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Publications: [News] [Books] [Technical Reports and Submitted Manuscripts] [Refereed Journal Publications] [Book Chapters and Conference Proceedings] [PhD Dissertation]
Berkeley Electronic Press Selected Works Website
NEWS
UC Berkeley Division of Biostatistics Working Paper Series [www.bepress.com/ucbbiostat]
Multiple Testing
Procedures with Applications to Genomics
(2008). S. Dudoit and M. J. van der Laan.
Springer Series in Statistics.
Order: [Springer] [Amazon]
Books
Multiple Testing
Procedures with Applications to Genomics
(2008). S. Dudoit and M. J. van der Laan.
Springer Series in Statistics.
Order: [Springer] [Amazon]
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 in Statistics for Biology and Health.
Order: [Springer] [Amazon]
Contents, R code, and data: [Bioconductor]
Technical Reports and Submitted Manuscripts
S. Dudoit, H. N. Gilbert, and M. J. van der Laan (2007). Resampling-based empirical Bayes multiple testing procedures for controlling generalized tail probability and expected value error rates: Focus on the false discovery rate and simulation study. [Tech report #228] [Website Companion]
D. Shilane, R. H. Liang, and S. Dudoit (2007). Loss-based estimation with evolutionary algorithms and cross-validation. [Tech report #227]
D. Shilane, J. Martikainen, S. Dudoit, and S. Ovaska (2006). A general framework for statistical performance comparison of evolutionary computation algorithms. [Tech report #204]
S. Dudoit, S. Keles, and M. J. van der Laan (2006). Multiple tests of association with biological annotation metadata. [Tech report #202]
A. Barrier, M. J. van der Laan, and S. Dudoit (2005). Prognosis of stage II colon cancer by non-neoplastic mucosa gene expression profiling. [Tech report #179]
A. Barrier, M. J. van der Laan, and S. Dudoit (2005). Colon cancer prognosis prediction by gene expression profiling. [Tech report #178]
D. Rubin, S. Dudoit, and M. J. van der Laan (2005). A method to increase the power of multiple testing procedures through sample splitting. [Tech report #171]
B. Durbin, S. Dudoit, and M. J. van der Laan (2005). Optimization of the architecture of neural networks using a Deletion/Substitution/Addition algorithm. [Tech report #170]
M. D. Birkner, K. S. Pollard, M. J. van der Laan, and S. Dudoit (2005). Multiple testing procedures and applications to genomics. [Tech report #168] [SAS code]
S. Dudoit, M. J. van der Laan, and M. D. Birkner (2004). Multiple testing procedures for controlling tail probability error rates. [Tech report #166]
Y. Wang and S. Dudoit
(2004). Quantification and visualization of LD patterns and
identification of haplotype blocks. [Tech report #150]
M. J. van der Laan, S. Dudoit, and A. W. van de Vaart (2004). The cross-validated adaptive epsilon-net estimator. [Tech report #142]
M. J. van der Laan and S. Dudoit (2003). Unified cross-validation methodology for selection among estimators and a general cross-validated adaptive epsilon-net estimator: Finite sample oracle inequalities and examples. [Tech report #130]
S. Dudoit (2003). IBD configuration transition matrices and linkage score tests for unilineal relative pairs. [Tech report #128]
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. [R News website]
Refereed Journal Publications
2008
D. Shilane, J. Martikainen, S. Dudoit, and S. J. Ovaska (2008). A general framework for statistical performance comparison of evolutionary computation algorithms. Information Sciences, Vol. 178, No. 14, p. 2870-2879. [Journal website]
S. Dudoit, S. Keles, and M. J. van der Laan (2008). Multiple tests of association with biological annotation metadata. In D. Nolan and T. P. Speed (eds), Probability and Statistics: Essays in Honor of David A. Freedman, Vol. 2 of IMS Collections, p. 153-218. [Project Euclid] [arXiv]
B. Durbin, S. Dudoit, and M. J. van der Laan (2008). A deletion/substitution/addition algorithm for classification neural networks, with applications to biomedical data. In S. Gupta and R. Mukerjee (eds), Statistical Design and Analysis in the Health Sciences III, Special Issue of Journal of Statistical Planning and Inference, Vol. 138, No. 2, p. 464-488. [Journal website]
2007
A. Barrier, F. Roser, P.-Y. Boelle, B. Franc, C. Tse, D. Brault, F. Lacaine, S. Houry, P. Callard, C. Penna, B. Debuire, A. Flahault, S. Dudoit, and A. Lemoine (2007). Prognosis of stage II colon cancer by non-neoplastic mucosa gene expression profiling. Oncogene, Vol. 26, No. 18, p. 2642--2648. [Journal website]
2006
M. J. van der Laan, S. Dudoit, and A. W. van der Vaart (2006). The cross-validated adaptive epsilon-net estimator. Statistics & Decisions, Vol. 24, No. 3, p. 373-395. [Journal website]
A. W. van der Vaart, S. Dudoit, and M. J. van der Laan (2006). Oracle inequalities for multi-fold cross validation. Statistics & Decisions, Vol. 24, No. 3, p. 351-371. [Journal website]
A. Barrier, P.-Y. Boelle, F. Roser, J. Gregg, C. Tse, D. Brault, F. Lacaine, S. Houry, M. Huguier, B. Franc, A. Flahault, A. Lemoine, and S. Dudoit (2006). Stage II colon cancer prognosis prediction by tumor gene expression profiling. Journal of Clinical Oncology, Vol. 24, No. 29, p. 4685-4691. [Journal website] [Website companion]
D. Rubin, M. J. van der Laan, and S. Dudoit (2006). A method to increase the power of multiple testing procedures through sample splitting. Statistical Applications in Genetics and Molecular Biology, Vol. 5, No. 1, Article 19. [Journal website] [Tech report #171]
S. Keles, M. J. van der Laan, S. Dudoit, and S. E. Cawley (2006). Multiple testing methods for ChIP-Chip high density oligonucleotide array data. Journal of Computational Biology, Vol. 13, No. 3, p. 579-613. [Journal website] [Tech report #147]
Y. Wang, L. P. Zhao, and S. Dudoit (2006). A fine-scale linkage-disequilibrium measure based on length of haplotype sharing. American Journal of Human Genetics, Vol. 78, No. 4, p. 615-628. [Journal website] [Tech report #192]
T. Hothorn, P. Buhlmann, S. Dudoit, A. M. Molinaro, and M. J. van der Laan (2006). Survival ensembles. Biostatistics, Vol. 7, No. 3, p. 355-373. [Journal website] [Tech report #174]
Software: R packages mboost (various boosting algorithms) and party (random forest for censored data).
Vignette for Section 6 analyses: [PDF] [.Rnw]
> vignette("SurvivalEnsembles", package = "mboost")
F. Chiappini, A. Barrier, R. Saffroy, M. -C. Domart, N. Dagues, D. Azoulay, M. Sebagh, B. Franc, S. Chevalier, B. Debuire, S. Dudoit, and A. Lemoine (2006). Exploration of global gene expression in human liver steatosis by high-density oligonucleotide microarray. Laboratory Investigation, Vol. 86, No. 2, p. 154-165. [Journal website]
2005
K. S. Pollard, M. D. Birkner, M. J. van der Laan, and S. Dudoit (2005). Test statistics null distributions in multiple testing: Simulation studies and applications to genomics. Numero double special Statistique et Biopuces, Journal de la Societe Francaise de Statistique, Vol. 146, No. 1-2, p. 77-115. [Website companion] [Tech report #184]
A. Barrier, P.-Y. Boelle, A. Lemoine, C. Tse, D. Brault, F. Chiappini, F. Lacaine, S. Houry, M. Huguier, A. Flahault, and S. Dudoit (2005). Gene expression profiling of nonneoplastic mucosa may predict clinical outcome of colon cancer patients. Diseases of the Colon and Rectum, Vol. 48, No. 12, p. 2238-2248. [Journal website]
A. Barrier, N. Olaya, F. Chiappini, F. Roser, O. Scatton, C. Artus, B. Franc, S. Dudoit, A. Flahault, B. Debuire, D. Azoulay, and A. Lemoine (2005). Ischemic preconditioning modulates the expression of several genes, leading to the overproduction of IL-1Ra, iNOS, and Bcl-2 in a human model of liver ischemia-reperfusion. The FASEB Journal, Vol. 19, No. 12, p. 1617-1626. [Journal website]
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]
2004
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. Keles, M. J. van der Laan, and S. Dudoit (2004). Asymptotically optimal model selection method with right censored outcomes. Bernoulli, Vol. 10, No. 6, p. 1011-1037. [Abstract] [Tech report #124]
M. J. van der Laan, S. Dudoit, and K. S. Pollard (2004). Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 15. [Journal website] [Tech report #141]
M. J. van der Laan, S. Dudoit, and K. S. Pollard (2004). Multiple testing. Part II. Step-down procedures for control of the family-wise error rate. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 14. [Journal website] [Tech report #139]
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]
A. M. Molinaro, S. Dudoit,
and M. J. van der Laan
(2004). Tree-based
multivariate regression and density estimation with
right-censored data. In S. Dudoit, R. C. Gentleman, and M. J. van
der Laan (eds), Multivariate Methods in Genomic Data
Analysis, Special Issue of Journal
of
Multivariate Analysis, Vol. 90, No. 1, p. 154-177. [Tech
report #135]
M. J. van der Laan, S. Dudoit, and S. Keles (2004). Asymptotic optimality of likelihood-based cross-validation. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 4. [Journal website] [Tech report #125]
2003
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. Keles, M. J. van der Laan, S. Dudoit, B. Xing, and M. B. Eisen (2003). Supervised detection of regulatory motifs in DNA sequences. Statistical Applications in Genetics and Molecular Biology, Vol. 2, No. 1, Article 5. [Journal website] [Tech report #131]
Y. Ge, S. Dudoit, and T. P. Speed (2003). Resampling-based multiple testing for microarray data analysis. TEST, Vol. 12, No. 1, p. 1-44 (plus discussion p. 44-77). [PDF] [Tech report #633]
S. Dudoit, J. P. Shaffer, and J. C. Boldrick (2003). Multiple hypothesis testing in microarray experiments. Statistical Science, Vol. 18, No. 1, p. 71-103. [PDF] [Project Euclid] [Tech report #110]
S. Dudoit and J. Fridlyand (2003). Bagging to improve the accuracy of a clustering procedure. Bioinformatics, Vol. 19, No. 9, p. 1090-1099. [Journal website] [Tech report #600]
S. Dudoit, R. C. Gentleman,
and J. Quackenbush (2003).
Open
source tools for microarray analysis. Biotechniques Supplements,
Microarrays and Cancer: Research and Applications, p. 45-51. [Journal website]
S.
Dudoit and D. R.
Goldstein (2003). Extensions to a score test for genetic linkage
with identity by descent data. In D. R. Goldstein (ed), Science and Statistics: A Festschrift for
Terry Speed, Vol. 40 of Institute
of Mathematical Statistics, Lecture Notes-Monograph Series, p.
307-319.
2002
H. Y. Chang, J. T. Chi, S. Dudoit, C. Bondre, M. van de Rijn, D. Botstein, and P. O. Brown (2002). Diversity, topographic differentiation, and positional memory in human fibroblasts. Proc. Natl. Acad. Sci., Vol. 99, No. 20, p. 12877-12882. [Website companion]
S. Dudoit and J. Fridlyand (2002). A prediction-based resampling method to estimate the number of clusters in a dataset. Genome Biology , Vol. 3, No. 7, p. 0036.1-0036.21. [Journal website] [Tech report #600]
X. Chen, S. T. Cheung, S. So, S. T. Fan, C. Barry, J. Higgins, K.-M. Lai, J. Ji, S. Dudoit, I. O. L. Ng, M. van de Rijn, D. Botstein, and P. O. Brown (2002). Gene expression patterns in human liver cancers. Molecular Biology of the Cell, Vol. 13, No. 6, p. 1929-1939. [Website companion]
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, p. 108-136. [Tech report #584]
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, Y. H. Yang, 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]
J. C. Boldrick, A. A. Alizadeh, M. Diehn, S. Dudoit, C. L. Liu, C. E. Belcher, D. Botstein, L. M. Staudt, P. O. Brown, and D. A. Relman (2002). Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc. Natl. Acad. Sci., Vol. 99, No. 2, p. 972-977. [Website companion]
S. Dudoit, Y. H. Yang, 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, p. 111-139. [PDF] [Tech report #578]
2001
D. R. Goldstein, S. Dudoit, and T. P. Speed (2001). Power and robustness of a score test for linkage analysis of quantitative traits using identity by descent data on sib pairs. Genetic Epidemiology, Vol. 20, No. 4, p. 415-431. [Journal website]
2000
M. J. Callow, S. Dudoit, E. L. Gong, T. P. Speed, and E. M. Rubin (2000). Microarray expression profiling identifies genes with altered expression in HDL deficient mice. Genome Research, Vol. 10, No. 12, p. 2022-2029. [Journal website]
D. R. Goldstein, S. Dudoit, and T. P. Speed (2000). Power of a score test for quantitative trait linkage analysis of relative pairs. Genetic Epidemiology, Vol. 19(Suppl 1), p. S85-S91. [Journal website]
S. Dudoit and T. P. Speed (2000). A score test for the linkage analysis of qualitative and quantitative traits based on identity by descent data on sib-pairs. Biostatistics, Vol. 1, No. 1, p. 1-26. [Journal website] [Tech report #556]
1999
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]
S. Dudoit and T. P. Speed
(1999). Triangle constraints
for sib-pair
identity by descent probabilities under a general multilocus model for
disease susceptibility. In M. E. Halloran and S. Geisser (eds), Statistics
in Genetics, Vol. 112 of IMA Volumes in Mathematics and its
Applications, Springer, New York, p. 181-221. [Springer
website] [Tech
report #527]
Book Chapters and Conference Proceedings
K. S. Pollard, S. Dudoit,
and M. J. van der Laan (2005). Multiple testing procedures: the multtest
package and
applications to genomics. In R. C. Gentleman, V. J. Carey, W.
Huber, R. Irizarry, and S. Dudoit
(eds), Bioinformatics and
Computational Biology
Solutions Using R and Bioconductor, Springer, New York,
Chapter 15, p. 249-271. [Tech report #164]
[Bioconductor R package multtest]
R. Gentleman, B. Ding, S. Dudoit, and J. Ibrahim (2005). Distance measures in DNA microarray data analysis. In R. C. Gentleman, V. J. Carey, W. Huber, R. Irizarry, and S. Dudoit (eds), Bioinformatics and Computational Biology Solutions Using R and Bioconductor, Springer, New York, Chapter 12, p. 189-208.
S. Dudoit and M. J. van der Laan (2003). Unified cross-validation methodology for estimator selection and applications to genomics. Bulletin of the International Statistical Institute, 54th Session Proceedings, Vol. LX, Book 2, p. 412-415. [PDF] [ISI website, IPM-76: Gene expression data]
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]
[PDF]
S. Dudoit and J. Fridlyand (2003). Classification in microarray experiments. In T. P. Speed (ed), Statistical Analysis of Gene Expression Microarray Data, Chapman & Hall/CRC, Chapter 3, p. 93-158.
S. Dudoit and J. Fridlyand (2003). Introduction to classification in microarray experiments. In D. P. Berrar, W. Dubitzky, and M. Granzow (eds), A Practical Approach to Microarray Data Analysis, Kluwer, Chapter 7, p. 132-149.
S. Dudoit, Y. H. Yang, 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, p. 141-152. [Tech report #589]
PhD Dissertation
S. Dudoit (1999). Linkage analysis of complex human traits using identity by descent data, PhD dissertation. [Postscript]