The University of Arizona

ECOL 453/553
EVOLUTIONARY & FUNCTIONAL
GENOMICS
 

COURSE INFORMATION

FALL 2008

ECOL/BIOC/MCB 453/553
Evolutionary and Functional Genomics   4 units

Course coordinator: Michael Nachman

Lecture: Tues Thurs 2:00 – 3:15, Biosciences West (BSW) 219
Computational Lab: Tues Thurs 3:30 - 4:50, Koffler Building (KOFFL) 209

ON THIS PAGE:

Overview
Instructors
Reading
Required Activities
Encouraged Activities
Grading
Policy on Cheating
Research Projects (including deadlines)

OVERVIEW

The life sciences are being transformed by massive infusions of sequence data together with new computational advances and database capabilities. Central to this transformation are the determination of complete genome sequences and the exploitation of these sequences to answer biological questions. This exploitation involves integration of the new sequence information with established methods and information in genetics. However, because much of genomics depends on comparative sequence analysis, an understanding of evolutionary processes is also essential. This course surveys the basic findings and approaches in the developing field of genomics. We will cover conceptual aspects as well as methodology and technical advances that are central to obtaining and exploring genome sequences. A consideration of how the evolutionary process shapes genomes will be a continuing theme in the course. This course is part of a graduate training program in Evolutionary and Functional Genomics, funded by the National Science Foundation. (UA IGERT program).

Organization:

The course consists of a lecture/reading portion and a hands-on computational portion. Lectures will be complemented by readings from textbooks and the primary scientific literature. In the computational portion, basic tools for exploiting genomic sequence databases will be introduced and put into use by students.

INSTRUCTORS

Lecure portion:

Main instructors:

Michael Nachman (Professor, Ecology & Evolutionary Biology) coordinator
nachman@u.arizona.edu, 626-4595, BSW 334
office hours: F 2-3, or by appointment

Howard Ochman (Regents Professor, Biochemistry & Molecular Biophysics)
hochman@email.arizona.edu, 626-8355, LSS 233
office hours: MWF 11-12, or by appointment

Michael Sanderson (Professor, Ecology & Evolutionary Biology)
sanderm@email.arizona.edu
office hours: to be announced

Computational Lab Portion:

Instructor:

Travis Wheeler (Dept. Computer Science)
twheeler@cs.arizona.edu, BSW 419
office hours: M 1-2:30, or by appointment

Teaching Assistant:

Patrick Degnan (Dept. Ecology & Evol. Biology)
pdegnan@email.arizona.edu, LSS 2nd floor lobby
office hours: W 2-3:30, or by appointment

READING

Text for lecture portion:

A Primer of Genome Science. 2nd ed. By Greg Gibson and Spencer V. Muse. 2004. Sinauer Associates, Sunderland MA.

Supplemental (optional): Genomes 3. By T. A. Brown. 2006. John Wiley and Sons. This is a useful molecular biology text that has a genome-level orientation. It is a good reference book in molecular genetics. An earlier edition, Genomes 2 (2002), is available on line; see the course website.

Three additional texts will be on reserve at the science library for the computational biology lectures by Prof. Sanderson. These are intended to provide further background and additional detail regarding these topics for the interested student. The texts are:

Ewens, W. J., and G. R. Grant. 2005. Statistical methods in bioinformatics, 2nd edition. Springer, New York. QH 506 E94S 2005

Felsenstein, J. 2004. Inferring Phylogenies. Sinauer Press, Sunderland, MA. QH83 .F45 2004

Gusfield, D. 1997. Algorithms on strings, trees and sequences. Cambridge University Press, New York. QA76.9.A43 G87 1997

Additional readings:

REQUIRED ACTIVITIES: Students are expected to —

Attend all lectures and all laboratory sessions. Please inform Nachman/Wheeler by email in advance if you must miss a session due to illness or emergency.

Complete the required reading before the associated class section. In a few cases, the readings will be changed in advance of the lecture; changes will be announced in class and on the website.

Participate in class discussions on the readings.

Complete the assigned exercises individually, without conferring with other students or other individuals, and turn them in on time.

Complete the midterm exam and final exam.

Participate in lecture, including one in-class presentation (grads only).

Complete the project/poster/short report on time (see guidelines).

ENCOURAGED ACTIVITIES: The following will help you learn more —

Think and ask questions during lectures. Don't assume that you will figure it out later from notes or from what is posted on the web. The Powerpoint slides are supplementary to the lectures and cannot be used as a substitute.

Ask questions outside of lectures.

Read beyond the assigned readings. Among the best journals to check out are Science, Nature, PLoS-Biology, Proceedings of the National Academy of Science, Bioinformatics, and Genome Research. Use PubMed to find papers on various topics in genomics.

Spend time exploring on-line resources in genomics; we will introduce you to some. The textbook site has useful material and links (http://www.sinauer.com/genomics/).

Form discussion or help groups to go over readings, lecture material, or computer exercises. For exercises, you can discuss questions but students must answer them individually. (See Grading, below.)

Attend seminars on campus in the area of genomics. We will announce some in class.

GRADING

Further explanation of grading system:

Homework exercises are complementary to lecture material and must be completed on time. Homework exercises may have extra questions for the 553 students that are not required for the 453 students. All submitted material must be the work of the individual student, writing the answers alone, based on their own understanding. For homework exercises, students can discuss the material in groups, but the completion of the answers must be done alone and independently.

Research projectpoints (required for 553 only) will be divided between overall project content and scope (9/15), and communication of the project including proposal and presentation of idea to class (3/15), report (3/15).

*Students enrolled as 453 may do a project and receive some points; please contact instructors.

Class participation points for grad students (enrolled in 553) will be awarded based on (1/3) participation in class discussions. This includes showing evidence of having completed and thought about assigned readings, one in-class presentation, (1/3) participation in the computer lab, and (1/3) contribution to the projects.

For 453 students, the participation points will be awarded based on between (1/2) participation in lecture discussions (showing evidence of having completed the readings) and (1/2) participation in lab discussions.

FINAL GRADES:

Scores will correspond to grades as follows: 91-100 = A, 81-90 = B, 71-80 = C, 61-70 = D, 60 and below = E.

Policy on Incomplete Grades, Late Assignments:

No grades of "I" will be given except in cases of unforeseeable emergencies. Work not turned in will receive zero points. Late assignments will be penalized during grading except in cases of documented emergency.

POLICY ON CHEATING

As stated above, students are required to write exercises and exams independently. Cases of cheating, or of helping others to cheat, will be penalized to the maximum extent allowed at the University. We encourage discussion of problem sets, but the writing of the answers must be done by individual students by themselves. The exams must be done individually without discussion. No copying, pasting, or paraphrasing based on published or internet materials is allowed. Your words should be your own, based on your own understanding of the material.

On the projects, students are encouraged to discuss the problems or methods with other class members, instructors or others and to seek advice from any available source.

RESEARCH PROJECTS - Required for graduate students, optional for undergraduates

Students will work in pairs but are encouraged to discuss their projects with instructors, students (or anyone else). Project topics will be suggested; students may choose their own with our approval. Students should write a 1-page proposal for their project, due (date to be announced), and the in-class presentations of the project ideas will also occur on that day. This proposal (and the presentation) should include the idea being tested or explored, a statement of the previous findings relevant to the project, the data that will be used, and the methods that will be applied. A few relevant literature references should be cited.

Each grad student will turn in a short report (8-10 pages) that outlines the project and its main results, plus conclusions.

Major deadlines for Research Projects (to be announced):