Computational biology & radiobiology research by our group
- Topics mainly concern mathematical/computational modeling of ionizing radiation-influenced
or sporadic carcinogenesis, second cancers after
radiotherapy, large-scale
DNA structure, and chromosome
damage by ionizing radiation.
- Techniques
involve mathematics, modeling and
programming, not experiments.
Data is obtained by colleagues at various
labs worldwide or is in the literature. Mathematical techniques include
differential equations, probability theory,
Monte-Carlo computer simulations, polymer
physics, mass-action and stochastic
chemical kinetics, Markov chains and other random
processes, population dynamics, and
ecological-evolutionary modeling of somatic
cell populations, all at
a rather applied level. Programming is
mainly in Fortran, Java, Mathematica, C++,
HTML.
- 2009-2010
Current Projects.
Our main project at the moment is cancer risk
estimation for astronauts in cooperation with the
Center for Cancer Systems Biology at Tufts. In addition, we are
working on mathematical modeling of the blast
crisis in CML, with a transformation model
involving cell-cell fusion. This is being carried
out with the cooperation of three new students
in the URAP program (see below)
- Team.
We have a small theory
group (e.g. one or two postdocs, one grad student and several undergrad research assistants).
Some current or past members of our team are the following.
- Ray Sachs home page
and Ray Sachs contact information.
-
Hatim Fakir
home page.
Dr. Fakir is a postdoc in our group. His
main interests are mathematical modeling of
radiation-influenced carcinogenesis and
tumor growth mechanisms and internal
microdosimetry.
-
Javier Arsuaga
home page.
Dr. Arsuaga is a former postdoc in our group. His
main interests are chromosome structure and DNA repair. His
approach to these problems relies on a combination of experimental and
computational work.
-
Mariel Vazquez
home page.
Dr. Vazquez is a former postdoctoral fellow in our group. She
is interested in studying the structure of DNA and how it is affected by
vital biological processes such as DNA recombination and repair.
-
Dan Levy
home page. Dan
is a former postdoc in our group.
He developed algorithms for quantifying
mFISH chromosome aberration patterns. He also worked on
genomic phylogenetics.
-
URAP.
Our group has undergraduate students each semester; some are
in the UCB undergraduate research apprentice program (URAP).
- Publications.
Titles, abstracts, and some full papers for
Sachs: Publications 1997-1998;
Publications 1999-2000;
Publications 2001-2002;
Publications 2003-2005;
Publications 2006-2008.
- Federal Grants.
Brief descriptions.
- Software:
-
Programs for simulating and analyzing radiation produced
chromosome aberrations are available
at the
CRC (Computational Radiation Cytogenetics)
web site maintained at UCB by Sachs.
-
TangleSolve
Topological analysis of site-specific recombination; from Vazquez'
web site.
"...the universe is not only stranger than we suppose, but stranger than we
can suppose." -- JBS Haldane
Research