Sandrine Dudoit, Ph.D.Associate Professor of Biostatistics
PHONE: (510) 643-1108
FAX: (510) 643-5163
LOCATION: 109 Haviland
E-MAIL: sandrine@stat.berkeley.edu
WEB SITE: http://www.stat.berkeley.edu/~sandrine
Research Interests
- Design and analysis of gene expression experiments using DNA microarrays (e.g. microarray experiments monitering transcript levels, ChlP-Chip experiments for identifying transcription factor binding sites, alternative microarray experiments)
- Nucleotide and protein sequence analysis (e.g. identification of regulatory motifs in DNA sequences)
- Genetic mapping of complex human traits (e.g. linkage analysis, linkage disequilibrium analysis, SNP-based association studies)
- Analysis of biological metadata (e.g. Gene Ontology annotation)
- Loss-based estimation with cross-validation (classification, density estimation, model selection, prediction)
- Multiple hypothesis testing
Selected Publications
Bioinformatics and Computational Biology Solutions Using R and Bioconductor (2005). Edited by R. Gentleman, V. Carey, W. Huber, R. Irizarry, and S. Dudoit. Springer Series: Statistics for Biology and Health. Contents, R code, and data: [Bioconductor]
A. Barrier, A. Lemoine, P.-Y. Boelle, C. Tse, D. Brault, F. Chiappini, J. Breittschneider, F. Lacaine, S. Houry, M. Huguier, M. J. van der Laan, T. P. Speed, B. Debuire, A. Flahault, and S. Dudoit (2005). Colon cancer prognosis prediction by gene expression profiling. Oncogene, Vol. 24, No. 40, p. 6155-6164. [Journal website] [Tech report #178] [Daily Cal]
S. Dudoit and M. J. van der Laan (2005). Asymptotics of cross-validated risk estimation in estimator selection and performance assessment. Statistical Methodology, Vol. 2, No. 2, p. 131-154. [Journal website] [Tech report #126]
R. C. Gentleman,V. J. Carey, D. J. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R. Irizarry, F. Leisch, C. Li, M. Maechler, A. J. Rossini, G. Sawitzki, C. Smith, G. K. Smyth, L. Tierney, Y. H. Yang, and J. Zhang (2004). Bioconductor: Open software development for computational biology and bioinformatics. Genome Biology, Vol. 5, No. 10, Article R80. [Journal website] [Tech report # 1]
S. Dudoit, M. J. van der Laan, and K. S. Pollard (2004). Multiple testing. Part I. Single-step procedures for control of general Type I error rates. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 13. [Journal website] [Tech report #138]
S. Dudoit, M. J. van der Laan, S. Keles, A. M. Molinaro, S. E. Sinisi, and S. L. Teng (2003). Loss-based estimation with cross-validation: Applications to microarray data analysis. In G. Piatetsky-Shapiro and P. Tamayo (eds), Microarray Data Mining, Special Issue of SIGKDD Explorations, Vol. 5, No. 2, p. 56-68 [Tech report #137]
S. Dudoit, J. Fridlyand, and T. P. Speed (2002). Comparison of discrimination methods for the classification of tumors using gene expression data. Journal of the American Statistical Association, Vol. 97, No. 457, p. 77-87. [Tech report #576]
S. Dudoit and T. P. Speed (1999). A score test for linkage using identity by descent data from sibships. Annals of Statistics, Vol. 27, No. 3, p. 943-986. [Tech report #528]
Other Interests
Professor Dudoit is also involved in the development of statistical software for biological data analysis and is a core member of the Bioconductor Project.
Profile updated: February 12, 2007