CPBS 7711:
Methods and Tools in Biomedical Informatics

Tuesdays and Thursdays, 1-2:30pm
RC-1 South Tower, Room L18-6106
Anschutz Medical Campus, UC Denver

Prof. Larry Hunter  
Office: RC-1 S. Room L18-6101  
Phone: 303-724-3574  
E-mail: Larry.Hunter@ucdenver.edu  
Office hours by appointment  

Gargi Datta, TA   
E-mail: gargi.datta@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

Course description 

An introduction to the theory and practice of bioinformatics and computational biology. Topics include: the analysis of macromolecular sequences, structures, gene expression arrays, proteomics, and management of the biological literature. Requirements and prerequisites

Goals for the course: The course will familiarize students with the tools and principles of contemporary bioinformatics. By the end of the course, students will have a working knowledge of a variety of publicly available data and computational tools important in bioinformatics, and a grasp of the underlying principles that is adequate for them to evaluate and use novel techniques as they arise in the future.

This course is also the beginning of 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 many of the instructors in the computational bioscience program. Prof. Hunter is the course director; please raise any concerns or questions about the course with him. If you have questions about the materials presented, please start by talking with the T.A.

Much of the material presented in this course will be in the form of lectures. Generally, we dislike lecture courses, but there is so much material that you have to know in order to be a well educated researcher in bioinformatics (and to pass the preliminary exam!) that we feel we have no choice. Do know that we want you to ask questions, raise topics you'd like to know more about, and otherwise make this course more your own.


  • Check this area for announcements about the course.


Each of the following topics will be covered in one or more class lectures. This list is tentative until the lecture is posted. Lecture notes, readings and external links will be posted here before or after each class depented on speaker preference. The professor for each topic is indicated by last name. Classes will be held in RC1N - P18 6123.

8/26/14 Welcome/What is Bioinformatics Hunter
Educational Mission

8/28/14 Sci Comm: Class Project Overview Hunter
NIH's Grants information page
NIH's general review process. Pay particular attention to the Review Criteria.
NIH's information page for peer reviewers and applicants. There is a FAQ, writing advice, and tips.
Martin Kryzwinski's great web site for making better figures.
9/2/14 Genetics Pollock
Link to Powerpoint
9/4/14 MolBio databases Dowell
Link to Powerpoint

9/9/14 Expression Array Analysis Phang
Link to Powerpoint

9/11/14 RNAseq/ChipSeq/Methylseq De
Link to Powerpoint


9/16/14 Genome Analysis Costello
Link to Powerpoint

9/18/14 SciComm: How to Propose Research and Review Proposals Hunter

9/23/14 Computational Phylogeny Pollock

Link to Powerpoint        

9/25/14 Microbiome and Metagenomics Lozupone
Link to Powerpoint

9/30/14Software Testing Cohen
Link to Powerpoint

10/2/14 Machine Learning Leach
Link to Powerpoint

10/7/14 Sequence Search and Alignment Miller
Link to Powerpoint Link to Paper

10/9/14 Multiple Sequence Alignment Pollock
Link to Powerpoint

10/14/14 Sequence Assembly and NextGen sequencing Leach
Link to Powerpoint

10/16/14 Statistics Kechris
Link to Powepoint

10/21/14 Protien Structure and Prediction Strong
Link to Powepoint

10/23/14 Molecular Mechanics, Dynamics, Docking Strong
Link to Powepoint

10/29/14 PPI Networks Goldberg--WEDNESDAY
TIME DIFFERENT--12:30pm start in normal location RC1 S6106
Link to Powepoint Link to Ted Talk Lecture

10/30/14 TED Talks #1 (De, Hunter, Leach, Miller, Pollock)
HELD IN RC1 North 6107 Robinson Conference Room

11/4/14 BioViz Goerg

11/6/14 TED Talks #2 (Cohen, Dowell, Goerg, Lozupone, Tabakoff)
HELD IN RC1 North 6107 Robinson Conference Room

11/11/14SciComm: Reviewing Journal Articles Kechris
Link to Powerpoint Link to Journal Article Link to Assignment

11/13/14 TED Talks #3 (Costello, Kechris, Phang, Strong)
HELD IN RC1 North 6107 Robinson Conference Room


11/18/14 Knowledge-based Analysis Hunter

11/20/14 BioNLP Cohen
Link to Powerpoint #1 Link to Powerpoint #2 Link to Powerpoint #3

11/27/14 NO CLASS--Thanksgiving Holiday

12/2/14 SciComm: Present Reveiws of Journal Articles Kechris

12/4/14 SciComm: Presenting Research Orally/Conference Participation Hunter
SciComm: Scientific Writing Wethington

12/9/14 Present Project Proposals (All Faculty)


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, and an oral presentation of the project plan. The project will be executed in 7712 in the 2nd semester (including a presentation of a progress report, 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. The dedication and intensity you bring to these tasks is a good predictor of your likely success as an independent researchers, 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 (yes, including core).

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