2007-8 Bioinformatics Qualifying Examination
Examining Faculty
- Alexey Onufriev (committee chair)
- Yang Cao
- Joao Setubal
This page is pretty much finalized. The exam date is set, but check for possible updates.
The exam will take place on Sat., Feb. 9 at 2 pm. Please report to 2160 Torgersen Hall, the "conference room" in the back. The whole thing should take approximately 2 hours. Bring the papers, notes, blank sheets, etc. Above all, bring your clear, well-rested heads.
Format of the Examination
The exam is divided into 3 major themes. These will
include the following:
Structural Bioinformatics, Algorithms in Bioinformatics, and
Modeling and Simulation. We will
explore each theme via a set of related papers in the reading list below.
We expect you to read all the papers in the
reading list and obtain a detailed understanding of each paper. We
also expect you to acquire any pre-requisite or background knowledge
required to understand these papers. The exam has two parts:
- Written examination
Write a 1 page synopsis on each paper.
Use 11pt or 12pt times
font (\usepackage{times} in Latex) with 0.5 inch margins on
each side and
single-spaced type. Submit the combined synopsis as one file
in PDF format
by email to Alexey Onufriev
(alexey at cs vt dot edu)
by 5PM on January 31, 2007. Tell us
what problems you think each paper solves, what advantages and
disadvantages the solutions have, what the significance of
each paper is, and how would you improve the techniques used.
Also, you MUST answer specific questions that we ask on each
paper, the list is given below. Format: quote the question
and provide your answer below. The space used for the answers to
the specific questions does
not count towards the page limit of the synopsis; the answers
page should directly follow the synopsis page
for the corresponding paper. No more than 1 page per each answer,
UNLESS otherwise stated in the specific question.
- Oral Examination
The oral examination will involve in-depth questions on the
issues you have covered in the synopsis.
We encourage you to
read other related papers on these themes to understand how
research in each theme is evolving. We will elicit your
opinion on potential avenues of research in each theme.
Questions will drill down into the statistical, algorithmic,
and computational details of the papers in the reading list.
We will also examine your understanding of the biological
relevance and significance of the papers. The exam will be
45-60 minutes long.
Reading List (complete )
All the papers are available in the library, most of the papers should
also available on-line. You should be able to access them from a VT
computer.
- Structural Bioinformatics
- Contact order, transition state
placement and the refolding rates of single domain proteins. Plaxco, K.W., Simons, K.T., and Baker, D., J. Mol. Biol. 277, 985-994 (1998).
- Modeling and Simulation
- Approximate accelerated stochastic simulation of chemically reacting systems, Gillespie DT, JOURNAL OF CHEMICAL PHYSICS 115 (4):
1716-1733 JUL 22 2001
- Algorithms in Bioinformatics
- Finding motifs using random projections
J. Buhler and M. Tompa, Journal of Computational Biology, 9:225-242, 2002.
If you have any specific questions about the Bioinformatics qualifier, please send email to Alexey Onufriev (alexey at cs vt dot edu). Make
sure that your message has the phrase "bioinformatics qualifier" in
the subject line. You might find the following book(s) useful for general reference: (1) Structural Bioinformatics, by Bourne and Weissig.
(2) Dan Gusfield's book used in Dr. Heath's Algorithms in Bioinformatics course
(3) The book that Dr. Zhang uses in CS 4984, "Introduction to Bioinformatics Algorithms"
(4) System Modelling in Cellular Biology, From Concepts to Nuts and Bolts
Edited by Zoltan Szallasi, Jrg Stelling and Vipul Periwal, 2006,
ISBN: 978-0-262-19548-5