Jeff Thompson - Denison University

From GEP Wiki
Jump to: navigation, search

Genomics at Denison University

Course Structure

"Genomics" was offered for the first time at Denison University during the Spring 2008 term, and was offered again in Spring 2011 and Spring 2013. The course is a four-credit upper level elective for Biology majors (and others that have completed the required Biology "core" courses). The course was structured to meet two times per week for 80 minutes lecture periods, on Tuesdays and Thursdays, and an additional three hour "lab" period Thursday afternoons. Every other Thursday, the morning "lecture" period was used as a split-class journal discussion/computer work time, to provide additional times to work on the laptops and enable discussions with smaller groups. Fifteen students registered for the course, primarily junior and senior Biology and Biochemistry majors.

The "laboratory" portion of the course revolved around a series of major lab projects. The first is a sequence assembly project, not connected to the GEP. Students assembled ~10 kb contigs of sequencing data spanning the upstream region of the beta-globin gene cluster of a variety of vertebrate species, which they subsequently used for comparative analysis between species to identify putative regulatory elements. The class used SeqMan (DNAStar, Inc.), and sequencing data were obtained from the Trace Archives database at NCBI. The class spent four weeks on this project, culminating in a short publication style report (2008, 2011) or an oral presentation (2013).

The second project involved the annotation of sequences from the D. erecta 3L chromosome (Spring '08), the D. grimshawii dot chromosome (Spring '11), and the D. biarmipes dot chromosome (Spring '13).  Each student worked independently on their own sequence in Spring '08, while in Spring '11 and '13, students worked in pairs on assigned sequences.  In the most recent offering, four weeks of the course was dedicated to this work (3 hours per week in lab, plus some additional "lecture" class time). In addition to gene model development, students were also provided instructions for additional analyses, including ClustalW analysis, UTR mapping, repeat analysis, etc. Students were asked to develop their own specific questions that they wished to analyze about their sequences, and to select appropriate analyses to answer these questions. As with the first project, students were required to write a formal publication style laboratory report on their work (2008, 2011) or an oral presenation (2013).

A third project was added to the course in 2013, a transcriptome analysis of a yeast strain that possesses a temperature sensitive mutation in histone H3.  Working in pairs, students isolated mRNA from wildtype and mutant strains at the non-permissive temperature, which was subsequently analysed using Affymetrix microarrays, done through the Microarray Facility at the James Cancer Center at The Ohio State University.  One week was spent purifying the mRNA, and second week was used to do the data analysis.  A third week was used to take a field trip to the microarray facility to see how the work is done.  The project culminated in a short written report.


For the most part, the first run of this course went reasonably well. A decent balance of topics was achieved, although the coverage on genome expression at the end was rushed and shortened relative to the original plans. Journal discussions were lively, and connected well with topics covered in class. Both lab projects worked quite well. Students admittedly found both projects to be challenging, and it took them several weeks to become acclimated before things began to move along. I had two teaching assistants in Spring '08 who had completed the GEP training course (but had obviously not taken the course itself), which helped a lot. But because of the time between offerings, no TAs were used in Spring '11 and '13 (which did not pose any notable prob).  The 2013 course is currently in progress, and is going well.  I have made a pedagological shift to oral presentations in this course, in part as a means of diversifying the types of work that students do in my upper-level courses.

Course Syllabus (2013 version)

Genomics is the study of the entire genetic contents of a given cell or organism, with the ultimate goal of understanding how all of the genes in a given genome cooperatively function and interact with one another to orchestrate the biological activities in the organism. This course will cover fundamental concepts in genomics, ranging from how whole genome sequences are assembled, how potential genes are identified and characterized within the genome, how genomes differ within and between species, how genomes are functionally organized and expressed, and how genomes evolve over time. The laboratory component of this course will be a mix of computer-based and “wet lab” multi-week projects, including participation in a collaborative research project with the Genome Sequencing Center at Washington University in St. Louis. There will be a notable emphasis on oral communication in this course, with multiple presentation and discussion opportunities incorporated into the curriculum.

General Course Information:

Instructor: Dr. Jeff Thompson
Office: Talbot Hall 413
Phone: ext. 5581
Lectures: TR 10:00-11:20 AM Talbot 210
Lab: R 1:30-4:20 PM Talbot 210
Office Hours: MF, 3-4 pm; T, 1:30-2:30 pm

Students are welcome to meet with me individually, as needed, during the office hour times listed above. Scheduled meetings at other times are welcome as well. My weekly schedule can be accessed via the Denison Google Calendar system (instructions are posted on Blackboard); find an open time and let me know when you would like to meet with me. I am here to help you, and I hope you will make use of my availability to maintain a strong performance in this course.

Text & Materials: The textbook selected for this course is Genomes, 3rd Edition, by T.A. Brown (Garland Science; ISBN 9780815341383). Most handouts and other miscellaneous documents will be made available on the Blackboard web site or in class. I also recommend the purchase of a USB flash drive for storage/backup of computer data generated in the lab.

Lectures: Attendance at all lectures is strongly recommended. Lecture handouts covering ~2 weeks of material will be posted on Blackboard. These handouts include a topical outline, copies of images presented in class, recommended text readings, and other relevant information. It is advisable to bring this handout to class for note-taking purposes.

Exams: Two exams will be administered in class during the semester, as indicated on the course schedule (see below). Each exam will cover the material from the previous ~5 weeks of class, focusing on comprehension of fundamental concepts and application of concepts to analytical problems. A cumulative final exam will be given on Wednesday May 1st, 2-4 pm.

Lab Projects: Laboratory work completed for this class will be primarily computer based, making use of online genome databases and DNA sequence analysis programs. There will be three multi-week projects: the assembly of a partial genomic sequence from raw DNA sequencing data available online, a compositional analysis (i.e. “annotation”) of a genomic DNA sequence, and a microarray “transcriptome” analysis of a mutant yeast strain. The first two projects will culminate with oral presentations (the last project will require a short written analysis); details on the projects and the presentation requirements will be posted on Blackboard.

The annotation project is part of a collaboration with the Genomics Educational Partnership (GEP). GEP is a consortium of faculty from around the country (including myself) that develops large-scale genomic research projects for use in undergraduate courses, coordinated through the Genome Sequencing Center at Washington University in St. Louis. Students who participate in GEP projects have the potential to be co-authors on primary research papers published by GEP that make use of these data. Details on the requirements for becoming a co-author will be outlined in the corresponding lab project handout.

“Adopt a Genome” Presentations: Pairs of students will “adopt” a species whose genome has been sequenced and analyzed. Relevant primary literature on the genome of the species will be identified, and each group will give a presentation to the class during the last week of the semester on their findings. Specifics on the project and the presentation format will be addressed in a separate handout posted on Blackboard.

'Journal Article Discussio'n: Five Thursdays will be dedicated to discussion of primary research articles related to topics covered in the lecture. The discussions will be held as split-class sessions (back-to-back sessions with half of the class at one time). Students are expected to read papers before class and actively participate in the discussion. Students will be expected to use the other half of the discussion period for lab/computer work. Guidelines regarding discussion expectations are posted on Blackboard.

Late Work/Missed Exams: Timely completion of work is an essential component for success in this class. All assignments are due on the date indicated by the instructor, and it is your responsibility to make sure that your work is turned in on time. Any work turned in late will be subject to a 10% per day deduction from the total possible number of points. Any exceptions to this policy must be arranged with the instructor prior to the due date, and will only be granted for extenuating circumstances, at the discretion of the instructor.

Typically there are no make-up opportunities for missed in-class exams, regardless of the circumstances (it simply takes too long to write new exams). For any missed exam that is deemed “excused” by the professor (documented illness, family emergency, etc.), the value of that exam will be added to the value of the final exam (i.e. if you miss an exam that is worth 20% of the final grade, the final exam value will be increased from 25% to 45%). Unexcused exam absences will result in a “zero” for that exam.

Grading: Scores from various assignments and activities will be used to determine
the final course grade, based on the following distribution:

Semester Exams (2) 15% each, 30% total
Final Exam 20%
Lab Project Presentations (2) 10% each; 20% total
Lab Data Sheet 2%
“Adopt a Genome” Presentation 13%
Journal Discussion Participation 3% each; 15% total

Letter grades will be assigned based on the following scale: A-/A = 90-100; B-/B/B+ = 80-89.9; C-/C/C+ = 70-79.9; D-/D/D+ = 60-69.9; F < 60. Breakpoints between the +/- grade modifiers will be established at the end of the semester, based on the distribution of the overall class scores. The minimum score for a particular grade may be shifted down at the professor’s discretion, but it will not be shifted up (i.e. the minimum score for an A- might be moved below 90, but it will not be raised above 90). Additional variables, such as trends during the semester (i.e. steadily improving/declining scores) and degree of engagement in the course may be taken into account when determining the final grade of individuals who are “on the edge” between grades. Feel free to contact me at any time to determine your current grade status.

Course Evaluations: Course evaluations are to be completed online in class on Tuesday April 16th. All students are required to complete an evaluation for this course. These evaluations play an important role in aiding the professor in the future design of this course, as well as being used by the Denison administration for tenure and promotion decisions. Please take this responsibility seriously in providing an honest and thoughtful evaluation of the course.

Disability Statement: Any student who feels he or she may need an accommodation based on the impact of a disability should contact me privately as soon as possible to discuss his or her specific needs. I rely on the Academic Support & Enrichment Center in 104 Doane to verify the need for reasonable accommodations based on documentation on file in that office.

Academic Integrity: It is expected that all students in this class will understand and embrace academic integrity to the highest extent. Academic dishonesty is defined as “intellectual theft”. It includes, but is not limited to, providing or receiving assistance in a manner not authorized by the instructor in the creation of work to be submitted for evaluation. All work done for this course must be completed by you and only you (unless indicated for a particular assignment), and all sources used in completing assignments must be properly cited, following the guidelines in The Bedford Handbook (see Chapter 52). Any assignments that are found to be in violation of this code (work copied from others students, plagiarized from published works, etc.) will be given a “zero”. Furthermore, as indicated in the Code of Academic Integrity (see, instructors must refer all acts of academic dishonesty to the Associate Provost, and may result in failure of the course, suspension, or expulsion. Neither ignorance nor carelessness is an acceptable defense for violating academic integrity policies.

Course Schedule (2013)

Week 1: Jan. 15. 17

T, R: Genome Assembly
Lab: Assembly and Analysis of beta-Globin Upstream Sequences from Various Vertebrates

Week 2: Jan. 22, 24

T: Assembly, cont.
R: journal discussion/computer time
Lab: Assembly project, cont.

Week 3: Jan. 29, 31

T, R: Genome Annotation
Lab: Assembly project, cont.

Week 4: Feb. 5,7

T:  Annotation, cont.
R: journal discussion/computer time
Lab: Assembly project, cont.

Week 5: Feb. 12, 14

T, R: Genome Anatomy
Lab: Assembly project presentations

Week 6: Feb. 19, 21

T: Exam I
R: Anatomy, cont.

Week 7: Feb. 26, 28

T: Anatomy, cont.
R: journal discussion/computer time
Lab: Annotation of a dot chromosome sequence from Drosophila biarmipes

Week 8: Mar. 5, 7

T, R: Genome Expression
Lab: Dot Chromosome Annotation, cont.

Mar. 11-15

No Classes: Spring Break Week

Week 9: Mar. 19, 21

T, R: Expression, cont.
Lab: Dot Chromosome Annotation, cont.

Week 10: Mar. 26, 28

T: Expression, cont.
R: journal discussion/computer time
Lab: Dot Chromosome Annotation, cont.

Week 11: Apr. 2, 4

T, R: Genome Evolution
Lab: Annotation project presentations

Week 12: Apr. 9, 11

T: Exam II
R: Evolution, cont.
Lab: trip to OSU microarray facility

Week 13: Apr. 16, 18

T: Evolution, cont.
R:  journal discussion
Lab: Microarray analysis of mutant yeast transcriptome

Week 14: Apr. 23, 25

T, R: "Adopt-a-Genome" presentations
Lab: Evolution, cont.

FINAL EXAM: Wednesday May 1st, 1-4 pm