January 5, 2023

EPID/MICROBIOL 582 - Molecular Epidemiology

8:30 am

Event Description

Course Information

Instructor: Evan Snitkin, PhD

Course Assistants: Ali Pirani and Hasan Abu-Amara

Session: Jan 5, 2022 – April 18, 2022

Weekly class meeting: Mondays and Wednesdays, 8:30-10:00am, 1112 SPH2

Office hours: M/W 10:30am-noon

Contact: esnitkin@umich.edu


The course is scheduled to be in person, but I will also be using Zoom to record each session and allow for virtual guest speakers. Please check your version of zoom, and make sure you are using version 5.3.0 or higher and are viewing using an app (either on a computer or mobile phone). This enables use of newer zoom features, such as allowing participants to choose a breakout room of their choice.

Course Description

Molecular Epidemiology (but really Genomic Epidemiology) --- Provide an overview of cutting-edge approaches for microbial genomic analysis, with a focus on their application in the emerging field of genomic epidemiology. Lectures will be reinforced with discussions and extensive hands-on training. Students will gain experience e on the command-line and in performing downstream analysis and visualization in R.

Course Goals/Foundational Competencies (FC)

● To gain hands on experience in the analysis of microbial genomic data

● To gain experience in interpreting microbial genomic data to inform public health action

Learning Objectives

Specifically, you will be able to:

1. Navigate the Unix command line and submit jobs to a compute cluster

2. Run a suite of modern tools for bacterial genomic analysis Epid/Microbiol 582 Syllabus, Winter 2022

3. Execute bacterial genomic workflows starting with data download/quality control and leading all the way through processed results that are suitable for interpretation

4. Analyze bacterial genomic data sets to summarize their strain distribution, antibiotic resistance potential and identify putative cases of recent transmission

5. Describe challenges associated with studying transmission using bacterial genomic data


Please find flyer in downloads below with course requirements and schedule