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I am an
assistant professor in the Department of Epidemiology and
Biostatistics, Division
of Biostatistics, at UCSF. I am also a member of UCSF
Comprehensive Cancer Center Biostatistics Core
where I lead genomics analysis efforts and of CBMB (Center for
Bioinformatics and Molecular Biostatistics) which is a center providing
statistical support for molecular, genomics and genetics data. My main
research interests concern
the application of statistics to problems in genomics and cancer.
In particular, my research work has centered on the development
of statistical methodology and software for the analysis of gene
expression and DNA copy number number data,
I graduated
from School 239 in Saint
Petersburg, formerly Leningrad. After moving to the US, I
obtained a
bachelor’s degree in mathematics from the University of California in
Berkeley
and then enrolled in the Ph.D program in the Department of Statistics at
the University of California,
Berkeley where I worked under the supervision of Terry Speed on
the analysis
of high-dimensional genomics data. During my graduate studies, I
took a part in Human
Genome Project assisting with conversion to high-throughput
sequencing techniques as part of initially LBNL (Lawrence Berkeley National Labs)
and later JGI (Joint
Genome Institute) team. Additionally, I was involved with
identification of epistasis in mouse linkage studies at WEHI (Walter & Eliza
Institute of Medical Research) and with the development of statistical
methods for the analysis of gene expression data. During my postoc, I
worked in the lab of Ajay Jain on the
problems related to the analysis of the copy number data.
Research
Research Interests
Publications
Presentations
Teaching
This fall I am co-teaching BMI course
(statistical methods
for the analysis of the microarray data). Additionally,
together
with other CBMB members, we put together a workshop for the microarray
community:
Microarrays:
Case Studies and Advanced Analyses.
Last year, together with Dr. Mark van der Laan,
I co-advised Peter Dimitrov who has assisted in developing
R/Bioconductor package aCGH
for the analysis of the array CGH data.
In the Spring 2005, Hanni Willenbrock, a
Ph.D student in CBS DTU, Denmark,
will spend a semester in my lab working on the projects concerning
analysis of expression and array CGH data.
I have been active in providing informal statistical service to the
members of the UCSF Comprehensive
Cancer Center.
Workshops
Software
I am a maintainer of aCGH package on R/Bioconductor. At the
moment, it contains graphical and computational tools for visualization
and testing of the array CGH data as well Hidden Markov Model based
methods for finding copy number transitions. The latter part of the
package utilizes HMM software written by Jim Lindsey and the two
packages, repeated and its dependency, rmutil, need to
be downloaded and installed from his website: http://popgen0146uns50.unimaas.nl/~jlindsey/rcode.html.
[aCGH.tar.gz] [aCGH.zip]
Links
Computational Collaborators
Experimental Collaborators
General
Personal : This
section is password protected.
