Johns Hopkins School of Public Health

Rafael A. Irizarry

Selected Publications and Manuscript

Wang et al. (2006) Estimating genome-wide copy number using allele specific mixture models [web page].

Carvalho B, Bengtsson H Speed TP and Irizarry RA (2006) Exploration, normalization, and genotype calls of high density oligonucleotide SNP array data [web page].

Irizarry RA, Cope L, Wu Zhijin (2006) Feature-level exploration of the Choe et al. Affymetrix GeneChip contol dataset. [web page]. 100 MAs from GEO [PDF] 60MB

Cope L, Hartman SM, Golmann HWH, Tiesman JP, and Irizarry RA. (2005) Analysis of Affymetrix GeneChip Data Using Amplified RNA. [web page]

Irizarry, RA, Wu, Z and Jaffee, H (2005) Comparison of Affymetrix GeneChip Expression Measures. [web page]

Wu, Z and Irizarry, RA (2005) A Statistical Framework for the Analysis of Microarray Probe-Level Data [web page]

Irizarry, RA et al. (2004) Multiple Lab Comparison of Microarray Platforms. [web page]

Irizarry, RA (2004) Parameters with Musical Interpretations. Chance 17: 30-38. [Sound examples].

Kendziorski, C Irizarry, RA, Chen, K, Haag, JD, Gould, MN To Pool or Not to Pool: A Question of Microarray Experimental Design . [web-page]. Submitted.

Wu, Z and Irizarry, RA, Stochastic Models Inspired by Hybridization Theory for Short Oligonucleotide Arrays . Proceedings of RECOMB 2004 [Full-text-PDF]. J Comput Biol. 2005 Jul-Aug;12(6):882-93.

Gautier, L, Cope, LM, Bolstad, BM, and Irizarry, RA (2002) affy - A package for the analysis of Afftmetrix GeneChip data at the probe level.. Bioinformatics. [Web-Page]

Wu, Zhijin, Irizarry, RA, Gentleman, R, Martinez Murillo, F, Spencer, F (2003) A Model Based Background Adjustement for Oligonucleotide Expression Arrays. J Amer Stat Assoc 99:909-917. [Full-text-PDF]

Cope, LM, Irizarry, RA, Jaffee, H, Wu, Z, Speed, TP (2004) A Benchmark for Affymetrix GeneChip Expression Measures. Bioinformatics 20: 323-331. [Web-page Supplemental-material-PDF]

Irizarry, RA, Bolstad BM, Collin, F, Cope, LM, Hobbs, B, and, Speed, TP (2003) Summaries of Affymetrix GeneChip Probe Level Data. Nucleic Acids Research. Vol. 31, No. 4 e15 [Abstract, HTML, Software] Before downloading the paper please read this.

Irizarry, RA, Ooi, SL, Wu, Z, and Boeke, Jef (2003) Use of Mixture Models in a Microarray-Based Screening Procedure for Detecting Differentially Represented Yeast Mutants. Statistical Applications in Genetics and Molecular Biology. Vol. 2, Issue 1. [Web Page]

Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, Antonellis, KJ, Scherf, U, Speed, TP (2003) Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Biostatistics. Vol. 4, Number 2: 249-264. [Abstract, PDF, PS, Complementary Color Figures-PDF, Software,]

Bolstad, B.M., Irizarry RA, Astrand, M, and Speed, TP (2003), A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance Bioinformatics. 19(2):185-193.

Irizarry, RA (2002). Choosing the smoothness parameter for smoothing splines by minimizing an estimate of risk. [Abstract, Full text-PDF, Full text-Postscript].

Scharfstein DO and Irizarry RA (2002), Generalized Additive Selection Models for the Analysis of Non-ignorable Missing Data. To appear in Biometrics[Postscript][PDF] [Software]

Irizarry, RA (2002). Weighted estimation of harmonic components in a musical sound signal. Journal of Time Series Analysis. 23: 29-48. [Abstract, Full text-PDF].

Irizarry, RA, Parmigiani, P, Guo, M, Dracheva, T, and Jen, J.(2001). A Statistical Analysis of Radiolabeled Gene Expression Data Proceedings of Interface 2001. [Abstract, Full text-PDF].

Irizarry, RA, Tankersley, CG, Frank, R, and Flanders, SE Assessing Homeostasis through Circadian Patterns. Biometrics. 57: 1228-1237 [Abstract, Full text-PDF, Full text-postscript].

Irizarry, RA (2001). Local Harmonic Estimation in Musical Sound Signals. Journal of the American Statistical Association. [Abstract, Full text-PDF, Full text-postscript].

Irizarry, RA (2001). Local Regression with Meaningful Parameters. American Statistician. 55: 72-79 [Abstract, Full text-PDF].

Irizarry, RA (2001). Information and Posterior Probability Criteria for Model Selection in Local Likelihood Estimation . Journal of the American Statistical Association. 96: 303-315.[Abstract, Full text-PDF, Full text-postscript].

Irizarry, RA (2000). Asymptotic distribution of estimates for a time-varying parameter in a harmonic model with multiple fundamentals. Statistica Sinica 10: 1041-1067. [Abstract, Full text-PDF].

Brillinger, DR, Morettin, PA, Irizarry, RA, and Chiann C (2000). Some Wavelet-Based Analyses of Markov Chain Data. Signal Processing. 80: 1607-1627. [Abstract, Full text-PDF,Full text-postscript]

Brillinger, DR and Irizarry, RA (1998). An investigation of the second- and higher- order spectra of music. Signal Processing. 65: 161-178. [Full text-postscript]

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