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 group testing theory, dynamic programming, Markov models, local search as well as many other optimization techniques. Topics discussed in this course include the following:

• Sequence Alignment, Multiple Sequence Alignment

• Computational Genomics and Proteomics

• Protein Structure Identification and Prediction

• High-throughput screening

• Pooling Designs

• Biological Networks

• Functional Groups

• R. Durbin, S.R. Eddy, A. Krogh, and G. Mitchison, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, 1998. ISBN: 0521629713

•  M.S. Waterman, Introduction to Computational Biology: Maps, Sequences, and Genomes, Chapman & Hall, 1995. ISBN: 0412993910

• P.A. Pevzner, Computational Molecular Biology: An Algorithmic Approach, MIT Press, 2000. ISBN: 0262161974

•  D.-Z. Du and F. K. Hwang, Pooling Design and Nonadaptive Group Testing: Important Tools for DNA Sequencing, World Scientific, 2006. ISBN: 9812568220

• 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.

• Each team will study a number of research papers assigned by the instructor in details.
• Prepare and make a presentation and lead classroom discussion.
• The team who handles the presentation will not required to submit the review report on that lecture.

• By the second week, students will be formed into a number of "research groups." Each group may consist of 2 to 3 students.
• The "research topics" will be chosen in consultation with the instructor.
• A project may consist of:
  • Performing some experiments to verify and compare 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 maximum.

• Students in each group are also responsible for "peer reviewing" the project of another group. This includes the following:
  • 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 team
  • 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 review)
• 45% on the project, which will be divided as follows:
  • 5% for the research proposal (by the fifth week)
  • 10% for the midterm report (by the tenth week)
  • 30% for the final report

• A >= 90%, 90% > A- >= 87%, 87% > B+ >= 85%, 85% > B >= 80%, 80% > B- >= 77%, 77% > C+ >= 75%, 75% > C >= 70%

• You may discuss with other students on the review reports. However, you must write up the reports on your own independently.