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Genomics Spring 2025 Course Description
This course is tailored for graduate students with a basic understanding of genomics who aim to deepen their expertise in advanced concepts and applications in the field. The curriculum covers a wide range of topics including the mapping and sequencing of genomes, the latest computational and experimental techniques for identifying genomic variants, and the study of epigenetic modifications such as DNA methylation and chromatin accessibility. Students will also delve into methods for inferring transcription factor binding sites and motifs. High-throughput techniques for ascribing function to DNA, RNA, and protein sequences, including single-cell RNA sequencing, whole-genome sequencing, massively parallel reporter assays, chromosome conformation capture (Hi-C) analysis, metagenomics, and proteogenomic, will also be discussed. Finally, the use of genomic techniques and resources for studies of human disease will be addressed.
A significant focus will be placed on equipping students with the essential bioinformatics skills required to navigate and utilize databases that store sequence data, expression data, and other types of genome-wide information. Through practical problem sets, students will learn to manipulate and analyze large datasets typical of genomic analyses by developing simple computer scripts. While the course will enable students to become proficient in the use of computational tools and databases, specific programming skills and the theoretical underpinnings of these tools are covered in a separate course, Bio 5495 Computational Molecular Biology, taught by Dr. Michael Brent.
Due to space limitations in our teaching lab, enrollment for lab credit is capped at 30 students, with priority given to those enrolled in the DBBS programs. Other students may enroll in the lecture component only, with the instructor’s permission. Those with prior experience in computer programming are advised not to enroll for lab credit. Prereqs, Fundamentals of Molecular Cell Biology (Bio 5068), Nucleic Acids and Protein Biosynthesis (Bio 548), or Introduction to Coding and Statistical Thinking in Genetics and Genomics (Bio 5075). To enroll in just the lecture section, register for 3 credits. To enroll in both the lecture and lab sections, register for 4 credits. Credit variable, max 4 units.
Lectures
Mon, Wed 10:00-11:30am
Computer Lab
Fri 10:00-11:30am
Late penalty: No credit after Friday at 11:59pm
NO EXTENSIONS
Course Directors
Ting Wang, twang@genetics.wustl.edu, room 5211, Couch Research Building, 4515 McKinley Ave.
Sheng Chih (Peter) Jin, jin810@wustl.edu, room 6213, Couch Research Building, 4515 McKinley Ave.
Teaching Assistants
Humza Hemani, Haina Jin, Bart Olszowy, Cassidy Pitts, Lloyd Tripp, Jimmy Zhong
Please post questions on Piazza or use this email to contact the TAs: genomics.bio5488@gmail.com
TA Office Hours
Fri 10:00-11:30am (Holden Auditorium, FLTC)
Discussion Forum
Piazza: http://piazza.com/wustl/spring2025/biol5488
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.
You will not need to install additional software for the course. However, some software can make your life easier. We recommend a text editor like VSCode or notepad++ and FileZilla to move files between RIS and your computer. In addition, if you’d like to work remotely (ie not on WashU wifi, either eduroam or WUSM-secure) you will need to use the VPN. Instructions for downloading and installing the VPN can be found here: vpn-Windows-all-11.16.23.pdf | Powered by BoxLinks to an external site.
The lab server is hosted through RIS/OOD which is an interactive web-browser interface that connects to remote computer resources. This allows us to host the course materials, software and code environments in one space without additional programs. Please try to connect to the remote server before class on Friday (1/17/2025). Instructions can be found here: Compute Quick Start — RIS Services User Manual documentation.
Assignment Policies
Please see this link for assignment policies.
Syllabus
Link to syllabus.