- Name: Dr. My T. Thai
- Office: E566 CISE
- Phone: (352)392-6842
- Office Hours: T: 12:30pm-2:30pm
This course focuses on the design
and analysis of algorithms and models for problems motivated from
molecular biology research. The course also provides some
computational techniques, such as dynamic programming, Markov models,
local search as well as many other
optimization techniques. Topics discussed in this course include the
Sequence Alignment, Multiple
Genomics and Proteomics
Structure Identification and Prediction
- There is no formal prerequisites for this
course. However, students should have enough background in algorithms, i.e,
- Owing to
the rapid evolution of the subject, there is no formal required book
for this class. A collection of research related articles and reading
assignments will be provided at the Schedule
- Recommended Textbooks:
R. Durbin, S.R. Eddy, A. Krogh,
and G. Mitchison, Biological Sequence Analysis: Probabilistic
Models of Proteins and Nucleic Acids,
Cambridge University Press,
Introduction to Computational Biology: Maps, Sequences, and Genomes,
Chapman & Hall, 1995.
Pevzner, Computational Molecular Biology: An Algorithmic Approach,
MIT Press, 2000. ISBN: 0262161974
Course Work and
- Paper Review:
- Each student is required to submit a
paper review for the "required reading" papers. The review is about 1
page long and must be submitted at the beginning of the class on
the day of lecture. The review should follow this format:
- A short summary about the problem studied in
the paper. (About 2 to 5 sentences)
- What are the strengths of the paper?
- What are the weaknesses of the paper?
- Other comments and directions on how to
improve the paper.
- Paper Presentation:
- Each team will study a number of research
papers assigned by the instructor in details.
- Prepare and make a presentation and lead
- The team who handles the presentation will
not required to submit the review report on that lecture.
- Group Project:
- By the second week, students will be formed
into a number of "research groups." Each group may consist of 2 to 3
- The "research topics" will be chosen in
consultation with the instructor.
- A project may consist of:
- Performing some experiments to verify and
existing ideas/approaches. These experiments must reveal some critical
analysis and insights of each approach.
- Providing in-depth analysis
- Proposing original ideas/conducting original
work to improve the existing ideas or approaches
- The project must be done by following this
procedure. Detail of due date will be given in the Schedule page:
- By the third week, each group selects one or
two research topics in consultation with the instructor.
- By the fifth week, a "research proposal"
must be submitted which describes the scope of the project, lists the
issues to be addressed, and outlines approaches to be taken. Several
recommended papers related to the project must also be provided. The
research proposal is about 4 pages long, single space.
- By the tenth week, a project midterm report
must be submitted. It is about 7 pages long.
- By the last day of class, the final project
report in the format of a journal paper is due. It is 11 pages
- Peer Review:
- Students in each group are also responsible
for "peer reviewing" the project of another group. This includes the
- Writing a review report and posing a list of
suggested questions/comments. This is done through reading the
references, project proposal, and the progress report of the other
- Reviewing and evaluating the final project
report of the other team.
- There will be two homework assignments
- 15% on presentations
- 20% on two homework assignments
- 20% on review reports (including peer
- 45% on the project, which will be divided as
- 5% for the research proposal (by the fifth
- 10% for the midterm report (by the tenth
- 30% for the final report
- Cut-off points:
- A >= 90%, 90% > B >= 80%, 80% >
C >= 70%
- All the assignments must be submitted at the
beginning of the due date. No late submission will be
- Academic Integrity Policy:
- You may discuss with other students on
the review reports. However, you must write up
the reports on your own independently.