Survey of Genome Technologies (Conjoint 546)


Instructor: Roger Bumgarner, Department of Microbiology

Contact info:, 206-732-6137


Course Syllabus Fall, 2012

This site will be updated several times during the quarter

Note!! - reading materials in the form of pdfs are from journals to which UW

has an electronic subscription. These pdfs are not to be redistributed to those outside the UW.


 Lecture Title

Sept. 25th, 2012

"First generation" sequencing technologies and genome assembly


Reading Materials:


United States Patent 4,811,218 Hunkapiller, et al. March 7, 1989


What is the future of electrophoresis in large-scale genomic sequencing?

C.P Fredlake Electrophoresis 2006, 27, 3689–3702


Sept. 27th,  2012

 Next Generation sequencing technologies (1)


Reading Materials:



Oct. 2nd, 2012


 Next Generation Sequencing technologies (2)


Reading Materials:


Homework assignment #1 – News and Views 




1)     - see for a description of the format for a Nature News and Views article

2)     Don’t just summarize the article, discuss the general importance at a higher level.

3)     Make it interesting – good title, good lead-in etc.

4)     Read 3-4 News and Views articles prior to starting to write your own.



Due by 11:59PM 10/10/11.




Oct. 4th, 2012

Single Molecule Sequencing Methods and Complete Genomics Technology



Oct 9th , 2012

DNA Microarrays and their Applications




Oct. 11th, 2012

Genotyping technologies




Quiz #1 – Due10/19 @ 11:59PM


Oct. 16th, 2012

Proteomics (part 1)


Reading materials:



 Oct. 18th , 2012


Proteomics technologies (part 2)


Reading Materials:


Oct. 23st, 2012

Technologies and Methods for Metabolomics

Reading materials:


Oct. 25th, 2012


Systems Biology: Methods for Network Inference





Quiz #2

Due Nov. 2nd, at 11:59PM.



Grades and grading philosophy

Grading for this class

30% Attendance - you can't learn if you don't attend.

10% You are expected to provide one potential question (and associated answer) for each reading assignment.  The question should be designed to measure whether someone has read and understood the reading assignment.  These questions will be used in the quizzes.  For each reading assignment, a question/answer combination should be emailed to me within 1 week of the lecture.

40% Two homework assignments - Homework will consist of preparing two reviews of articles provided (students will be able to select from a small list of 3-4 articles for each assignment). Reviews will be prepared according to the format Nature recommends for "News and Views" articles - see for a description of the format.

20% One midterm and one final quiz - these will be multiple choice exams and the questions will only cover the assigned reading materials. This is a mechanism to encourage you to read said materials.

Grading philosophy

My belief is that their are two primary roles of homework and/or exams:

1) A mechanism for the instructor to discover what he or she could improve upon - e.g. if most students can't answer a given exam or homework question, perhaps the instructor did not actually teach what he or she thought.

2) A mechanism for extending the instruction beyond what can be accomplished within the classroom time.

I have no desire whatever to separate students into different bins - the marketplace will do that soon enough. However, I am required to provide a grade for this course which is based on something that can be readily evaluated and defended. Hence the grading rubric above.