CSCE 628 Computational Biology
Instructor: Sing-Hoi Sze
Meeting: MWF 9:10-10 HRBB 126
Office Hourse: MWF 8:40-9:10 HRBB 328B or by appointment
What is Computational Biology
Computational Biology is the application of computational techniques to
solve problems in biology, which involves DNA and proteins.
Traditionally, people from various disciplines, such as computer science,
mathematics and statistics, formulate and address these problems within
their own disciplines. More recently, multi-disciplinary
collaborations become the norm, which include participations of biologists and
The main purpose of the course is to expose students to various active
research areas in computational biology. Everyone who is interested in
computational biology is encouraged to take the course.
For most topics, considerable time will be spent on presenting latest
research ideas, mostly from the computer science point of view. Emphasis will
be placed on problem formulation, where many problems in genomics and
proteomics will be seen as graph-theoretic or optimization problems.
The focus of the lectures is on presenting the newest computational
approaches from research papers after briefly describing classical approaches
in each area.
- Computational formulations and algorithms for biological sequence
- Combinatorial and statistical approaches to motif finding and applications.
- Scalable algorithms for comparative genomics and whole genome comparisons.
- Study of genome rearrangements and inferring evolutionary relationships.
- Approaches for gene clustering and protein classification.
- Algorithms for finding common substructures in biological networks.
- Techniques for high-throughout sequence assembly.
- Homework Assignments (40%): short written assignments handed out every one
or two weeks.
- Two midterms (20% each).
- Presentation (20%): towards the end of the semester, each student will give
a presentation on a topic of interest.
- Graduate classification or approval of instructor.
- No required text. Materials and papers are drawn from the literature.