Nate Mortimer

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Genomics at Illinois State University

Course Overview

This course is designed to introduce students to experimental approaches in genomics and bioinformatics. We will approach the material from both practical and theoretical viewpoints. Students will conduct original genomics research, including genome annotation and bioinformatic analysis of genome wide data sets. The course goals are to enhance critical thinking and computational skills through problem-solving, and to improve written and oral communications skills.

The course is intended for upper level undergraduate and graduate students.

Implementation

Fall 2017 is the first implementation of the parasitoid wasp genome project. There is an annotated schedule in the Syllabus section, and I will add more details at the end of the semester. 

Lessons Learned and Future Plans

Syllabus for BSC 355

Schedule

Week 1 Introduction to Gene Annotation

Week 2 Introduction to Gene Annotation

During these weeks the students learn to use the UCSC Browser and to do gene annotation using the Understanding Eukaryotic Genes material

Week 3 Beginning Annotation Project

In this week, I introduce the students to the research aspects of the project. This includes having the students read the primary literature for discussion in class (the Visser, et al. paper for the parasitoid wasp project). The students then come up with hypotheses about the project, and we discuss how they can be tested using genomics. We then talk about the different types of genomics analysis we can use (i.e. phylogenies, functional annotations, protein structure) and about how careful gene annotation provides the data we need for these analyses.

Week 4 First Gene Annotation/Lab Meetings

Week 5 Gene Annotation Project

Week 6 Gene Annotation Project/Lab Meetings

Week 7 Gene Annotation Project

The students spend several weeks completing their annotations. During these weeks I have a couple of lab meeting style meetings with each group. In the first meeting the students will outline their plan of action - how they will break up the work, their annotation workflow. The second meeting is a status update.

Week 8 Beyond Annotation

Week 9 Beyond Annotation/Lab Meetings

Week 10 Beyond Annotation/Presentations

In the Beyond Annotation section, the students use their protein sequence data from their annotation projects to explore protein evolution using phylogenetics, and protein function using KEGG and the Conserved Domain Database. During this time the students will have another status update lab meeting, and the GEP portion of the course concludes with a Presentation encompassing the Annotation and Beyond Annotation projects.

Week 11 Introduction to Galaxy

Week 12 Galaxy Project/Lab Meetings

Week 13 Galaxy Project

Week 14 Galaxy Project/Lab Meetings

Week 15 Galaxy Project/Presentations