Sandrine Dudoit, PhD
Professor, Division of Biostatistics, School
of Public Health, and Department of Statistics
Chair and Head Graduate Advisor, Graduate Group in Biostatistics
University of California,
185 Li Ka Shing Center, #3370
Berkeley, CA 94720-3370
Tel: (510) 643-1108
Fax: (510) 643-5163
D. Risso, J. Ngai, T. P. Speed, and S. Dudoit.
The role of spike-in standards in the normalization of RNA-seq.
In S. Datta and D. Nettleton, editors, Statistical Analysis of Next Generation Sequencing Data, Frontiers in Probability and the Statistical Sciences, Chapter 9, pages 169-190. Springer International Publishing, 2014.
D. Risso, J. Ngai, T. P. Speed, and S. Dudoit. Normalization of RNA-seq data using factor analysis of control genes or samples. Nature Biotechnology, 2014. (Advanced online publication) [HTML].
Remove unwanted variation from RNA-Seq data.
D. Risso and S. Dudoit.
[Bioconductor R package: devel]
Research and Teaching Activities
My research and teaching activities concern the development and
application of statistical methods and software for the analysis
of biomedical and genomic data.
Statistical methodology. My methodological research
interests regard high-dimensional inference and include
exploratory data analysis (EDA), visualization, loss-based
estimation with cross-validation (e.g., density estimation,
regression, model selection), and multiple hypothesis testing.
Applications to biomedical and genomic research. Much of my
methodological work is motivated by statistical inference
questions arising in biological research and, in particular, the
design and analysis of high-throughput microarray and sequencing
gene expression experiments, e.g., mRNA-Seq for transcriptome
analysis and genome annotation and ChIP-Seq for DNA-protein
interaction profiling (e.g., transcription factor binding). My
contributions include: exploratory data analysis, normalization
and expression quantitation, differential expression analysis,
class discovery, prediction, integration of biological annotation
metadata (e.g., Gene Ontology (GO) annotation).
Statistical computing. I am also interested in statistical
computing and, in particular, reproducible research. I am a
founding core developer of the Bioconductor Project (http://www.bioconductor.org), an open-source and open-development software project for the analysis of biomedical and genomic data.
Curriculum Vitae and Biography
Curriculum Vitae: [PDF]
Graduate Group in
Biostatistics, UC Berkeley
in Computational and Genomic Biology, UC Berkeley
Group in Computational Science and Engineering (CSE), UC
Center for Computational
(CCB), UC Berkeley
California Institute for
Quantitative Biosciences (QB3)
Berkeley Stem Cell
Molecular Biostatistics (CBMB), UC San Francisco