Biology Reference
In-Depth Information
Irizarry, R. A., Wu, Z., and Jaffee, H. A. (2006). Comparison of Affymetrix GeneChip expres-
sion measures. Bioinformatics 22, 789-794.
Kauffmann, A., Gentleman, R., and Huber, W. (2009). arrayQualityMetrics—a bioconductor
package for quality assessment of microarray data. Bioinformatics 25, 415-416.
Kauffmann, A. and Huber, W. (2010). Microarray data quality control improves the detection
of differentially expressed genes. Genomics 95, 138-142.
Khanin, R. and Wit, E. (2005). Design of large time-course microarray experiments with two
channels. Appl. Bioinform. 4, 253-261.
Lee, S. I. and Batzoglou, S. (2003). Application of independent component analysis to micro-
arrays. Genome Biol. 4, e76.
Lee, W. P. and Tzou, W. S. (2009). Computational methods for discovering gene networks
from expression data. Brief. Bioinform. 10, 408-423.
Leek, J. T., Scharpf, R. B., Bravo, H. C., Simcha, D., Langmead, B., Johnson, W. E.,
Geman, D., Baggerly, K., and Irizarry, R. A. (2010). Tackling the widespread and critical
impact of batch effects in high-throughput data. Nat. Rev. Genet. 11, 733-739.
Lemoine, S., Combes, F., and Le Crom, S. (2009). An evaluation of custom microarray appli-
cations: the oligonucleotide design challenge. Nucleic Acids Res. 37, 1726-1739.
Liao, J. C., Boscolo, R., Yang, Y. L., Tran, L. M., Sabatti, C., and Roychowdhury, V. P. (2003).
Network component analysis: reconstruction of regulatory signals in biological systems.
Proc. Natl. Acad. Sci. U.S.A. 100, 15522-15527.
Liebermeister, W. (2002). Linear modes of gene expression determined by independent com-
ponent analysis. Bioinformatics 18, 51-60.
Liu, X. S., Brutlag, D. L., and Liu, J. S. (2002). An algorithm for finding protein-DNA binding
sites with applications to chromatin-immunoprecipitation microarray experiments. Nat.
Biotechnol. 20, 835-839.
McCarthy, D. J. and Smyth, G. K. (2009). Testing significance relative to a fold-change thresh-
old is a TREAT. Bioinformatics 25, 765-771.
Madeira, S. C. and Oliveira, A. L. (2004). Biclustering algorithms for biological data analysis:
a survey. IEEE/ACM Trans. Comput. Biol. Bioinform. 1, 24-45.
M¨der, U., Nicolas, P., Richard, H., Bessi`res, P., and Aymerich, S. (2011). Comprehensive
identification and quantification of microbial transcriptomes by genome-wide unbiased
methods. Curr. Opin. Biotechnol. 22, 32-41.
M¨der, U., Schmeisky, A. G., Fl´rez, L. A., and St¨lke, J. (2012). SubtiWiki—a comprehen-
sive community resource for the model organism Bacillus subtilis . Nucleic Acids Res. 40,
D1278-D1287.
Nam, D. and Kim, S. Y. (2008). Gene-set approach for expression pattern analysis. Brief.
Bioinform. 9, 189-197.
Nielsen, H. B., Wernersson, R., and Knudsen, S. (2003). Design of oligonucleotides for micro-
arrays and perspectives for design of multi-transcriptome arrays. Nucleic Acids Res. 31,
3491-3496.
Nicolas, P., Leduc, A., Robin, S., Rasmussen, S., Jarmer, H., and Bessi ` res, P. (2009). Tran-
scriptional landscape estimation from tiling array data using a model of signal shift and
drift. Bioinformatics 25, 2341-2347.
Nicolas, P., M¨der, U., Dervyn, E., Rochat, T., Leduc, A., Pigeonneau, N., Bidnenko, E.,
Marchadier, E., Hoebeke, M., Aymerich, S., Becher, D., Bisicchia, P., Botella, E.,
Delumeau, O., Doherty, G., Denham, E. L., Devine, K. M., Fogg, M., Fromion, V.,
Goelzer, A., Hansen, A., H ¨ rtig, E., Harwood, C. R., Homuth, G., Jarmer, H.,
Search WWH ::




Custom Search