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Keck Home Page > DNA Microarray Resource > Publications

Publications

Microarray Experimental Design

 

  1. Dobbin K, Shih JH, Simon R. Questions and answers on design of dual-label microarrays for identifying differentially expressed genes. J Natl Cancer Inst. 2003 Sept 17;95(18):1362-9.

  2. Shih JH, Michalowska AM, Dobbin K, Ye Y, Qiu TH, Green JE. Effects of pooling mRNA in microarray class comparisons. Bioinformatics. 2004 July 9 [epub].

  3. Yoo C, Cooper GF. A Computer-based Microarray Experiment Design-system for Gene-regulation Pathway Discovery.
    Proc AMIA Symp. 2003;:733-7.

  4. Glonek GF, Solomon PJ. Factorial and time course designs for cDNA microarray experiments.
    Biostatistics. 2004 Jan;5(1):89-111.

  5. Lee I, Dombkowski AA, Athey BD. Guidelines for incorporating non-perfectly matched oligonucleotides into target-specific hybridization probes for a DNA microarray.
    Nucleic Acids Res. 2004 Feb 02;32(2):681-90. Print 2004.

  6. Mimmack ML, Brooking J, Bahn S. Quantitative polymerase chain reaction: validation of microarray results from postmortem brain studies.
    Biol Psychiatry. 2004 Feb 15;55(4):337-45.

  7. Kerr MK. Design considerations for efficient and effective microarray studies.
    Biometrics. 2003 Dec;59(4):822-8.

  8. McShane LM, Shih JH, Michalowska AM. Statistical issues in the design and analysis of gene expression microarray studies of animal models.
    J Mammary Gland Biol Neoplasia. 2003 Jul;8(3):359-74. Review.

  9. Brown JS, Kuhn D, Wisser R, Power E, Schnell R. Quantification of sources of variation and accuracy of sequence discrimination in a replicated microarray experiment. Biotechniques. 2004 Feb;36(2):324-32.

  10. Shioda T. Application of DNA microarray to toxicological research.
    J Environ Pathol Toxicol Oncol. 2004;23(1):13-31. Review.

  11. 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.

  12. Wilson CL, Pepper SD, Hey Y, Miller CJ. Amplification protocols introduce systematic but reproducible errors into gene expression studies.
    Biotechniques. 2004 Mar;36(3):498-506.

  13. Barrera L, Benner C, Tao YC, Winzeler E, Zhou Y. Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays.
    BMC Bioinformatics. 2004 Apr 20;5(1):42.

  14. Bhattacharya S, Long D, Lyons-Weiler J. Overcoming confounded controls in the analysis of gene expression data from microarray experiments.
    Appl Bioinformatics. 2003;2(4):197-208.

  15. Sartor M, Schwanekamp J, Halbleib D, Mohamed I, Karyala S, Medvedovic M, Tomlinson CR. Microarray results improve significantly as hybridization approaches equilibrium.
    Biotechniques. 2004 May;36(5):790-6.

  16. Mary-Huard T, Daudin JJ, Robin S, Bitton F, Cabannes E, Hilson P. Spotting effect in microarray experiments.
    BMC Bioinformatics. 2004 May 19;5(1):63.

  17. Yao B, Rakhade SN, Li Q, Ahmed S, Krauss R, Draghici S, Loeb JA. Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells.
    BMC Bioinformatics. 2004 Jul 23;5(1):99.

  18. Conway T, Schoolnik GK. Microarray expression profiling: capturing a genome-wide portrait of the transcriptome.
    Mol Microbiol. 2003 Feb;47(4):879-89.

  19. Townsend JP, Hartl DL. Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments.
    Genome Biol. 2002;3(12):RESEARCH0071.

  20. Simon R, Radmacher MD, Dobbin K, McShane LM. Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification.
    J Natl Cancer Inst. 2003 Jan 1;95(1):14-8.

  21. Sasik R, Calvo E, Corbeil J. Statistical analysis of high-density oligonucleotide arrays: a multiplicative noise model.
    Bioinformatics. 2002 Dec;18(12):1633-40.

  22. Churchill GA. Fundamentals of experimental design for cDNA microarrays.
    Nat Genet. 2002 Dec;32 Suppl:490-5.

  23. Murphy D. Gene expression studies using microarrays: principles, problems, and prospects.
    Adv Physiol Educ. 2002 Dec;26(4):256-70.

  24. Hwang D, Schmitt WA, Stephanopoulos G, Stephanopoulos G. Determination of minimum sample size and discriminatory expression patterns in microarray data.
     Bioinformatics. 2002 Sep;18(9):1184-93.

  25. Yang YH, Speed T. Design issues for cDNA microarray experiments.
    Nat Rev Genet. 2002 Aug;3(8):579-88.

  26. Simon R, Radmacher MD, Dobbin K. Design of studies using DNA microarrays.
    Genet Epidemiol. 2002 Jun;23(1):21-36.

  27. Bilban M, Buehler LK, Head S, Desoye G, Quaranta V. Normalizing DNA microarray data.
    Curr Issues Mol Biol. 2002 Apr;4(2):57-64.

  28. Finkelstei D, Ewing R, Gollub J, Sterky F, Cherry JM, Somerville S. Microarray data quality analysis: lessons from the AFGC project. Arabidopsis Functional Genomics Consortium.

  29. Foster WR, Huber RM. Current themes in microarray experimental design and analysis.
    Drug Discov Today. 2002 Mar 1;7(5):290-2.

  30. Kane MD. Aligning experimental design with bioinformatics analysis to meet discovery research objectives.
    Cytometry. 2002 Jan 1;47(1):50-1.

  31. Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, Bushel P, Afshari C, Paules RS. Assessing gene significance from cDNA microarray expression data via mixed models.
    J Comput Biol. 2001;8(6):625-37.

  32. Lobenhofer EK, Bushel PR, Afshari CA, Hamadeh HK. Progress in the application of DNA microarrays.
    Environ Health Perspect. 2001 Sep;109(9):881-91.

  33. Hess KR, Zhang W, Baggerly KA, Stivers DN, Coombes KR. Microarrays: handling the deluge of data and extracting reliable information.
    Trends Biotechnol. 2001 Nov;19(11):463-8.

  34. Draghici S, Kuklin A, Hoff B, Shams S. Experimental design, analysis of variance and slide quality assessment in gene expression arrays.
    Curr Opin Drug Discov Devel. 2001 May;4(3):332-7.

  35. Mills JC, Gordon JI. A new approach for filtering noise from high-density oligonucleotide microarray datasets.

  36. Tseng GC, Oh MK, Rohlin L, Liao JC, Wong WH. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects.
    Nucleic Acids Res. 2001 Jun 15;29(12):2549-57.

  37. Quackenbush J. Computational analysis of microarray data.
     Nat Rev Genet. 2001 Jun;2(6):418-27.

Microarray Protocol

  1. Spiess AN, Mueller N, Ivell R. Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations.
    BMC Genomics. 2003 Nov 10;4(1):44.

  2. Ojaniemi H, Evengard B, Lee DR, Unger ER, Vernon SD. Impact of RNA extraction from limited samples on microarray results.
    Biotechniques. 2003 Nov;35(5):968-73.

  3. Nasedkina TV, Zharinov VS, Isaeva EA, Mityaeva ON, Yurasov RN, Surzhikov SA, Turigin AY, Rubina AY, Karachunskii AI, Gartenhaus RB, Mirzabekov AD.Clinical screening of gene rearrangements in childhood leukemia by using a multiplex polymerase chain reaction-microarray approach.
    Clin Cancer Res. 2003 Nov 15;9(15):5620-9.

  4. Lim EH, Aggarwal A, Agasthian T, Wong PS, Tan C, Sim E, Tan L, Goh PS, Wang SC, Khoo KL, Mukherjee A, Khoo SM, Chua G, Nilsson B, Lee KH, Tan P. Feasibility of using low-volume tissue samples for gene expression profiling of advanced non-small cell lung cancers.
    Clin Cancer Res. 2003 Dec 1;9(16 Pt 1):5980-7.

  5. Schoor O, Weinschenk T, Hennenlotter J, Corvin S, Stenzl A, Rammensee HG, Stevanovic S. Moderate degradation does not preclude microarray analysis of small amounts of RNA.
    Biotechniques. 2003 Dec;35(6):1192-6, 1198-201.

  6. Murray EJ. Improved method for generating microarray probes using submicrogram amounts of total RNA.
    Mol Biotechnol. 2003 Feb;23(2):171-7.

  7. Wang J, Hu L, Hamilton SR, Coombes KR, Zhang W. RNA amplification strategies for cDNA microarray experiments.
    Biotechniques. 2003 Feb;34(2):394-400.

  8. Xiang CC, Chen M, Kozhich OA, Phan QN, Inman JM, Chen Y, Brownstein MJ. Probe generation directly from small numbers of cells for DNA microarray studies.
    Biotechniques. 2003 Feb;34(2):386-8, 390, 392-3.

  9. 't Hoen PA, de Kort F, van Ommen GJ, den Dunnen JT. Fluorescent labelling of cRNA for microarray applications.
    Nucleic Acids Res. 2003 Mar 1;31(5):e20.

  10. Zhao H, Hastie T, Whitfield ML, Borresen-Dale AL, Jeffrey SS. Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis.
    BMC Genomics. 2002 Oct 30;3(1):31.

  11. Iacobas AD, Urban M, Spray DC. New protocol in spotting microarray technique.
    Rom J Physiol. 2000 Jan-Dec;37(1-4):69-80.

  12. Weidenhammer EM, Kahl BF, Wang L, Wang L, Duhon M, Jackson JA, Slater M, Xu X. Multiplexed, targeted gene expression profiling and genetic analysis on electronic microarrays.
    Clin Chem. 2002 Nov;48(11):1873-82.

  13. Brody JP, Williams BA, Wold BJ, Quake SR. Significance and statistical errors in the analysis of DNA microarray data.
    Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12975-8.

  14. Liss B. Improved quantitative real-time RT-PCR for expression profiling of individual cells.
    Nucleic Acids Res. 2002 Sep 1;30(17):e89.

  15. Hu L, Wang J, Baggerly K, Wang H, Fuller GN, Hamilton SR, Coombes KR, Zhang W. Obtaining reliable information from minute amounts of RNA using cDNA microarrays.
    BMC Genomics. 2002 Jun 21;3(1):16.

  16. Yu J, Othman MI, Farjo R, Zareparsi S, MacNee SP, Yoshida S, Swaroop A. Evaluation and optimization of procedures for target labeling and hybridization of cDNA microarrays.
    Mol Vis. 2002 Apr 26;8:130-7.

  17. Warrington JA, Shah NA, Chen X, Janis M, Liu C, Kondapalli S, Reyes V, Savage MP, Zhang Z, Watts R, DeGuzman M, Berno A, Snyder J, Baid J. New developments in high-throughput resequencing and variation detection using high density microarrays.
    Hum Mutat. 2002 Apr;19(4):402-9.

  18. Wu L, Thompson DK, Li G, Hurt RA, Tiedje JM, Zhou J. Development and evaluation of functional gene arrays for detection of selected genes in the environment.
    Appl Environ Microbiol. 2001 Dec;67(12):5780-90.

  19. Zhang Y, Price BD, Tetradis S, Chakrabarti S, Maulik G, Makrigiorgos GM. Reproducible and inexpensive probe preparation for oligonucleotide arrays.
    Nucleic Acids Res. 2001 Jul 1;29(13):E66-6.

  20. Mahalingam R, Fedoroff N. Screening insertion libraries for mutations in many genes simultaneously using DNA microarrays.
    Proc Natl Acad Sci U S A. 2001 Jun 19;98(13):7420-5.

  21. Hertzberg M, Sievertzon M, Aspeborg H, Nilsson P, Sandberg G, Lundeberg J. cDNA microarray analysis of small plant tissue samples using a cDNA tag target amplification protocol.
    Plant J. 2001 Mar;25(5):585-91.

  22. Sengupta R, Tompa M. Quality control in manufacturing oligo arrays: a combinatorial design approach.
    Pac Symp Biocomput. 2001;:348-59.

  23. Manduchi E, Grant GR, McKenzie SE, Overton GC, Surrey S, Stoeckert CJ Jr. Generation of patterns from gene expression data by assigning confidence to differentially expressed genes.
    Bioinformatics. 2000 Aug;16(8):685-98.

  24. Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G. Making and reading microarrays.
    Nat Genet. 1999 Jan;21(1 Suppl):15-9.

 

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Last modified: 21-Feb-2007