Sandrine Dudoit: Research Group Members

Group Members: [MA and MPH Students] [PhD Students] [Postdoctoral Fellows] [Visiting Scholars] [Alumni]

MA and MPH Students

PhD Students

James H. Bullard (Fall 2006 -- )
Graduate Group in Biostatistics, UC Berkeley.
Projects. Statistical and computational methods for the design and analysis of high-throughput gene expression experiments based on DNA microarrays and next-generation sequencing: transcriptome analysis using mRNA-Seq; genome annotation in S. cerevisiae using tiling microarrays; microarray-based assays (16s small-subunit rRNA microarrays) for the quantitative detection of microorganisms in complex environmental and medical samples.

Houston N. Gilbert (Spring 2006 -- )
Graduate Group in Biostatistics, UC Berkeley.
Projects. Multiple hypothesis testing; DNA microarray-based genetic mapping and gene expression studies; genome-wide association studies.

Kasper D. Hansen (Fall 2005 -- )
Graduate Group in Biostatistics, UC Berkeley.
Projects. Statistical and computational methods for the design and analysis of high-throughput gene expression experiments based on DNA microarrays and next-generation sequencing: transcriptome analysis using mRNA-Seq; genome annotation in S. cerevisiae using tiling microarrays; microarray-based study of gene regulation by alternative splicing in D. melanogaster; microarray-based assays (16s small-subunit rRNA microarrays) for the quantitative detection of microorganisms in complex environmental and medical samples; ChIP-Chip experiments for identifying transcription factor binding sites and histone modification.

Postdoctoral Fellows

Dr. Elizabeth A. Purdom (Spring 2007 -- )
Division of Biostatistics and Department of Statistics, UC Berkeley.
Projects. Statistical and computational methods for transcriptome analysis using next-generation sequencing.

Visiting Scholars

Alumni

MA and MPH Students

Matthieu Cornec (Fall 2002 -- Spring 2003)
Department of Statistics, UC Berkeley/Ecole Nationale de la Statistique et de l'Administration Economique, Malakoff, France.
Projects. Risk inference using cross-validation.
Current position. Institut National de la Statistique et des Etudes Economiques (INSEE), Paris, France.

Fabian L. Gallusser (Summer 2005 -- Summer 2006)
Graduate Group in Biostatistics, UC Berkeley.
Projects. Statistical and computational methods for the analysis of alternative splicing microarray experiments; Bioconductor R package cosmo for COnstrained Search for MOtifs in DNA (cosmo Projects).
Current position. Associate Product Marketing Manager, Google, Paris, France.

Benjamin A. Goldstein (Spring 2007)
MPH Degree Program in Epidemiology/Biostatistics, UC Berkeley.
Thesis title. Comparative Analysis of FDR-Controlling Procedures to Identify Genetic Associations in Complex Diseases.
Current position. PhD Program in Biostatistics, UC Berkeley.

Sylvia E. Keuter Sudat (Fall 2008)
Graduate Group in Biostatistics, UC Berkeley.
Thesis title. An Application of Statistical Clustering Methods to the Investigation of Patterns of Gene Expression within the Arabidopsis Receptor-like Kinase Superfamily.
Current position. PhD Program in Biostatistics, UC Berkeley.

Jennifer L. Poirier (Spring 2007)
Graduate Group in Biostatistics, UC Berkeley.
Thesis title. A Comparative Analysis of Regression Methods.
Current position.

PhD Students

David A. Shilane (Fall 2005 -- Summer 2008)
Graduate Group in Biostatistics, UC Berkeley.
Dissertation title. Optimization Studies with Multiple Testing, Loss-Based Estimation, and Confidence Intervals for Negative Binomials of High Dispersion.
Projects. Loss-based estimation with evolutionary algorithms and cross-validation.
Current position. Biostatistician, Department of Health Research and Policy, Stanford University.

Yan Wang (Fall 2002 -- Spring 2006)
Graduate Group in Biostatistics, UC Berkeley.
Dissertation title. Statistical Methods for Evaluating Linkage Disequilibrium and Its Patterns Using Length of Haplotype Sharing.
Projects. Genetic mapping of complex human traits using single nucleotide polymorphisms (SNP); quantification and visualization of genome-wide linkage disequilibrium patterns; identification of haplotype blocks.
Current position. Gilead Sciences, Seattle, WA.

Postdoctoral Fellows

Professor Mathias Drton (Summer 2004 -- Spring 2005)
Department of Mathematics, UC Berkeley.
Projects. Multiple testing procedures in graphical model selection.
Current position. Assistant Professor, Department of Statistics, University of Chicago.

Dr. Blythe P. Durbin (Fall 2003 -- Summer 2005)
Division of Biostatistics, UC Berkeley.
Projects. Optimization of neural network architecture using loss-based Deletion/Substitution/Addition (DSA) algorithm.
Current position. Senior Biostatistician, Early Clinical Development, Oncology, Genentech Inc.

Dr. Steffen Durinck (Fall 2007 -- Spring 2008)
Division of Biostatistics, UC Berkeley, and Life Sciences Division, Lawrence Berkeley National Laboratory.
Projects. Statistical and computational methods for transcriptome analysis using next-generation sequencing.
Current position. Bioinformatics Scientist, DNA Sequencing Business, Illumina Inc.

Professor Sunduz Keles (Fall 2003 -- Spring 2004)
Division of Biostatistics, UC Berkeley.
Projects. Loss-based estimation with cross-validation; supervised detection of regulatory motifs in DNA sequences; identification of transcription factor binding sites in ChIP-Chip experiments; tests of association between gene expression measures and Gene Ontology annotation; software for automating access to data from HTML forms.
Current position. Assistant Professor, Department of Biostatistics and Medical Informatics and Department of Statistics, University of Wisconsin, Madison.

Professor Katherine S. Pollard (Summer 2003 -- Fall 2003)
Division of Biostatistics, UC Berkeley.
Projects. Multiple hypothesis testing: software implementation in the Bioconductor R package multtest and applications to the identification of differentially expressed and co-expressed genes in high-throughput gene expression experiments.
Current position. Associate Professor, Division of Biostatistics, UC San Francisco, and Associate Investigator, Gladstone Institutes.

Visiting Scholars

Dr. Alain Barrier (January 2004 -- July 2006)
Praticien Hospitalo-Universitaire, Hopital Tenon and Universite Pierre et Marie Curie -- Paris 6, France.
Projects. Development and application of statistical and computational methods for cancer prognosis prediction based on microarray gene expression measures.

Dr. Melanie Courtine (Fall 2003)
Laboratoire d'Informatique, Universite Pierre et Marie Curie -- Paris 6, France.
Projects. Development and application of statistical and computational methods for genetic studies of human obesity (ObeLinks Project).

Kasper D. Hansen (July 2004 -- August 2005)
Department of Biostatistics, Copenhagen University, Denmark.
Projects. Statistical software design for loss-based estimation with cross-validation.

Dr. David O. Nelson (January 2003 -- July 2006)
Lawrence Livermore National Laboratory.

Professor Alejandro Sanchez Pla (May 2003 -- September 2003)
Department of Statistics, Faculty of Biology, University of Barcelona, Spain.
Projects. Microarray data analysis; gene annotation.