Evolutionary Genomics

BEES 608J/BIOL608J, Spring 2003, 1-2 credits


Instructors: Dr. Sara Via (sv47@umd.edu) and Dr. Gerald Wilkinson (gw10@umd.edu)

Meetings: Wed 12-2, Room 1111, Plant Sciences Bldg

Required Text: A Primer of Genome Science by Greg Gibson and Spencer Muse, Sinauer 2002.

Recommended Background: Coursework in genetics.

Overview: The goal of this graduate seminar is to learn how new techniques for measuring gene and protein expression can be used to address and answer evolutionary questions. Participants will use a new book, A Primer of Genome Science, to identify techniques of interest. After an organizational meeting to decide on topics, recent papers which apply these techniques to evolutionary problems will be discussed each week. Examples of potential topics include EST sequencing, subtractive hybridization, serial analysis of gene expression, cDNA microarrays, quantitative PCR, SNP genotyping and reverse genetic approaches, such as RNA interference.

Format: This seminar course will meet once a week for 2 hours. After assessing the background and interest of individuals in the class, a schedule of topics for the semester will be developed and discussion leaders will be assigned for the semester. Each week one member of the class will be responsible for leading discussion on the topic for the week. Each week part or all of one book chapter will be assigned for all members of the class to read and, on occasion, we may also require that everyone attempt to work through some of the exercises that are available online at http://www.sinauer.com/genomics. In addition, pairs of class mates will read at least one additional paper on their own and come prepared to summarize the content of that paper to the group.

Grading: If enrolled for one credit, grades will be based on attendance, participation in discussions, and presentation. If enrolled for two credits, a short grant proposal must also be completed. The proposal should be between 2,000 and 2,500 words (no more than 10 double-spaced pages). The proposal must contain a short introduction to the conceptual issue rather than full literature review, and should emphasize why the chosen approaches/techniques are appropriate for the question, and how they will provide the answer.

Additional Sources

Kamberova, G. and Shah, S. 2003 DNA Array Image Analysis: Nuts and Bolts

Knudsen, S. 2002 A Biologist's Guide to Analysis of DNA Microarray Data. John Wiley & Sons, New York. [review]

Speed, T.P. 2003 Statistical Analysis of Gene Expression Data.


Trex genome site: http://www.ensembl.org/withdrawn_trex/

Class Schedule

Date

Topic (click for assignment)

Reading

Presenters

Feb 5

Genome projects

Ch. 1

Wilkinson

Feb 12

Genome sequencing

pp. 63-90

Mignault

Feb 26

Genome annotation and gene families

pp. 91-120

Zwiers

March 5

Microarrays

pp. 123-146

Washington

March 12

Differential display

pp. 147-158

Amitin, Cook

March 19

Guest presentation: Annotating the bee genome

Dr. Jay Evans

March 26

Spring break!

 

April 2

Transcriptome examples

pp. 160-175

Anand, South

April 9

SNP variation and applications

pp. 241-270

Pfeifer, Lesnik

April 16

Guest presentation: Microarray methods

 

Dr. Eric Baehrecke

April 23

SNP discovery and genotyping

pp. 271-292

West, Johns

April 30

Functional proteomics

pp. 183-212

Christianson, Russo

May 7

Functional genomics

pp. 212-236

Hrrbo, Coffin

 

 

 

 

May 14

Integrative genomics

Ch. 6

Class