1.088/1.881/HST.538: Genomics and Evolution of Infectious Diseases (3-0-9)

Time: TuTh 1:00p-2:30p

Location: Remote!


Prof Tami Lieberman

tami at mit


Brian Do

briando at mit

Course description: Provides a thorough introduction to the forces driving pathogen evolution, practical experience with bioinformatics and computational tools, and discussions of topics relevant to public health today. Topics include mechanisms of genome variation in bacteria and viruses, population genetics, outbreak detection and tracking, strategies to impede the evolution of drug resistance, emergence of new disease, and microbiomes and metagenomics. Includes discussion of primary literature and computational assignments.

Prerequisites: Biology (GIR), 1.000 or 6.0001 (some programming), or permission of instructor. As this class touches on multiple subjects, experience with either probability (18.05) or genetics (7.03) is strongly recommended but not required.

Textbook/readings : There is no textbook for this course, which covers both fundamental and cutting-edge material. Readings for class will be posted on the class website (Canvas site TBA). These should be read before class, as discussions in class will build on them.

Some class time will be dedicated to critical discussion of primary literature (indicated with an underline in syllabus). Reading primary literature can be quite time consuming, so please plan accordingly.

Programming: You are welcome to use any programming language you like to solve problem sets. For some problem sets, we will provide pointers and helpful starting code in Python, but we can also help you with your questions using R or MATLAB.

For Spring 2021: In-class examples, psets, and journal clubs will include investigation of SARS-CoV2, but this will only be a fraction of the class, We will continue to cover many other infectious diseases.


Much of the learning in this course will be done via hands on problem sets. This course has 5 homeworks/problem sets (due at the end of the week) and 3 short in-class quizzes.

  • 60% Problem sets (5)

  • 30% Short in-class quizzes (3)

  • 10% Participation in paper discussions

Late assignments will not be accepted without prior approval. If approved beforehand, there will still be a reduction of 10% of the points available per day late. This penalty may be waived due to extenuating circumstances.

See example syllabus from 2020 below (note fewer classes due to interruption mid-semester; In addition, more pre-class readings will be provided in 2021 in order to spend more classtime reinforcing concepts).

1.088 / 1.881 / HST.538 Syllabus for Web