Genomics Spring 2018 Course Description

This course is designed for beginning students who want to become familiar with the basic concepts and applications of genomics.  The course covers a wide range of topics including how genomes are mapped and sequenced as well as the latest computational and experimental techniques for predicting genes, splice sites, and promoter elements.  High throughput techniques for ascribing function to DNA, RNA, and protein sequences including Next Generation Sequencing, interspecies genome comparisons and genome-wide knock-out collections will also be discussed.  Finally, the use of genomic techniques and resources for studies of human disease will be discussed.

A heavy emphasis will be put on students acquiring the basic skills needed to navigate databases that archive sequence data, expression data and other types of genome-wide data.  Through problem sets the students will learn to manipulate and analyze the large data sets that accompany genomic analyses by writing simple computer scripts. While students will become sophisticated users of computational tools and databases, programming and the theory behind it are covered elsewhere, in Michael Brent’s class, Bio 5495 Computational Molecular Biology.

Because of limited space in our teaching lab, enrollment for lab credit will be limited to 24 students. Priority will be given to students in the DBBS program. Others interested in the course may enroll for the lectures only. If you have previous experience in computer programming, we ask that you do not enroll for the laboratory credit. To enroll in just the lecture section, register for 3 credits. To enroll in both the lecture and lab sections, register for 4 credits.


Mon, Wed 10:00-11:30am

4th floor classroom (room 4001B), McKinley Scott Research Building, 4515 McKinley Ave.

Computer Lab

Fri., 10:00-11:30am

4th floor classroom (room 4001B), McKinley Scott Research Building, 4515 McKinley Ave.

Course Masters

Ting Wang, twang@genetics.wustl.edu, room 5211, McKinley Scott Research Building, 4515 McKinley Ave.
Donald Conrad, dconrad@genetics.wustl.edu, room 6213, McKinley Scott Research Building, 4515 McKinley Ave.

Teaching Assistants

Alan Du, Gervette Penny, Nicolette Laird, Wenjun Kong

Bio5488 TA E-mail, bio5488wustl@gmail.com. Please use this email to contact the TAs.

TA Office Hours

Mondays 11:30am-12:30pm and by appointment, 4th floor classroom (room 4001B), McKinley Scott Research Building, 4515 McKinley Ave.
*Due to room reservation conflicts, office hours may be held in room 5001C/D McKinley Scott Research Building. Email notice will be sent out in case of location changes.
**Please e-mail if you will be coming after the first 30 minutes**

Python Help Sessions 

Starting 1/23, Tuesdays 5:30-7:00pm 6001B McKinley Scott Research Building, 4515 McKinley Ave.

Snacks will be provided as well as help with homework assignments from tutors!

Discussion Forum

Please use the google sheet (link to come) to post questions about the lectures/assignments. Note there are tabs at the bottom of the sheet for questions on each section of the class (material for Exam #1 and material for Exam #2), as well as for each homework. It’s likely that if you have a question, one of your classmates will have the same one, so this forum should serve as a resource for everyone!

Textbooks and Resources

Although there will be a heavy emphasis on bringing students up to speed in the computational skills necessary to analyze genome-wide data, we do not assume that students have extensive computer skills.  Those students who are not familiar with command line operating systems (Unix, Linux) or basic programming should should look through John McCutcheon’s Linux Primer.
Here is a quick unix reference sheet.

This class will teach students to write simple scripts using Python.

Please install software as instructed prior the first lab section if you are planning to take it.

Assignment Policies 

Please see this link for assignment policies.

Page last modified 12/29/2017.