Y. H. Yang*, Y. Y. Xiao* and M. Segal (2004). Identifying differentially expressed genes from microarray experiments via statistic synthesis.  Bioinformatics (accepted)

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.

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]

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].

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.

S. Dudoit and Y. H. Yang (2002). 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 (To appear).
[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]

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].

Statistical methods in the design and analysis of gene expression data from c{DNA} microarray experiment.