer","year":"2005","unstructured":"Sch\u00e4fer, J., Strimmer, K.: An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics\u00a021, 754\u2013764 (2005)","journal-title":"Bioinformatics"},{"key":"2_CR19","doi-asserted-by":"publisher","first-page":"2153","DOI":"10.1214\/aoms\/1177696719","volume":"41","author":"R. Dykstra","year":"1970","unstructured":"Dykstra, R.: Establishing the positive definiteness of the sample covariance matrix. The Annals of Mathematical Statistics\u00a041, 2153\u20132154 (1970)","journal-title":"The Annals of Mathematical Statistics"},{"key":"2_CR20","doi-asserted-by":"publisher","first-page":"3593","DOI":"10.1093\/nar\/gkg567","volume":"31","author":"J. Helden van","year":"2003","unstructured":"van Helden, J.: Regulatory sequence analysis tools. Nucleic Acids Research\u00a031, 3593\u20133596 (2003)","journal-title":"Nucleic Acids Research"},{"key":"2_CR21","first-page":"445","volume-title":"Proceedings of the Fifteenth International Conference on Machine Learning","author":"F. Provost","year":"1998","unstructured":"Provost, F., Fawcett, T., Kohavi, R.: The case against accuracy estimation for comparing induction algorithms. In: Proceedings of the Fifteenth International Conference on Machine Learning, pp. 445\u2013453. Morgan Kaufmann, San Francisco (1998)"},{"key":"2_CR22","doi-asserted-by":"publisher","first-page":"861","DOI":"10.1016\/j.patrec.2005.10.010","volume":"27","author":"T. Fawcett","year":"2006","unstructured":"Fawcett, T.: An introduction to ROC analysis. Pattern Recognition Letters\u00a027, 861\u2013874 (2006)","journal-title":"Pattern Recognition Letters"},{"key":"2_CR23","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1177\/0272989X8900900307","volume":"9","author":"R.J. McClish","year":"1989","unstructured":"McClish, R.J.: Analyzing a portion of the ROC curve. Medical Decision Making\u00a09, 190\u2013195 (1989)","journal-title":"Medical Decision Making"},{"key":"2_CR24","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1148\/radiology.201.3.8939225","volume":"201","author":"Y.L. Jiang","year":"1996","unstructured":"Jiang, Y.L., Metz, C.E., Nishikawa, R.M.: A receiver operating characteristic partial area index for highly sensitive diagnostic tests. Radiology\u00a0201, 745\u2013750 (1996)","journal-title":"Radiology"},{"key":"2_CR25","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1093\/biomet\/68.3.589","volume":"68","author":"B. Efron","year":"1981","unstructured":"Efron, B.: Nonparametric estimates of standard error: the jackknife, the bootstrap and other methods. Biometrika\u00a068, 589\u2013599 (1981)","journal-title":"Biometrika"}],"container-title":["Lecture Notes in Computer Science","Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-01184-9_2","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,12]],"date-time":"2024-03-12T14:29:37Z","timestamp":1710253777000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-01184-9_2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009]]},"ISBN":["9783642011832","9783642011849"],"references-count":25,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-01184-9_2","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2009]]}}}