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Publications

Refereed publications

2007

Woodruff PG, Boushey HA, Dolganov GM, Barker CS, Yang YH, Donnelly S, Ellwanger A, Sidhu SS, Dao-Pick TP, Pantoja C, Erle DJ, Yamamoto KR, Fahy JV. (2007) Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids. Proc Natl Acad Sci U S A, 104(40), 15858-63.
Williams, E., Xiao, Y.Y, Sickles, H., Shafer, P., Yona, G., Yang, Y.H. and Lin, D.M. (2007) Novel subdomains of the mouse olfactory bulb defined by molecular heterogeneity in the nascent external plexiform and glomerular layers. BMC Developmental Biology 7:48, 2007.
Xiao, Y.Y., Segal, M., Yang, Y.H. and Yeh, R. F. A multi-array multi-SNP genotyping algorithm for Aymetrix SNP microarray. Bioinformatics Jun15; 23(12): 1459-67, 2007.
Winn, V.D., Haimov-Kochman, R., Paquet, A.C., Yang, Y.J., Madhusudhan, M.S., Gormley, M., Feng, K.T., Bernlohr, D.A., McDonagh, S., Pereira, L., Sali, A. and Fisher, S.J. Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term. Endocrinology 148(3), 1059-79, 2007.

2005

Kuperman DA, Lewis CC, Woodruff PG, Rodriguez MW, Yang Y.H., Dolganov GM, Fahy JV, Erle DJ. (2005) Dissecting asthma using focused transgenic modeling and functional genomics. J Allergy Clin Immunol. 2005 Vol 116(2), pp. 305--311.
Barker, C. S., Griffin, C., Dolganov, G. M., Hanspers, K., Yang, J. Y. & Erle, D. J. (2005) Increase DNA hybridization specificity using sscDNA targets. BMC Genomics 6, p.57.
Xiao, Y*., Yang, Y.H*., Burckin, T.A., Shiue, L., Hartzog, G.A. and Segal, M.R. (2005) Analysis of a Splice Array Experiment Elucidates Roles of Chromatin Elongation Factor Spt4-5 in Splicing, PLoS Comput Biol, 1, e39.
Xiao, Y., Segal, M.R. and Yang, Y.H. (2005) Stepwise normalization of two-channel spotted microarrays, Statistical Applications in Genetics and Molecular Biology, 4, Article 4.
Gonzalez, R., Yang, Y. H., Grin, C., Allen, L., Tigue, Z. and Dobbs, L. (2005). Freshly-isolated Rat Alveolar Type I Cells, Type II Cells, and Cultured Type II Cells Have Distinct Molecular Phenotypes. Am J Physiol Lung Cell Mol Physiol. Vol. 288(1), L179–89.
Y. H. Yang*, Y. Y. Xiao* and M. Segal (2005). Identifying differentially expressed genes from microarray experiments via statistic synthesis. Bioinformatics, Vol 21, pp. 1984--1093.

2004

D. Lin*, Y. H. Yang*, J. Scolnick, L. Brunet, H. Marsh, V. Peng, Y. Okazaki, Y. Hayashizaki, T. P. Speed and J. Ngai (2004). Spatial patterns of gene expression in the olfactory bulb. PNAS. Vol. 101(34), pp.12718--12723.
M.W. Rodriguez, A. C. Paquet, Y.H. Yang and D. J. Erle (2004) Differential gene expression by integrin beta7+and beta7-memory T helper cells BMC Immunology, pp. 5--13.
Gentleman R. C., Carey V. J., Bates D. M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier, L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li, C., Maechler M., Rossini A. J., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J. Y., and Zhang J. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biology, Vol. 5: R80.

2003

D.J Erle and Y.H. Yang (2003) , Asthma investigators begin to reap the fruits of genomics. Genome Biology 4(11): 232.
Y.H. Yang and N. Thorne (2003) Normalization for Two-color cDNA Microarray Data. Science and Statistics: A Festschrift for Terry Speed, D. Goldstein (eds.), IMS Lecture Notes, Monograph Series, Vol 40, pp. 403--418. [pdf]
E. Diaz, Y. H. Yang, K. C. Loh, M. Tessier-Lavigne, T. P. Speed, and J. Ngai (2003). Molecular analysis of positional identity in the developing mouse retina. PNAS. Vol. 100 (9), pp. 5491--5496. [pdf]
G. K Smyth, Y. H. Yang, T. P. Speed (2003). Statistical issues in microarray data analysis. In: Functional Genomics: Methods and Protocols, M. J. Brownstein and A. B. Khodursky (eds.), Methods in Molecular Biology Volume 224, Humana Press, Totowa, NJ, pages 111-136. [pdf]

2002

Y.H.Yang and T. P. Speed (2002) Design issues for cDNA microarray experiments. Nature Review Genetics Vol. 3, pp. 579--558. [Journal's Web] [pdf]
T. P. Speed and Y. H Yang (2002). Direct versus indirect designs for cDNA microarray experiments. Sankhya : The Indian Journal of Statistics, Vol. 64, Series A, Pt. 3, pp 706-720. [Journal's Web] [pdf]
E. Díaz, Y. Ge, Y.H. Yang, K.C. Loh, T.A. Serafini, Y. Okazaki, Y. Hayashizaki, T.P. Speed, J. Ngai, and P. Scheiffele (2002).
Molecular Analysis of Gene Expression in the Developing Pontocerebellar Projection System. Neuron. Vol. 36 (3), pp. 417--434
Y. H. Yang, M. J. Buckley, S. Dudoit, and T. P. Speed (2002). Comparison of methods for image analysis on cDNA microarray data. Journal of Computational and Graphical Statistics, Vol. 11, No. 1, pp. 108--136. [UCB Tech report #584].
Y. H. Yang, S. Dudoit, P. Luu, D. M. Lin, V. Peng, J. Ngai, and T. P. Speed (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research, Vol. 30, No. 4, e15. [Journal website] [pdf].
Y. H. Yang, S. Dudoit, T. P. Speed, and M. J. Callow (2002). Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica, Vol. 12, No. 1, pp. 111--139. [UCB Tech report #578] [article].

Before 2001

Y. H. Yang, M. J. Buckley and T. P. Speed (2001). Analysis of cDNA microarray images. Briefings in Bioinformatics, Vol. 2, pp. 341-349. [pdf]
Buckley, M. and Yang, J. (1997) Regularised shortest-path extraction . Pattern Recognition Letters, Vol 18, pp. 621-629.

Chapters in Books

Yang, Y. H. and Paquet, A. C. (2005). Preprocessing Two-Color Spotted Arrays In: R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.), Bioinformatics and Computational Biology Solutions using R and Bioconductor, Springer, New York, pp.49 -- 70.
S. Dudoit and Y. H. Yang (2003). Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger (eds), The Analysis of Gene Expression Data: Methods and Software, Springer, New York, p. 73--101. [Table of contents] [Rnw file] [PDF].
Y.H. Yang and T. P. Speed (2003). Design and Analysis of Comparative Microarray Experiments In T. P Speed (ed) Statistical Analysis of Gene Expression Microarray Data, Chapman & Hall. [Amazon]
C.A. Ball, Y. Chen, S. Panavally, G. Sherlock, T. Speed, P.T. Spellman, Y.H. Yang (2003). Section7: An introduction to microarray bioinformatics. In D. Bowtell and J. Sambrook (eds), DNA Microarrays: A Molecular Cloning Manual. Cold Spring Harbor Press. [CSHL]

Other manuscripts

S. Dudoit, Y. H. Yang, and B. Bolstad (2002). Using R for the Analysis of DNA Microarray Data. R News, Vol. 2, No. 1, p. 24--32. [Rnews website].
Y. H. Yang, S. Dudoit, P. Luu, and T. P. Speed (2001). Normalization for cDNA microarray data. In M. L. Bittner, Y. Chen, A. N. Dorsel, and E. R. Dougherty (eds), Microarrays: Optical Technologies and Informatics, Vol. 4266 of Proceedings of SPIE. [UCB Tech report #589].

Ph.D. Thesis

Statistical methods in the design and analysis of gene expression data from cDNA microarray experiment. [ps] [Correction]