Biology Reference
In-Depth Information
Bolstad, B. M., Collin, F., Simpson, K. M., Irizarry, R. A., and Speed, T. P. (2004). Experi-
mental design and low-level analysis of microarray data. Int. Rev. Neurobiol. 60, 25-58.
Bolstad, B. M., Irizarry, R. A., Astrand, M., and Speed, T. P. (2003). A comparison of nor-
malization methods for high density oligonucleotide array data based on bias and variance.
Bioinformatics 19, 185-193.
Bourgon, R., Gentleman, R., and Huber, W. (2010). Independent filtering increases detec-
tion power for high-throughput experiments. Proc. Natl. Acad. Sci. U.S.A. 107,
9546-9551.
Buck, M. J. and Lieb, J. D. (2004). ChIP-chip: considerations for the design, analysis, and appli-
cation of genome-wide chromatin immunoprecipitation experiments. Genomics 83, 349-360.
Buescher, J. M., Liebermeister, W., Jules, M., Uhr, M., Muntel, J., Botella, E., Hessling, B.,
Kleijn, R. J., Le Chat, L., Lecointe, F., M¨der, U., Nicolas, P., Piersma, S., R¨gheimer, F.,
Becher, D., Bessieres, P., Bidnenko, E., Denham, E. L., Dervyn, E., Devine, K. M.,
Doherty, G., Drulhe, S., Felicori, L., Fogg, M. J., Goelzer, A., Hansen, A.,
Harwood, C. R., Hecker, M., Hubner, S., Hultschig, C., Jarmer, H., Klipp, E.,
Leduc, A., Lewis, P., Molina, F., Noirot, P., Peres, S., Pigeonneau, N., Pohl, S.,
Rasmussen, S., Rinn, B., Schaffer, M., Schnidder, J., Schwikowski, B., van Dijl, J. M.,
Veiga, P., Walsh, S., Wilkinson, A. J., Stelling, J., Aymerich, S., and Sauer, U. (2012).
Global network reorganization during dynamic adaptations of Bacillus subtilis metabo-
lism. Science 335, 1099-1103.
Bussemaker, H. J., Li, H., and Siggia, E. D. (2001). Regulatory element detection using cor-
relation with expression. Nat. Genet. 27, 167-171.
Bustin, S. A., Benes, V., Nolan, T., and Pfaffl, M. W. (2005). Quantitative real-time
RT-PCR—a perspective. J. Mol. Endocrinol. 34, 597-601.
Canelas, A. B., Harrison, N., Fazio, A., Zhang, J., Pitk ¨ nen, J. P., van den Brink, J.,
Bakker, B. M., Bogner, L., Bouwman, J., Castrillo, J. I., Cankorur, A.,
Chumnanpuen, P., Daran-Lapujade, P., Dikicioglu, D., van Eunen, K., Ewald, J. C.,
Heijnen, J. J., Kirdar, B., Mattila, I., Mensonides, F. I., Niebel, A., Penttil¨, M.,
Pronk, J. T., Reuss, M., Salusj¨rvi, L., Sauer, U., Sherman, D., Siemann-Herzberg, M.,
Westerhoff, H., de Winde, J., Petranovic, D., Oliver, S. G., Workman, C. T.,
Zamboni, N., and Nielsen, J. (2010). Integrated multilaboratory systems biology
reveals differences in protein metabolism between two reference yeast strains. Nat. Com-
mun. 1, 145.
Chandriani, S. and Ganem, D. (2007). Host transcript accumulation during lytic KSHV infec-
tion reveals several classes of host responses. PLoS One 2, e811.
Chomczynski, P. and Sacchi, N. (1987). Single-step method of RNA isolation by acid guani-
dinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162, 156-159.
Churchill, G. A. (2002). Fundamentals of experimental design for cDNA microarrays. Nat.
Genet. 32, 490-495.
Dufour, Y. S., Wesenberg, G. E., Tritt, A. J., Glasner, J. D., Perna, N. T., Mitchell, J. C., and
Donohue, T. J. (2010). chipD: a web tool to design oligonucleotide probes for high-density
tiling arrays. Nucleic Acids Res. 38, W321-W325.
Durand, S., Gilet, L., Bessi ` res, P., Nicolas, P., and Condon, C. (2012). Three essential
ribonucleases-RNase Y, J1, and III-control the abundance of a majority of Bacillus subtilis
mRNAs. PLoS Genet. 8, e1002520.
Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. (1998). Cluster analysis and dis-
play of genome-wide expression patterns. Proc. Natl. Acad. Sci. U.S.A. 95, 14863-14868.
Elemento, O., Slonim, N., and Tavazoie, S. (2007). A universal framework for regulatory ele-
ment discovery across all genomes and data types. Mol. Cell 28, 337-350.
Search WWH ::




Custom Search