CS598/BioE598: Algorithmic Genomic Biology (2015)

Instructor: Tandy Warnow, Founder Professor of Engineering

This is the description of the 2015 CS598/BioE598 AGB course. The 2016 course description is located at 598-2016.html.

Office hours: Mondays 10:00-11:45AM in 3235 Siebel; however, these will sometimes be moved due to travel or faculty candidate job talks. No office hours Monday March 30, 2015 (replaced by Monday, March 23, 2015, 10-11:45 AM) or April 13, 2015 (replaced by Tuesday April 14, 2015, 9-10:45 AM). Extra office hour Thursday May 7, 2015, 10:30-11:45 AM.

Course location: TR 11:00 AM - 12:20 PM, 1109 Siebel Center for Computer Science.

Course description: The main focus of the course is on phylogeny (evolutionary tree) estimation, but the course also covers the related problems of computing multiple sequence alignments, genome assembly, and analyzing microbiomes. Students will learn the mathematical and computational foundations in these areas, read the current literature, and do a team research project. The techniques involved include discrete algorithms, graph theory, simulations, and probabilistic analysis of algorithms. The course is appropriate for doctoral students in computer science, computer engineering, bioengineering, mathematics, and statistics; doctoral students in the biological sciences are also welcome, and will have different homework and exams.

Course textbook : Introduction to Computational Phylogenetics. This is a draft, and will evolve over the semester!

Pre-requisites: No biology background is required, but students should have some mathematical maturity, and at least one undergraduate course in algorithm design, data structures, or probability theory.

Students from departments outside Engineering, CS, Math, and Statistics: The course will be very mathematical, and being able to understand proofs and design methods with provable guarantees is the main point of this course. If you do not have the equivalent of an undergraduate degree in math, statistics, computer science, or some other engineering program, the course may not be appropriate for you. However, if you are a PhD student doing research in an area that relies strongly on phylogeny estimation, then please see me to discuss whether this course is appropriate for you.

Homework policy : Homeworks are due in class by 11:10 AM; homeworks handed in on time can receive full credit. Homeworks handed in after the deadline but before 24 hours after the deadline receive 80% of the grade. Homeworks handed in after 24 hours but before 48 hours receive 60% of the grade. No homeworks will be accepted after 48 hours past the deadline. The single worst homework grade will be dropped. You are encouraged to work with other students on the homework, but if you do this, this is what you should do. First, indicate on the homework who you worked with. Second, do not look at the other homework solutions when you write your own solutions; this includes not looking at someone else's write-up of a critique of some literature. Third, and more generally, must write your homework solutions entirely on your own, using your own language. Please do not under any circumstances copy homework solutions from anyone else, or let anyone copy from you.

Academic integrity: You are expected to abide by the university academic integrity standards, which means (among other things) that you should never copy anyone else's homework nor let anyone copy your homework. This is particularly important for your final project, especially if you refer to the scientific literature in your project. You must also never plagiarize, which means (among other things) that any text that you copy from another document must be properly attributed (with quotation marks around the copied material, and citation to the document from which you have copied the material). Even paraphrasing can count as plagiarism. All violations of academic integrity standards will be reported to the appropriate university offices. Serious violations will result in a failing grade for the course. Please see this page for a brief discussion of this issue, and the real academic integrity page.

Grading :

Reading Assignments: You are expected to do the assigned reading. This includes assigned material from the textbook, but also the scientific literature that I assign as reading.

Quizzes: These will be short (10 minute) quizzes, meant to confirm basic understanding of a technique or concept. If you have done the reading and homeworks, they will be straightforward. The worst quiz grade will be dropped.

Final Exam: This will be a closed book, comprehensive exam. Please see this review document.

Final Project: The course requires a final project of each student. You are strongly encouraged to do a research project, but you can also do a survey paper on some topic relevant to the course material. In both cases, your project should be a paper (of about 15 pages) in a format and style appropriate for submission to a journal. Research projects can involve two students, but survey papers must be done by yourself. Grades on the final project depend upon the kind of project you do. For a research paper, your grade will be 30% writing, 40% scientific/algorithmic rigor, and 30% impact. If you do a survey paper, the grade will be 30% writing, 30% summary of the literature you discuss, and 40% commentary (i.e., insight, critical and thoughtful discussion of the issues that come up). The final project counts for 15% of your course grade, and will be due on May 7, 11 AM, in hardcopy and in email. You must give this to me directly - in class or in my office hours. See this page for a list of possible final projects.

Class Presentation: Pairs of students will present scientific papers to the class. You will have 15 minutes for the presentation, with 10 minutes for questions. You will need to prepare a PPTX or PDF file for your presentation one week before your scheduled presentation, and will get feedback on the file from the instructor before you give the presentation. This counts for 5% of your final grade. See list of papers that you have each selected to present.

Course Schedule and Homework Assignments