Biology Reference
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Jules, M., Klipp, E., Le Chat, L., Lecointe, F., Lewis, P., Liebermeister, W., March, A.,
Mars, R. A. T., Nannapaneni, P., Noone, D., Pohl, S., Rinn, B., R¨gheimer, F.,
Sappa, P. K., Samson, F., Schaffer, M., Schwikowski, B., Steil, L., St¨ lke, J.,
Wiegert, T., Wilkinson, A. J., van Dijl, J. M., Hecker, M., V¨lker, U.,
Bessi`res, P., and Noirot, P. (2012). Condition-dependent transcriptome reveals high-level
regulatory architecture in
Bacillus subtilis
.
Science
335, 1103-1106.
Opgen-Rhein, R. and Strimmer, K. (2007). Accurate ranking of differentially expressed genes
by a distribution-free shrinkage approach.
Stat. Appl. Genet. Mol. Biol.
6, e9.
Patterson, T. A., Lobenhofer, E. K., Fulmer-Smentek, S. B., Collins, P. J., Chu, T. M., Bao, W.,
Fang, H., Kawasaki, E. S., Hager, J., Tikhonova, I. R., Walker, S. J., Zhang, L., Hurban, P.,
de Longueville, F., Fuscoe, J. C., Tong, W., Shi, L., and Wolfinger, R. D. (2006). Perfor-
mance comparison of one-color and two-color platforms within the MicroArray Quality
Control (MAQC) project.
Nat. Biotechnol.
24, 1140-1150.
Perocchi, F., Xu, Z., Clauder-M¨nster, S., and Steinmetz, L. M. (2007). Antisense artifacts in
transcriptome microarray experiments are resolved by actinomycin D.
Nucleic Acids Res.
35, e128.
Peters, J. M., Mooney, R. A., Kuan, P. F., Rowland, J. L., Keles, S., and Landick, R. (2009).
Rho directs widespread termination of intragenic and stable RNA transcription.
Proc. Natl.
Acad. Sci. U.S.A.
106, 15406-15411.
Preli
´
, A., Bleuler, S., Zimmermann, P., Wille, A., B¨hlmann, P., Gruissem, W., Hennig, L.,
Thiele, L., and Zitzler, E. (2006). A systematic comparison and evaluation of biclustering
methods for gene expression data.
Bioinformatics
22, 1122-1129.
Qiu, X., Brooks, A. I., Klebanov, L., and Yakovlev, N. (2005). The effects of normalization on
the correlation structure of microarray data.
BMC Bioinformatics
6, e120.
Quackenbush, J. (2001). Computational analysis of microarray data.
Nat. Rev. Genet.
2,
418-427.
Rasmussen, S., Nielsen, H. B., and Jarmer, H. (2009). The transcriptionally active regions in
the genome of
Bacillus subtilis
.
Mol. Microbiol.
73, 1043-1057.
Richter, A., Schwager, C., Hentze, S., Ansorge, W., Hentze, M. W., and Muckenthaler, M.
(2002). Comparison of fluorescent tag DNA labeling methods used for expression analysis
by DNA microarrays.
Biotechniques
33, 620-630.
Ruprecht, R. M., Goodman, N. C., and Spiegelman, S. (1973). Conditions for the selective
synthesis of DNA complementary to template RNA.
Biochim. Biophys. Acta
294,
192-203.
Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. (1995). Quantitative monitoring of
gene expression patterns with a complementary DNA microarray.
Science
270, 467-470.
Sharan, R., Maron-Katz, A., and Shamir, R. (2003). CLICK and EXPANDER: a system for
clustering and visualizing gene expression data.
Bioinformatics
19, 1787-1799.
Slonim, N., Atwal, G. S., Tkacik, G., and Bialek, W. (2005). Information-based clustering.
Proc. Natl. Acad. Sci. U.S.A.
102, 18297-18302.
Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential
expression in microarray experiments.
Stat. Appl. Genet. Mol. Biol.
3, e3.
Smyth, G. K. (2005). Limma: linear models for microarray data. In R. Gentleman, V.
Carey, S. Dudoit, R. Irizarry & W. Huber (Eds.),
Bioinformatics and Computational
Biology Solutions using R and Bioconductor
(pp. 397-420). New York: Springer.
Sorek, R. and Cossart, P. (2010). Prokaryotic transcriptomics: a new view on regulation, phys-
iology and pathogenicity.
Nat. Rev. Genet.
11, 9-16.
