An interdisciplinary program in Computational Molecular
Biology (CMB) has been established at the
University of
Washington (UW) and Fred Hutchinson Cancer Research Center (FHCRC).
The program involves graduate work towards a Ph.D. degree.
Students were admitted for the academic years beginning in
September 2000 and in each September afterwards. Students from diverse
undergraduate majors, including biology, chemistry, computer science,
mathematics, physics, statistics, and related areas, are encouraged to
apply.
Successful students will be admitted to one of the participating
UW departments below. Each of these has established a "CMB track"
for students in the program, with adjustments to the
usual departmental first-year requirements in order to allow the
student to satisfy the CMB requirements as well. Each department
determines which CMB students are admitted to it, is responsible for
their financial support, and awards their degrees. Transfer into a different
participating department is permitted at the end of the student's
first year, subject to approval by that department.
Participating departments include:
The University of Washington and the FHCRC have an unusually large number
of faculty members who specialize in different areas of computational and
mathematical biology.
They are spread across many departments, but they are in frequent contact and
cooperate in training students in programs such as the CMB and Statgen programs.
In the CMB program particularly active areas include genomics (Green, Felsenstein,
Olson, Nickerson, Noble, Akey, Swanson, Bergstrom, Henikoff, Trask, and Tompa) and
protein structure (Baker, Samudrala), and gene interaction (Ruzzo, Qian, Samudrala, and Gentleman).
The CMB program is just one of several at the University of
Washington which focus on the use of computational, statistical or
mathematical methods to study problems in biology. Other programs
which the student may wish to consider include
These programs are complementary, and students in any of them are encouraged to take
courses in the others. In particular, students from
non-CMB-participating departments and students from non-CMB tracks in
participating departments are eligible to take the CMB core
course and participate in journal club or research discussions.
The CMB program and the Statgen program cooperate particularly closely
as "sister programs" in training their students.
APPLICATION PROCESS:
- Applications should be submitted to one of the
participating University of Washington departments above (see links to
their department web pages above for address and detailed instructions).
Note that some of these departments have application deadlines as early as
December 15, and for international students there are deadlines as
early as November 1. The application should include the following:
- Cover letter. This should indicate
clearly that you wish to be considered for the CMB program; specify your preferred host department(s), if any; and indicate which of the prerequisites for the CMB program you have satisfied or will be satisfying prior to admission.
- You should also write us a letter (or email us) informing us that you have applied to
that department and want to be a Computational Molecular Biology student.
- Curriculum vitae
- GRE scores (as required by the department)
- Grade transcript
- 3 letters of recommendation. At least one of these should attest
to your suitability for computational research.
- Statement of purpose
- official UW application form
- any other materials required by the department (e.g. departmental application form).
- Upon receipt, the department will forward a copy of the application to the
CMB program admissions committee. This committee
will make an initial determination whether or not the student is
acceptable to the CMB program, advise the department of its opinion, and
also consider whether the student would be well-advised to apply
to any of the other CMB member
departments, based on the student's background and any stated
preferences.
- Applications will be considered by
the admissions committee of each relevant department, with the CMB
program admissions committee advising them.
The following minimal preparatory coursework requirements, which are
essential for a thorough understanding of the material covered in the
core CMB course, should have been satisfied by every CMB student
either prior to admission, or during the first year of graduate study
(preferably no later than the end of the winter quarter):
- 1 quarter of probability & statistics (the equivalent of
STAT 390 or STAT 394)
- 1 quarter of
computer programming, preferably including the writing of programs for
data analysis (the equivalent of CSE 142/ CSE 143)
- 1 quarter of algorithms and data structures (the equivalent of CSE 373)
- 2
quarters of molecular biology, biochemistry, and/or genetics (the equivalent of
GENOME 371/372,
and/or BIOC 440/441)
These should be at the advanced undergraduate level or higher, and at
least two of them should have been satisfied prior to admission. The
host department will in general have additional prerequisites. Due to
the course burden in many departments, it is strongly recommended that
all of the above be satisfied prior to admission if at all possible.
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.
Applied Math 423: Mathematical Biology: Introduction to Stochastic Models
