**Math 591-- Discrete Mathematical Biology**

** Spring 2012, TuTh 3:00--4:15 PM, Room TBA**

**Instructor:** Seth Sullivant, office: 3114 SAS Hall, email: smsulli2@ncsu.edu

**Office Hours: ** W 1:30-2:30 PM, Th 1:00-2:00 PM

**Required Text:** None

**Recommended Reading:** Durbin, Eddy, Krogh, and Mitchison*, Biological Sequence Analysis, *Felsenstein, *Inferring Phylogenies*, Semple and Steel, *Phylogenetics*, Wakeley, *Coalescent Theory*

**Prerequisites: **MA 405, 407, and 425 or consent of instructor.

**Course Description: **This course will focus on the mathematical study of
biological sequences (i.e. DNA, RNA, proteins). The mathematical
tools for studying these objects come from discrete mathematics
including graph theory, combinatorial optimization, polyhedral geometry,
and algebra. We will learn to employ these tools to study traditional
problems of computational biology with a view towards the interesting
mathematics that arise. Topics we might cover include: gene annotation,
sequence alignment, tree reconstruction, phylogenetic models, RNA secondary
structure, and the coalescent. No special knowledge of discrete math
or biology will be assumed, all concepts will be explained in the
course.

** Schedule: ** Is available here.

** Homework:** Homework will be assigned weekly and is due in class on Thursdays. Students must write up their own solutions. Please indicate on your homework any sources that you used in preparing solutions (e.g. if another student helped with a solution, or you found the solution in a book). Students are required to prepare homework solutions in LateX. A file explaining how to prepare your homework can be found here. Homework assignments can be found here.

**Note Taking: ** As part of the course,
each student will be required to prepared detailed LateXed notes of at least
two lectures. These lecture notes will be displayed on the course website
so that other students can use them as reference. During a week that
a student prepares lectures notes they will be excused from turning in
the homework.

**Final Project: ** There will be a final
project in the class which will consist of reading a research paper in
discrete mathematical biology preparing a short summary of the paper.
Suggested papers will be posted on the course website.

**Exams: ** There will be no Exams.

** Grades: ** Grades will be based on Homework (50%), Note-taking Assignment (20%), and Final Project (30%).

**Attendance:** Students are expected to arrive on time, to contribute to group work and class discussions, and to stay until the class ends. Attendance at all meetings of the class is expected. Occasional absences will be approved if they meet University policies.

**Adverse Weather:** Announcements regarding scheduled delays or the closing of the University due to adverse weather conditions will be broadcast on local radio and television stations and posted on the University homepage.

**Cell Phones:** Pagers, cellular phones and other types of telecommunication equipment are prohibited from use during class. Make sure that any pagers, phones or other equipment are turned off during the class period. If you have a special need to have your pager or phone on during class, please let me know.

**Academic Integrity Statement: **Students are required to follow the NCSU policy . “Academic dishonesty is the giving, taking, or presenting of information or material by a student that unethically or fraudulently aids oneself or another on any work which is to be considered in the determination of a grade or the completion of academic requirements or the enhancement of that student's record or academic career.’’ (NCSU Code of Student Conduct). The Student Affairs website has more information.

**Students with Disabilities:** Reasonable accommodations will be made for students with verifiable disabilities. In order to take advantage of available accommodations, students must register with Disabilities Services for Students.

**Class Evaluations:** Online class evaluations will be available for students to complete during the last two weeks of class. Students will receive an email message directing them to a website where they can login using their Unity ID and complete evaluations. All evaluations are confidential; instructors will never know how any one student responded to any question, and students will never know the ratings for any particular instructors.

**LateX Resources:**

- Essential LateX
- Essential Mathematical LateX
- LateX 2e introduction
- LATEX Software and Documentation
- Easy to install LateX for Windows
- Easy to install LateX for Macs