Microarray Databases
Lin FM, Huang HD, Chang YC, Horng JT. i-Genome: A database to summarize oligonucleotide data in genomes. BMC Genomics. 2004 Oct 9;5(1):78 [abstract]

Etim A, Zhou G, Wen X, Liu H, Ruotti V, Twigger S, Jin W, Matysiak B, Mathis J, Tonellato PJ, Datta MW. ChromSorter PC: a database of chromosomal regions associated with human prostate cancer. BMC Genomics. 2004 Apr 28;5(1):27 [abstract]

Osier MV, Zhao H, Cheung KH. Handling multiple testing while interpreting microarrays with the Gene Ontology Database. BMC Bioinformatics. 2004 Sep 06;5(1):124. [abstract]

Microarray Data Analysis
Shippy R, Sendera TJ, Lockner R, Palaniappan C, Kaysser-Kranich T, Watts G, Alsobrook J. Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations. BMC Genomics. 2004 Sep 02;5(1):61. [abstract]

Ramdas L, Cogdell DE, Jia JY, Taylor EE, Dunmire VR, Hu L, Hamilton SR, Zhang W. Improving signal intensities for genes with low-expression on oligonucleotide microarrays. BMC Genomics. 2004 Jun 14;5(1):35. [abstract]

Microarray Fabrication
Hessner MJ, Meyer L, Tackes J, Muheisen S, Wang X. Immobilized probe and glass surface chemistry as variables in microarray fabrication. BMC Genomics. 2004 Aug 04;5(1):53. [abstract]

RNA Amplification and Microarray Experimental Design
Schneider J, Buness A, Huber W, Volz J, Kioschis P, Hafner M, Poustka A, Sultmann H. Systematic analysis of T7 RNA polymerase based in vitro linear RNA amplification for use in microarray experiments. BMC Genomics. 2004 Apr 30;5(1):29. [abstract]

Forster T, Costa Y, Roy D, Cooke HJ, Maratou K. Triple-target microarray experiments: a novel experimental strategy. BMC Genomics. 2004 Feb 10;5(1):13. [abstract]

Li Y, Li T, Liu S, Qiu M, Han Z, Jiang Z, Li R, Ying K, Xie Y, Mao Y. Systematic comparison of the fidelity of aRNA, mRNA and T-RNA on gene expression profiling using cDNA microarray. J Biotechnol. 2004 Jan 8;107(1):19-28. [abstract]

Universal Standards
Novoradovskaya N, Whitfield ML, Basehore LS, Novoradovsky A, Pesich R, Usary J, Karaca M, Wong WK, Aprelikova O, Fero M, Perou CM, Botstein D, Braman J. Universal Reference RNA as a standard for microarray experiments. BMC Genomics. 2004 Mar 09;5(1):20. [abstract]

Hessner MJ, Singh VK, Wang X, Khan S, Tschannen MR, Zahrt TC. Utilization of a labeled tracking oligonucleotide for visualization and quality control of spotted 70-mer arrays. BMC Genomics. 2004 Feb 09;5(1):12. [abstract]

Microarray Validation
Brazeau DA. Combining genome-wide and targeted gene expression profiling in drug discovery: microarrays and real-time PCR. Drug Discov Today. 2004 Oct 1;9(19):838-45. [abstract]

Sample Recovery for Microarrays
Wong R, Tran V, Morhenn V, Hung SP, Andersen B, Ito E, Wesley Hatfield G, Benson NR. Use of RT-PCR and DNA microarrays to characterize RNA recovered by non-invasive tape harvesting of normal and inflamed skin. J Invest Dermatol. 2004 Jul;123(1):159-67. [abstract]

Bioinformatics
Flikka K, Yadetie F, Laegreid A, Jonassen I. XHM: a system for detection of potential cross hybridizations in DNA microarrays. BMC Bioinformatics. 2004 Aug 27;5(1):117. [abstract]

Imoto S, Higuchi T, Goto T, Tashiro K, Kuhara S, Miyano S. Combining microarrays and biological knowledge for estimating gene networks via bayesian networks. J Bioinform Comput Biol. 2004 Mar;2(1):77-98. [abstract]

Khatri P, Bhavsar P, Bawa G, Draghici S. Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W449-56. [abstract]

Seo J, Bakay M, Chen YW, Hilmer S, Shneiderman B, Hoffman EP. Optimizing signal/noise ratios in expression profiling: project-specific algorithm selection and detection p value weighting in affymetrix microarrays. Bioinformatics. 2004 Apr 29 [abstract]

Ameur A, Aurell E, Carlsson M, Westholm JO. Global gene expression analysis by combinatorial optimization. In Silico Biol. 2004 Mar 21;4(2):0020 [abstract]

Barash Y, Dehan E, Krupsky M, Franklin W, Geraci M, Friedman N, Kaminski N. Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays. Bioinformatics. 2004 Apr 12;20(6):839-46. Epub 2004 Jan 29. [abstract]

Diagnostics, BioMarkers and Cancer Research
Lin B, Vora GJ, Thach D, Walter E, Metzgar D, Tibbetts C, Stenger DA. Use of oligonucleotide microarrays for rapid detection and serotyping of acute respiratory disease-associated adenoviruses. J Clin Microbiol. 2004 Jul;42(7):3232-9. [abstract]

McElwaine S, Mulligan C, Groet J, Spinelli M, Rinaldi A, Denyer G, Mensah A, Cavani S, Baldo C, Dagna-Bricarelli F, Hann I, Basso G, Cotter FE, Nizetic D. Microarray transcript profiling distinguishes the transient from the acute type of megakaryoblastic leukaemia (M7) in Down's syndrome, revealing PRAME as a specific discriminating marker. Br J Haematol. 2004 Jun;125(6):729-42. [abstract]

Grant GM, Fortney A, Gorreta F, Estep M, Del Giacco L, Van Meter A, Christensen A, Appalla L, Naouar C, Jamison C, Al-Timimi A, Donovan J, Cooper J, Garrett C, Chandhoke V. Microarrays in cancer research. Anticancer Res. 2004 Mar-Apr;24(2A):441-8. [abstract]

Bailey WJ, Ulrich R. Molecular profiling approaches for identifying novel biomarkers. Expert Opin Drug Saf. 2004 Mar;3(2):137-51. [abstract]

Bacterial Microarrays
Vora GJ, Meador CE, Stenger DA, Andreadis JD. Nucleic acid amplification strategies for DNA microarray-based pathogen detection. Appl Environ Microbiol. 2004 May;70(5):3047-54. [abstract]

Sato N, Ohmori M, Ikeuchi M, Tashiro K, Wolk CP, Kaneko T, Okada K, Tsuzuki M, Ehira S, Katoh H, Okamoto S, Yoshimura H, Fujisawa T, Kamei A, Yoshihara S, Narikawa R, Hamano T, Tabata S, Kuhara S. Use of segment-based microarray in the analysis of global gene expression in response to various environmental stresses in the cyanobacterium Anabaena sp. PCC 7120. J Gen Appl Microbiol. 2004 Feb;50(1):1-8. [abstract]

Dharmadi Y, Gonzalez R. DNA microarrays: experimental issues, data analysis, and application to bacterial systems. Biotechnol Prog. 2004 Sep-Oct;20(5):1309-24. [abstract]

Effect of RNAlater® on Expression Patterns
Mutter GL, Zahrieh D, Liu C, Neuberg D, Finkelstein D, Baker HE, Warrington JA. (2004) Comparison of frozen and RNALater solid tissue storage methods for use in RNA expression microarrays. BMC Genomics 5:88. [article]