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Math/Bio 563
Mathematical Genetics

University of IdahoWashington State University

Fall 2009


Dates
11/05/09
Homework 6 Homework 7 and Homework 8  are now posted.  See syllabus for due dates.
        
 
Students should be contacting us soon regarding their presentations!

Click (here) to read Steven A. Frank's paper highlighting Price's contribution to Evolutionary Genetics




 For information on commuting to and from the campuses click (here)
Syllabus, Reading
Assignments and Homework


Handouts


Textbooks


REQUIRED
Evolutionary Theory
Mathematical and Conceptual Foundations
by Sean Rice

A list of typos
for Rice



Suggested reference books

Gene Genealogies, Variation and Evolution
by Hein, Schierup and Wiuf


Coalescent Theory, An Introduction
by John Wakeley

UI Professor:
Paul Joyce 
Dept. of Mathematics
Initiative for Bioinformatics and Computational
Biology (IBEST) 

University of Idaho

WSU Professor:

Richard Gomulkiewicz 

Department of Mathematics,
School of Biological Sciences


      Washington State University
E-mail:
joyce@uidaho.edu

Office

Brink Hall 413 

Phone: 

885-6338 

Office Hours for Paul Joyce:
Monday and Tueday 3:30-4:30 pm
or by appointment
E-mail: 
gomulki@wsu.edu

Office:

Biology Office: Eastlick 391
Math Office:     Neill 227

Phone:

335-2527

Office Hours for Richard Gomulkiewicz:
Mondays from 2:30-3:30 in Eastlick 391
Wednesdays from 2:00-3:00 in 
Neill 227, and by appointment.

Class Meeting

Tuesday
5:00- 6:15 pm

 TLC 223
UI CAMPUS

Class Meeting

Monday
5:10:-6:25 pm
TODD 204
WSU CAMPUS



 


 

Course Goals
(1) Gain exposure to, and experience with, major topics and methods in mathematical genetics; 

(2) Survey classical and contemporary literature in mathematical genetics.
 
 

Course format:

We plan to achieve the goals of the course through a series of instructor led “workshops” topics in mathematical genetics during the first part of the course and student led group discussions during the second part of the course.  One or two readings will usually be assigned per topic: one for background and a second for discussion. 

 For workshops, an instructor will briefly motivate the topic, outline the analyses, and summarize the main results.  The class will then work through the reading(s) as a group, stopping to clarify steps, methods, or concepts that are ambiguous.  Ideally, students who understand a step/method/concept will do the clarifying.  Of course, the instructors will help regulate the flow of discussion and contribute lucid explanations as necessary!  The instructors will also suggest homework problems which all students will be expected to attempt.  For this workshop format to succeed, it is critical that every student works to understand the readings prior to class.  If, in the course of reading the material, you don’t understand something (e..g., a term, concept, manipulation, or technique) make a note of it and go through the remaining material as best you can.  Be sure to bring your notes to class.

Student-led group discussions will cover topics chosen by students (topics—which may involve original research—must be pre-approved by the instructors).  Leaders should prepare handouts and readings that their fellow students will read prior to the discussion.
 
 

 










Internet Resources

Java Demonstrations of
the coalescent Process

Grading Criteria

Half of the grade in this course will based on the quality of a  student planned and executed group discussion during the second part of the course.  The other half of your grade will be based on in-class participation.  Your participation grade will be based on 
(a) attendance, (b) the contributions you make during discussions (including asking and answering questions, and making thoughtful comments), and (c) attempting and solving any assigned homework problems. 
 
 

Reading  Assignments: Readings will be assigned from current and classical literature.  You will be expected to  have read the assigned paper and participate in discussing the material.  You will be assigned four or five questions about the reading.  You will be required to answer each of the questions. 
 

 

Computer Programs
for Coalescent Models

Lamarc

Genetree

A recombination program
 

Some Computer Programs 
used in  Phylogenetic Analysis


List of phylogenetic software
by Joe Felsenstein 
 
 

 

Web Resources

To your left are a number of interesting web sites with information and computer software.   If you find any  web sites that you feel would be of interest to your instructors and/or fellow students, let me know (joyce@uidaho.edu).  I would be happy to post them.



Commuting between the two campuses
 This course is a joint effort between WSU and UI.  Tuesday's class will be at the University of Idaho starting at 5:00 pm and Monday's class is at WSU beginning at 5:10 pm. The Wheatland Express Bus Service http://www.wheatlandexpress.com/commuterfall.htm.  can take you directly to the campus, however the last bus departs before our class ends.  We will discuss commuting options in class. 


Click on the following link for a picture of  Todd Hall 204.    For a WSU campus map click
http://www.wsu.edu/campusmap/<>

The teaching an Learning Center (TLC) is located off the Idaho Commons.  Proceed south from the bus stop about a block to TLC 223.
  Click here http://www2.dfa.uidaho.edu/ceis/parkingtest/Maps/ColoredCampusMap.pdf for a University of Idaho map.