CPBS 7712: Research Methods in Biomedical Informatics
Spring 2012

Tuesdays and Thursdays, 1-2:45pm
RC-1 North Tower, Room P18-6123
Anschutz Medical Campus, UC Denver

Course Director: Prof. Larry Hunter  
Office: RC-1 S. Room L18-6100  
Phone: 303-724-3574  
E-mail: Larry.Hunter@ucdenver.edu  
Office hours by appointment  

Purpose This course is central to the educational mission of our Computational Bioscience PhD program. Please take the time to review the educational mission statement

Requirements and prerequisites

  • CPBS 7711 with a grade of B or higher, or permission of the instructor.  
  • Computational requirement: Access to a computer with an internet connection and the ability to create programs. In general, you will need access to the computational resources necessary to accomplish your course project. If additional university supplied tools are necessary, please contact the instructor as soon as possible.

Course description How to plan, develop, execute and report on research in computational biology. In this course, each faculty member in the computational bioscience program will present a number of lectures on the research currently being conducted in his or her laboratory. Students will plan, execute and report on a research project of their own. This course is a stage in the transition from well-educated students to independent researchers. The work in the course involves a series of supervised activities that introduce the activities of research. These will include:
  • Formulating an effective research plan
  • Critiquing the research plans of others
  • Revising research plans in light of critique
  • Reporting on research results, orally and in writing
  • Reviewing manuscripts that report on research results  

This is a team-taught course. You will get a chance to meet and interact with each of the core faculty in the computational bioscience program. These faculty include:

Prof. Hunter is the course director; please raise any concerns or questions about the course generally with him. Specific questions about any lecture or other material should be raised with the presenting faculty member. Contact information for each faculty member can be obtained by following the above links.




Each faculty member will present the research in his/her lab in a series of consecutive lectures and discusions. At various points during the year, the students will present and review research plans, partial results, and final results.


1/24/12 Welcome/Intro (Larry Hunter)

1/26/12 Research in the Hunter Lab Readings Links

1/31/12 Hunter Lab

2/2/12 OPEN

2/7/12 Research in the Leach Lab Links Slides

2/9/12 Research in the Goldberg Lab

2/14/12 Research in the Pollock Lab Links

2/16/12 Pollock Lab

2/21/12 Pollock Lab (Dr. Todd Castoe) Slides Reading

2/23/12 Research in the Görg Lab Links

2/28/12 Görg Lab

3/1/12 Peer review of research plans

3/6/12 Research in the Strong Lab

3/8/12 Strong Lab

March 12-16, 2012 Spring Break No Class

3/20/12 Student presentation of revised research plans

3/22/12 Research in the Cohen Lab

3/27/12 Cohen Lab

3/29/12 Cohen Lab

4/3/12 Research in the Kechris Lab Links

4/5/12 Kechris Lab
4/10/12 Kechris Lab

4/12/12 Research in the Kahn Lab

4/17/12 Leach Lab Slides

4/19/12 Leach Lab Slides

4/24/12 Student presentations of project updates

4/26/12 TBA

5/1/12 Researach in the Phang Lab Links Slides

5/3/12 Phang Lab Slides

5/8/12 Research in the Dowell Lab Readings Links Slides

5/10/12 Dowell Lab Slides Slides
5/15/12 No Class Final Exam Week
5/17/11 Student final presentations


  • Due Feb 23 Proposal for the course project. Due via email to professor and all other students before the start of class.
  • Due March 1 Written critique and 15 minute oral critique of each course project proposal. Due via email before the start of class, cc'ing all other students.
  • Due March 20 Presentation of revised research project. Due via email before the start of class, and 15 minute presentations during class.
  • Due April 24 Presentation of progress on course project. Due via email before the start of class, and 15 minute presentations during class.
  • Due May 17 Final presentation of course project. Due via email before 11am, and 15 minute presentations during usually scheduled class time.


The goal of this course is to get you familiar with the use of bioinformatics techniques in addressing real scientific problems. Grading will be largely on the basis of a course project. The project will involve several stages: producing a project plan, revising your plan in light of critique, presenting a status report on your progress, a final oral presentation, and a final written presentation. In addition to this work, you will be required to produce written critiques of others' research plans, and of others' written presentations of research results. The dedication and intensity you bring to these tasks is a good predictor of your likely success as an independent researcher, so we will add a subjective component to your grade that reflects what the faculty believe is the level of effort and committment you show toward the work; this includes showing up for class prepared, participating actively in discussions and activities, and in your ability to get high quality work done in the face of the many other requirements on your time.

While it may be hard for you to wrap your head around, no one will ever care about the grades you get in graduate school (assuming you pass, of course). Now the important thing is to make the transition to producing significant, original research that will make an impact on a broad community. Your ability to master existing material (both in textbooks and in original research publications) is assumed, and will be tested during your preliminary exam. What we hope to teach in this course (and will be evaluating you on) is the development of a creative and scholarly approach to doing new science.

Honor Code

The Graduate School requires that this honor code be included in all course syllabi.

Education at the University of Colorado, Denver is conducted under the honor system. All students who have entered health professional programs should have developed the qualities of honesty and integrity, and each student should apply these principles to his or her academic and subsequent professional career. All students are also expected to have achieved a level of maturity, which is reflected by appropriate conduct at all times.

Note that our educational mission statement includes even stronger goals for your professional behavior. Please feel free to raise issues related to those goals in class.

Computational Bioscience Program home page | Professor Hunter's home page