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. Quantitative
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
James H. Bullard
(Fall 2006
-- Fall 2009)
Graduate Group in Biostatistics, UC Berkeley.
Dissertation title. Statistical
Methods
and Software for High-throughput Gene Expression Experiments.
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.
Current position. Pacific
Biosciences.
Houston N. Gilbert
(Spring 2006 -- Spring 2009)
Graduate Group in Biostatistics, UC Berkeley.
Dissertation title. Multiple
Hypothesis
Testing: Methodology, Software Implementation, and
Applications to Genomics.
Projects. Multiple hypothesis
testing; DNA microarray-based genetic mapping and gene expression
studies;
genome-wide association studies.
Current position. Genentech.
Kasper D. Hansen
(Fall 2005 -- Fall 2009)
Graduate Group in Biostatistics, UC Berkeley.
Dissertation title. Analyses
of
High-Throughput Gene Expression Data.
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.
Current position. Postdoctoral
Fellow, Department of Biostatistics, Johns Hopkins University.
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. Genentech.
Postdoctoral Fellows
Dr. Gergana
Bounova (Summer 2010 -- Fall 2011)
Department of Statistics, UC Berkeley.
Projects.
Genome surveillance by small RNAs in
Tetrahymena;
inference of time-varying networks in genomics.
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.
Principal Statistician, UC Davis.
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. Life Sciences
Division, Lawrence Berkeley National Laboratory.
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.
Dr. Elizabeth A. Purdom
(Spring 2007
-- Spring 2009)
Division of Biostatistics and Department of Statistics, UC Berkeley.
Projects. Statistical and
computational methods for transcriptome analysis using
next-generation sequencing.
Current position. Assistant
Professor, Department of Statistics, UC Berkeley.
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.
Professor Niels
Richard Hansen (Fall 2010 -- Fall 2011)
Department of Mathematical Sciences, University of Copenhagen, Denmark.
Anne-Claire Haury, PhD student (Spring 2011)
Center for Computational Biology, Mines ParisTech/Institut Curie, France.
Projects. Molecular characterization
of cancer using joint analysis of high-throughput transcription and
genotype data.
Dr. David O.
Nelson (January
2003 -- July 2006)
Lawrence Livermore National Laboratory.
Davide Risso,
PhD student (Fall 2010 -- Spring 2011)
Department of Statistical Sciences, University of Padova,
Italy.
Projects. Genome annotation
and transcriptome analysis in
Saccharomyces using RNA-Seq.
Professor
Alejandro
Sanchez Pla
(May 2003 -- September 2003)
Department of Statistics, Faculty of Biology, University of Barcelona,
Spain.
Projects. Microarray
data analysis; gene annotation.