FIRST YEAR REQUIREMENTS:
Students will be assigned an advisor (a faculty member in the host
department familiar with the CMB program), who will help choose an
appropriate course of study consistent with the student's background
and with CMB and departmental requirements. As described more fully
below, all first-year CMB students will be required to complete the
2-quarter core CMB course, participate in the CMB journal club and
research reports, attend the seminar series, and do at least one
rotation in the lab of a participating faculty member. They will also
be required to satisfy any remaining prerequisites. These
requirements are in addition to the requirements of the host
department.
At the end of the first year, each student will choose a thesis
advisor from among participating faculty. Usually this advisor will be
in the originally selected host department, but transfer to another
department is permitted at this time, contingent on acceptance by the
new department. The thesis advisor's department will be responsible
for administering appropriate examinations and awarding the degree.
- Core CMB course (Genome 540/541). A 2-quarter course on protein and DNA
sequence analysis and molecular evolution. This will include a brief
review of basic molecular biology (structure & evolution of genes,
genomes and proteins), probabilistic models of sequences and of
sequence evolution, computational gene identification, pairwise
sequence comparison and alignment (algorithms and statistical issues),
multiple sequence alignment and evolutionary tree construction, and
protein sequence/structure relationships. These are the central
computational methods required to determine the "periodic table of
biology", i.e. the list of proteins and their evolutionary
relationships, which can be regarded as the first stage in the conversion of
molecular biology into a quantitative science. Moreover, the
statistical and algorithmic methods used (which include maximum
likelihood estimation, hidden Markov models, dynamic programming) have
wide applicability in other areas of computational/mathematical
biology.
The core course is taught
Winter/Spring, so as to leave the Autumn quarter free for meeting the
above prerequisites and for becoming well-integrated into the home
department.
- At least one rotation involving wet-lab work coupled with computationally
interesting data analysis. This can be co-mentored by a wet-lab biologist
together with a CMB participating faculty member. Some participating
departments may require additional rotations.
- Journal club (A/W/Sp); currently this is CSE 590c. Participation is required of all CMB students and is urged for all faculty members.
- Student research discussions (W/Sp). First year students will give a
1/2 hour report on their CMB rotations. More advanced students will
report periodically on their thesis work.
- Seminar series (A/W/Sp); currently this is the COMBI series. This will include outside speakers as well as
research presentations by participating CMB faculty. The latter will be
fairly extended and include ample discussion with students, since they
will be a primary mechanism by which students become familiar with the
various potential research areas prior to choosing a thesis advisor.
Each department's name is linked to its course catalog entry. For
specific information on individual courses, you can also consult
the departmental web pages, linked above. We do not maintain links to
individual course web pages as they change too frequently.
The number and content of the
electives that any student needs to take will be determined in consultation with the
thesis advisor and the requirements of the host department.
Questions about the program may be directed to any of the
participating faculty.
CONTACTING US
By email:
mkkuhner (at) gs.washington.edu
By mail:
Computational Molecular Biology Program
c/o Department of Genome Sciences
University of Washington
Box 357730
Seattle, WA 98195-7730
USA
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