378
V. Mittard-Runte et al.
Thieme F, Koebnik R, Bekel T et al (2005) Insights into genome plasticity and pathogenicity of the
plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete
genome sequence. J Bacteriol 187(21):7254–7266
Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing
radiation response. Proc Natl Acad Sci U S A 98(9):5116–5121
Usuka J, Zhu W, Brendel V (2000) Optimal spliced alignment of homologous cDNA to a genomic
DNA template. Bioinformatics 16(3):203–211
van Baren MJ, Brent MR (2006) Iterative gene prediction and pseudogene removal improves
genome annotation. Genome Res 16(5):678–685
Vapnik VN (1999) The nature of statistical learning theory. Springer, New York.
Velculescu VE, Zhang L, Vogelstein B et al (1995) Serial analysis of gene expression. Science
270(5235):484–487
von Mering C, Jensen LJ, Snel B et al (2005) STRING: known and predicted protein-protein
associations, integrated and transferred across organisms. Nucleic Acids Res 33:433–437
Vorhölter FJ, Schneiker S, Goesmann A et al (2008) The genome of Xanthomonas campestris pv.
campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan
biosynthesis. J Biotechnol 134(1–2):33–45
Wei C, Brent MR (2006) Using ESTs to improve the accuracy of de novo gene prediction. BMC
Bioinformatics 7:327
Wilkinson MD, Links M (2002) BioMOBY: an open source biological web services proposal. Brief
Bioinform 3(4):331–341
Wu J, Mao X, Cai T et al (2006) KOBAS server: a web-based platform for automated annotation
and pathway identification. Nucleic Acids Res 34:W720–W724
Wu TD, Watanabe CK (2005) GMAP: a genomic mapping and alignment program for mRNA and
EST sequences. Bioinformatics 21(9):1859–1875
Wu W, Xing EP, Myers C et al (2005) Evaluation of normalization methods for cDNA microarray
data by k-NN classification. BMC Bioinformatics 6:191
Yang YH, Speed T (2002) Design issues for cDNA microarray experiments. Nat Rev Genet
3(8):579–588
Yauk C, Berndt L, Williams A et al (2005) Automation of cDNA microarray hybridization and
washing yields improved data quality. J Biochem Biophys Methods 64(1):69–75
Yauk CL, Berndt ML, Williams A et al (2004) Comprehensive comparison of six microarray
technologies. Nucleic Acids Res 32(15):e124
Zhang MQ (2002) Computational prediction of eukaryotic protein-coding genes. Nat Rev Genet
3(9):698–709
Zhang Z, Schwartz S, Wagner L et al (2000) A greedy algorithm for aligning DNA sequences. J
Comput Biol 7(1–2):203–214
V. Mittard-Runte et al.
Thieme F, Koebnik R, Bekel T et al (2005) Insights into genome plasticity and pathogenicity of the
plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete
genome sequence. J Bacteriol 187(21):7254–7266
Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing
radiation response. Proc Natl Acad Sci U S A 98(9):5116–5121
Usuka J, Zhu W, Brendel V (2000) Optimal spliced alignment of homologous cDNA to a genomic
DNA template. Bioinformatics 16(3):203–211
van Baren MJ, Brent MR (2006) Iterative gene prediction and pseudogene removal improves
genome annotation. Genome Res 16(5):678–685
Vapnik VN (1999) The nature of statistical learning theory. Springer, New York.
Velculescu VE, Zhang L, Vogelstein B et al (1995) Serial analysis of gene expression. Science
270(5235):484–487
von Mering C, Jensen LJ, Snel B et al (2005) STRING: known and predicted protein-protein
associations, integrated and transferred across organisms. Nucleic Acids Res 33:433–437
Vorhölter FJ, Schneiker S, Goesmann A et al (2008) The genome of Xanthomonas campestris pv.
campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan
biosynthesis. J Biotechnol 134(1–2):33–45
Wei C, Brent MR (2006) Using ESTs to improve the accuracy of de novo gene prediction. BMC
Bioinformatics 7:327
Wilkinson MD, Links M (2002) BioMOBY: an open source biological web services proposal. Brief
Bioinform 3(4):331–341
Wu J, Mao X, Cai T et al (2006) KOBAS server: a web-based platform for automated annotation
and pathway identification. Nucleic Acids Res 34:W720–W724
Wu TD, Watanabe CK (2005) GMAP: a genomic mapping and alignment program for mRNA and
EST sequences. Bioinformatics 21(9):1859–1875
Wu W, Xing EP, Myers C et al (2005) Evaluation of normalization methods for cDNA microarray
data by k-NN classification. BMC Bioinformatics 6:191
Yang YH, Speed T (2002) Design issues for cDNA microarray experiments. Nat Rev Genet
3(8):579–588
Yauk C, Berndt L, Williams A et al (2005) Automation of cDNA microarray hybridization and
washing yields improved data quality. J Biochem Biophys Methods 64(1):69–75
Yauk CL, Berndt ML, Williams A et al (2004) Comprehensive comparison of six microarray
technologies. Nucleic Acids Res 32(15):e124
Zhang MQ (2002) Computational prediction of eukaryotic protein-coding genes. Nat Rev Genet
3(9):698–709
Zhang Z, Schwartz S, Wagner L et al (2000) A greedy algorithm for aligning DNA sequences. J
Comput Biol 7(1–2):203–214