Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995, 270: 467-470.
Article
PubMed
CAS
Google Scholar
Shalon D, Smith SJ, Brown PO: A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 1996, 6: 639-645.
Article
PubMed
CAS
Google Scholar
Stears RL, Martinsky T, Schena M: Trends in microarray analysis. Nat Med. 2003, 9: 140-145. 10.1038/nm0103-140.
Article
PubMed
CAS
Google Scholar
Kuipers OP, de Jong A, Baerends RJ, Van Hijum SA, Zomer AL, Karsens HA, den Hengst CD, Kramer NE, Buist G, Kok J: Transcriptome analysis and related databases of Lactococcus lactis. Antonie Van Leeuwenhoek. 2002, 82: 113-122. 10.1023/A:1020691801251.
Article
PubMed
CAS
Google Scholar
Bolotin A, Wincker P, Mauger S, Jaillon O, Malarme K, Weissenbach J, Ehrlich SD, Sorokin A: The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res. 2001, 11: 731-753. 10.1101/gr.GR-1697R.
Article
PubMed
CAS
PubMed Central
Google Scholar
Klaenhammer T, Altermann E, Arigoni F, Bolotin A, Breidt F, Broadbent J, Cano R, Chaillou S, Deutscher J, Gasson M, van de GM, Guzzo J, Hartke A, Hawkins T, Hols P, Hutkins R, Kleerebezem M, Kok J, Kuipers O, Lubbers M, Maguin E, McKay L, Mills D, Nauta A, Overbeek R, Pel H, Pridmore D, Saier M, van Sinderen D, Sorokin A, Steele J, O'Sullivan D, de Vos W, Weimer B, Zagorec M, Siezen R: Discovering lactic acid bacteria by genomics. Antonie Van Leeuwenhoek. 2002, 82: 29-58. 10.1023/A:1020638309912.
Article
PubMed
CAS
Google Scholar
Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Carter NM, Choi SK, Codani JJ, Connerton IF, Danchin A, .: The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature. 1997, 390: 249-256. 10.1038/36786.
Article
PubMed
CAS
Google Scholar
Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V, Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A, Chu L, Mazur M, Goltsman E, Larsen N, D'Souza M, Walunas T, Grechkin Y, Pusch G, Haselkorn R, Fonstein M, Ehrlich SD, Overbeek R, Kyrpides N: Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature. 2003, 423: 87-91. 10.1038/nature01582.
Article
PubMed
CAS
Google Scholar
Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, Durkin AS, Gwinn M, Kolonay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CL, McDonald LA, Feldblyum TV, Angiuoli S, Dickinson T, Hickey EK, Holt IE, Loftus BJ, Yang F, Smith HO, Venter JC, Dougherty BA, Morrison DA, Hollingshead SK, Fraser CM: Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science. 2001, 293: 498-506. 10.1126/science.1061217.
Article
PubMed
CAS
Google Scholar
Quackenbush J: Microarray data normalization and transformation. Nat Genet. 2002, 32 Suppl: 496-501. 10.1038/ng1032.
Article
PubMed
Google Scholar
Benes V, Muckenthaler M: Standardization of protocols in cDNA microarray analysis. Trends Biochem Sci. 2003, 28: 244-249. 10.1016/S0968-0004(03)00068-9.
Article
PubMed
CAS
Google Scholar
Fang Y, Brass A, Hoyle DC, Hayes A, Bashein A, Oliver SG, Waddington D, Rattray M: A model-based analysis of microarray experimental error and normalisation. Nucleic Acids Res. 2003, 31: e96-10.1093/nar/gng097.
Article
PubMed
PubMed Central
Google Scholar
Tilstone C: DNA microarrays: vital statistics. Nature. 2003, 424: 610-612. 10.1038/424610a.
Article
PubMed
CAS
Google Scholar
Kerr MK, Churchill GA: Statistical design and the analysis of gene expression microarray data. Genet Res. 2001, 77: 123-128. 10.1017/S0016672301005055.
PubMed
CAS
Google Scholar
Kerr MK, Churchill GA: Experimental design for gene expression microarrays. Biostatistics. 2001, 2: 183-201. 10.1093/biostatistics/2.2.183.
Article
PubMed
Google Scholar
Kerr MK, Martin M, Churchill GA: Analysis of variance for gene expression microarray data. J Comput Biol. 2000, 7: 819-837. 10.1089/10665270050514954.
Article
PubMed
CAS
Google Scholar
Spruill SE, Lu J, Hardy S, Weir B: Assessing sources of variability in microarray gene expression data. Biotechniques. 2002, 33: 916-3.
PubMed
CAS
Google Scholar
Chen JJ, Delongchamp RR, Tsai CA, Hsueh HM, Sistare F, Thompson KL, Desai VG, Fuscoe JC: Analysis of variance components in gene expression data. Bioinformatics. 2004, 20: 1436-1446. 10.1093/bioinformatics/bth118.
Article
PubMed
CAS
Google Scholar
Tu Y, Stolovitzky G, Klein U: Quantitative noise analysis for gene expression microarray experiments. Proc Natl Acad Sci U S A. 2002, 99: 14031-14036. 10.1073/pnas.222164199.
Article
PubMed
CAS
PubMed Central
Google Scholar
Piper MD, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J, Pronk JT: Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem. 2002, 277: 37001-37008. 10.1074/jbc.M204490200.
Article
PubMed
CAS
Google Scholar
Molecular Genetics publications: supplementary data for a generally applicable validation scheme. 2004, [http://molgen.biol.rug.nl/publication/validation_data]
Yuen T, Wurmbach E, Pfeffer RL, Ebersole BJ, Sealfon SC: Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res. 2002, 30: e48-10.1093/nar/30.10.e48.
Article
PubMed
PubMed Central
Google Scholar
Baum M, Bielau S, Rittner N, Schmid K, Eggelbusch K, Dahms M, Schlauersbach A, Tahedl H, Beier M, Guimil R, Scheffler M, Hermann C, Funk JM, Wixmerten A, Rebscher H, Honig M, Andreae C, Buchner D, Moschel E, Glathe A, Jager E, Thom M, Greil A, Bestvater F, Obermeier F, Burgmaier J, Thome K, Weichert S, Hein S, Binnewies T, Foitzik V, Muller M, Stahler CF, Stahler PF: Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling. Nucleic Acids Res. 2003, 31: e151-10.1093/nar/gng151.
Article
PubMed
PubMed Central
Google Scholar
Dombkowski AA, Thibodeau BJ, Starcevic SL, Novak RF: Gene-specific dye bias in microarray reference designs. FEBS Lett. 2004, 560: 120-124. 10.1016/S0014-5793(04)00083-3.
Article
PubMed
CAS
Google Scholar
Yue H, Eastman PS, Wang BB, Minor J, Doctolero MH, Nuttall RL, Stack R, Becker JW, Montgomery JR, Vainer M, Johnston R: An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. Nucleic Acids Res. 2001, 29: E41-E41. 10.1093/nar/29.8.e41.
Article
PubMed
CAS
PubMed Central
Google Scholar
Van Hijum SAFT, de Jong A, Buist G, Kok J, Kuipers OP: UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons. Bioinformatics. 2003, 19: 1580-1582. 10.1093/bioinformatics/btg203.
Article
PubMed
CAS
Google Scholar
Terzaghi BE, Sandine WE: Improved medium for lactic streptococci and their bacteriophages. Appl Microbiol. 1975, 29: 807-813.
PubMed
CAS
PubMed Central
Google Scholar
Van Hijum SAFT, García de la Nava J, Trelles O, Kok J, Kuipers OP: MicroPreP: a DNA microarray data preprocessing framework. Appl Bioinformatics. 2003, 241-244.
Google Scholar
García de la Nava J, Van Hijum SAFT, Trelles O: PreP: gene expression data pre-processing. Bioinformatics. 2003, 19: 2328-2329. 10.1093/bioinformatics/btg318.
Article
PubMed
Google Scholar
Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002, 30: e15-10.1093/nar/30.4.e15.
Article
PubMed
PubMed Central
Google Scholar
Swertz MA, De Brock EO, Van Hijum SA, de Jong A, Buist G, Baerends RJ, Kok J, Kuipers OP, Jansen RC: Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases. Bioinformatics. 2004, 20: 2075-2083. 10.1093/bioinformatics/bth206.
Article
PubMed
CAS
Google Scholar
Long AD, Mangalam HJ, Chan BY, Tolleri L, Hatfield GW, Baldi P: Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem. 2001, 276: 19937-19944. 10.1074/jbc.M010192200.
Article
PubMed
CAS
Google Scholar
García de la Nava J, Santaella DF, Alba JC, Carazo JM, Trelles O, Pascual-Montano A: Engene: the processing and exploratory analysis of gene expression data. Bioinformatics. 2003, 19: 657-658. 10.1093/bioinformatics/btg028.
Article
PubMed
Google Scholar
Kendall MG, Stuart A: The advanced theory of statistics. 1983, London, Charles Griffin & Company Ltd, III: Fourth
Google Scholar
Scheffé H: Analysis of variance. 1959, London, John Wiley and Sons
Google Scholar