1.088/ 1.881 / HST.538: Genomics and Evolution of Infectious Disease (MIT)

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

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

Location: 24-121


Prof Tami Lieberman

tami at mit

Preregistration is strongly encouraged and will assist us in TA allocation.

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. Previously taught as special subject 1.S993 in Spring 2019.

Prerequisites: Biology (GIR), 1.000 or 6.0002 (some programming), or permission of instructor. Further experience with probability and/or genetics is helpful but is not required. As enrollment of students from a wide variety of background is to be expected, unnecessary jargon and mathematics will be avoided.

Textbook: There is no textbook for this course, which covers both fundamental and cutting-edge material. Readings for class will be posted on the class Stellar website.


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% In-class quizzes (3)
  • 10% Participation in paper discussions

Collaboration: Problem sets are designed to be completed on their own. You are welcome to talk to classmates about principles for solving problems, but do not solve specific problems together.

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.

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.

Readings: Required readings should be read before class, as discussions in class will build on them. Readings for class are posted on the class Stellar website. Reading primary literature can take more time than anticipated, so please plan accordingly. Additional recommended readings will occasionally be provided; reading these before class will improve your learning.

The class schedule for Spring 2020's 1.088 is under construction. For reference, the schedule from last year is posted below. Among other changes, guest lectures this year will be replaced with more discussion of modern genomic pipelines, cloud computing, and more machine learning. Please note that this year (Spring 2020) there is no midterm and no final; these items are replaced with short in-class quizzes (~45 min each).

1.S993 Syllabus for Web