The Golden Spike: Citations

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See Genome Biology's access statistics for the Choe et al. Golden Spike paper here

The Choe et al. Golden Spike paper has been cited in the following papers:

Calza, S., W. Raffelsberger, et al. (2007). "Filtering genes to improve sensitivity in oligonucleotide microarray data analysis." Nucl. Acids Res. 35(16): e102-.

Steffen, L. S., J. R. Guyon, et al. (2007). "The zebrafish runzel muscular dystrophy is linked to the titin gene." Developmental Biology 309(2): 180-192.

Hulshizer, R. and E. M. Blalock (2007). "Post hoc pattern matching: assigning significance to statistically defined expression patterns in single channel microarray data." BMC Bioinformatics 8: 240.

McElwee, J. J., E. Schuster, et al. (2007). "Evolutionary conservation of regulated longevity assurance mechanisms." Genome Biol 8(7): R132.

Ghanaat-Pour, H., Z. Huang, et al. (2007). "Global expression profiling of glucose-regulated genes in pancreatic islets of spontaneously diabetic Goto-Kakizaki rats
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J Mol Endocrinol 39(2): 135-150.

Pepper, S. D., E. K. Saunders, et al. (2007). "The utility of MAS5 expression summary and detection call algorithms." BMC Bioinformatics 8: 273.

Tan, X. J., Y. X. Zhang, et al. (2007). "The comparison of different normalization methods in microarray data." Progress in Biochemistry and Biophysics 34(6): 625-633.

Dang, T. A. and T. K. Man (2007). "Classification of sarcomas using bioinformatics and molecular profiling." Curr Pharm Biotechnol 8(2): 83-91.

Gharaibeh, R. Z., A. A. Fodor, et al. (2007). "Software Note: Using probe secondary structure information to enhance Affymetrix GeneChip background estimates." Computational Biology and Chemistry 31(2): 92-98.

Zahurak, M., G. Parmigiani, et al. (2007). "Pre-processing Agilent microarray data." BMC Bioinformatics 8: 142.

Bruun, G. M., R. Wernersson, et al. (2007). "Improving comparability between microarray probe signals by thermodynamic intensity correction." Nucl. Acids Res. 35(7): e48-.

Schuster, E. F., E. Blanc, et al. (2007). "Correcting for sequence biases in present/absent calls." Genome Biol 8(6): R125.

Schuster, E. F., E. Blanc, et al. (2007). "Estimation and correction of non-specific binding in a large-scale spike-in experiment." Genome Biol 8(6): R126.

Wayland, M. T. and S. Bahn (2006). "Reproducibility of microarray studies: concordance of current analysis methods." Progress in Brain Research. Functional Genomics and Proteomics in the Clinical Neurosciences. S. E. H. a. S. Bahn, Elsevier: 109-125.

Mehta, T. S., S. O. Zakharkin, et al. (2006). "Epistemological issues in omics and high-dimensional biology: give the people what they want." Physiol Genomics 28(1): 24-32.

Mattes, W. B. (2006). "Cross-species comparative toxicogenomics as an aid to safety assessment." Expert Opin Drug Metab Toxicol 2(6): 859-74.

Trede, N. S., J. Medenbach, et al. (2007). "Network of coregulated spliceosome components revealed by zebrafish mutant in recycling factor p110." PNAS 104(16): 6608-6613.

Fodor, A. A., T. L. Tickle, et al. (2007). "Towards the uniform distribution of null p-values on Affymetrix microarrays." Genome Biol 8(5): R69.

Gaile, D. P. and J. C. Miecznikowski (2007). "Putative null distributions corresponding to tests of differential expression in the Golden Spike dataset are intensity dependent." BMC Genomics 8(1): 105.

Chen, Z., M. McGee, et al. (2007). "A distribution free summarization method for Affymetrix GeneChip(R) arrays." Bioinformatics 23(3): 321-327.

Opgen-Rhein, R. and K. Strimmer (2007). "Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach." Statistical Applications in Genetics and Molecular Biology 6.

Chen, J. J., C. A. Tsai, et al. (2007). "Gene selection with multiple ordering criteria." BMC Bioinformatics 8: 74.

Monaghan, J. R., J. A. Walker, et al. (2007). "Early gene expression during natural spinal cord regeneration in the salamander Ambystoma mexicanum." Journal of Neurochemistry 101(1): 27-40.

Liston, A., K. Hardy, et al. (2007). "Impairment of organ-specific T cell negative selection by diabetes susceptibility genes: genomic analysis by mRNA profiling." Genome Biol 8(1): R12.

Royce, T. E., J. S. Rozowsky, et al. (2006). [15] Extrapolating Traditional DNA Microarray Statistics to Tiling and Protein Microarray Technologies. Methods in Enzymology. DNA Microarrays, Part B: Databases and Statistics. Academic Press: 282-311.

Williams, B. A., R. M. Gwirtz, et al. (2006). [12] Genomic DNA as a General Cohybridization Standard for Ratiometric Microarrays. Methods in Enzymology. DNA Microarrays, Part A: Array Platforms and Wet-Bench Protocols. Academic Press: 237-279.

Yang, I. V. (2006). [4] Use of External Controls in Microarray Experiments. Methods in Enzymology. DNA Microarrays, Part B: Databases and Statistics. Academic Press: 50-63.

Perelman, E., A. Ploner, et al. (2007). "Detecting differential expression in microarray data: comparison of optimal procedures." BMC Bioinformatics 8: 28.

Chu, T. T., M. Y. Fink, et al. (2007). "Effective use of microarrays in neuroendocrine research." J Neuroendocrinol 19(3): 145-61.

Tolonen, A. C., J. Aach, et al. (2006). "Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability." Molecular Systems Biology 2.

Vardhanabhuti, S., S. J. Blakemore, et al. (2006). "A comparison of statistical tests for detecting differential expression using affymetrix oligonucleotide microarrays." Omics 10(4): 555-66.

Benton, M. G., S. Somasundaram, et al. (2006). "Analyzing the dose-dependence of the Saccharomyces cerevisiae global transcriptional response to methyl methanesulfonate and ionizing radiation." BMC Genomics 7: 305.

Wang, D., N. Amornsiripanitch, et al. (2006). "A Genomic Approach to Identify Regulatory Nodes in the Transcriptional Network of Systemic Acquired Resistance in Plants." PLoS Pathogens 2(11): e123.

Selman, C., N. D. Kerrison, et al. (2006). "Coordinated multitissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice." Physiol. Genomics 27(3): 187-200.

Katz, S., R. A. Irizarry, et al. (2006). "A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database." BMC Bioinformatics 7: 464.

McGee, M. and Z. X. Chen (2006). "Parameter estimation for the exponential-normal convolution model for background correction of affymetrix GeneChip data." Statistical Applications in Genetics and Molecular Biology 5.

Abdueva, D., D. Skvortsov, et al. (2006). "Non-linear analysis of GeneChip arrays." Nucl. Acids Res. 34(15): e105-.

Irizarry, R. A., L. M. Cope, et al. (2006). "Feature-level exploration of a published Affymetrix GeneChip control dataset." Genome Biol 7(8): 404.

Hein, A. M. and S. Richardson (2006). "A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates." BMC Bioinformatics 7(1): 353.

Hoffmann, M., D. Pohlers, et al. (2006). "Robust Computational Reconstitution - a new method for the comparative analysis of gene expression in tissues and isolated cell fractions." BMC Bioinformatics 7(1): 369.

Lemieux, S. (2006). "Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression." BMC Bioinformatics 7(1): 391.

Steinhoff, C. and M. Vingron (2006). "Normalization and quantification of differential expression in gene expression microarrays." Brief Bioinform 7(2): 166-177.

Yakoby, N., C. A. Bristow, et al. (2005). "Systems-level questions in drosophila oogenesis." Systems Biology, IEE Proceedings 152(4): 276-284.

Hu, P., J. Beyene, et al. (2006). "Tests for differential gene expression using weights in oligonucleotide microarray experiments." BMC Genomics 7: 33.

Novak, J. P., M. C. Miller, 3rd, et al. (2006). "Variation in fiberoptic bead-based oligonucleotide microarrays: dispersion characteristics among hybridization and biological replicate samples." Biol Direct 1: 18.

Liu, X., M. Milo, et al. (2006). "Probe-level measurement error improves accuracy in detecting differential gene expression." Bioinformatics 22(17): 2107-13.

Rattray, M., X. Liu, et al. (2006). "Propagating uncertainty in microarray data analysis." Brief Bioinform 7(1): 37-47.

Fu, C., L. Xi, et al. (2006). "Early hypothalamic response to age-dependent gene expression by calorie restriction." Neurobiology of Aging 27(9): 1315-1325.

Hsiao, A. and M. D. Kuo (2006). "High-throughput biology in the postgenomic era." J Vasc Interv Radiol 17(7): 1077-85.

Jeffery, I. B., D. G. Higgins, et al. (2006). "Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data." BMC Bioinformatics 7: 359.

Romero, R. and G. Tromp (2006). "High-dimensional biology in obstetrics and gynecology: Functional genomics in microarray studies." American Journal of Obstetrics and Gynecology 195(2): 360-363.

Sundaresh, S., D. L. Doolan, et al. (2006). "Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques." Bioinformatics 22(14): 1760-1766.

Tong, W., A. B. Lucas, et al. (2006). "Evaluation of external RNA controls for the assessment of microarray performance." 24(9): 1132-1139.

Zhang, L., S. J. Yoder, et al. (2006). "Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression." BMC Genomics 7: 153.

Barenco, M., J. Stark, et al. (2006). "Correction of scaling mismatches in oligonucleotide microarray data." BMC Bioinformatics 7: 251.

Hochreiter, S., Clevert, D.-A., and Obermayer, K. (2006). "A new summarization method for affymetrix probe level data". Bioinformatics 22, 943-949.

Wilson, C. L., A. H. Sims, et al. (2006). "Effects of oestrogen on gene expression in epithelium and stroma of normal human breast tissue" Endocr Relat Cancer 13(2): 617-628.

McElwee, J. J., E. Schuster, et al. (2006). "Diapause-associated metabolic traits reiterated in long-lived daf-2 mutants in the nematode Caenorhabditis elegans." Mechanisms of Ageing and Development 127(5): 458-472.

Lee, J.-Y., J. Colinas, et al. (2006). "Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots." PNAS 103(15): 6055-6060.

Millenaar, F. F., J. Okyere, et al. (2006). "How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results." BMC Bioinformatics 7: 137.

Cortez, K. J., C. A. Lyman, et al. (2006). "Functional genomics of innate host defense molecules in normal human monocytes in response to Aspergillus fumigatus." Infect Immun 74(4): 2353-65.

Metzner, C., B. Salmons, et al. (2006). "MMTV accessory factor Naf affects cellular gene expression." Virology 346(1): 139-50.

Timmons, J. A. and C. J. Sundberg (2006). "Oligonucleotide microarray expression profiling: Human skeletal muscle phenotype and aerobic exercise training." IUBMB Life 58(1): 15-24.

Havilio, M. (2006). "Signal deconvolution based expression-detection and background adjustment for microarray data." J Comput Biol, 13(1):63-80.

Qin, L. X., R. P. Beyer, et al. (2006). "Evaluation of methods for oligonucleotide array data via quantitative real-time PCR." BMC Bioinformatics 7: 23.

Estrada, B., S. E. Choe, et al. (2006). "An Integrated Strategy for Analyzing the Unique Developmental Programs of Different Myoblast Subtypes." PLoS Genetics 2(2): e16.

Puri, V., S. Puri, et al. (2006). "Effects of oestrogen on trigeminal ganglia in culture: implications for hormonal effects on migraine." Cephalalgia 26(1): 33-42.

Hu, Z. and G. R. Willsky (2006). "Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies." BMC Bioinformatics 7: 12.

Draghici, S., P. Khatri, et al. (2006). "Reliability and reproducibility issues in DNA microarray measurements." Trends in Genetics 22(2): 101-109.

Allison, D. B., X. Cui, et al. (2006). "Microarray data analysis: from disarray to consolidation and consensus." Nature Reviews Genetics 7(1): 55-65.

Weber, G. J., S. E. Choe, et al. (2005). "Mutant-specific gene programs in the zebrafish." Blood 106(2): 521-30.

Ploner, A., L. D. Miller, et al. (2005). "Correlation test to assess low-level processing of high-density oligonucleotide microarray data." BMC Bioinformatics 6(1): 80.

Lu, J., J. K. Tomfohr, et al. (2005). "Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach." BMC Bioinformatics 6: 165.

ERCC. (2005). "Proposed methods for testing and selecting the ERCC external RNA controls." BMC Genomics 6: 150.

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