1.S993 Genomics and Evolution of Infectious Diseases (3-0-9)

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

Location: 1-371


Prof Tami Lieberman

tami at mit


Jacob Baker

jsbaker 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. New class for Spring 2019, being introduced as a special subject.

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 are posted on the class Stellar website


This course has 5 homeworks/problem sets (due at the end of the week), a midterm, and a final exam.

  • 35% Problem sets / homeworks (5 -- lowest grade dropped)
  • 20% In-class midterm
  • 30% Final exam
  • 15% 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 MATLAB, but we can also help you with your questions using python or R.

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 primarily literature can take more time than anticipated, so please plan accordingly. Reading these papers closely and reinforcing them with in class discussion will provide good (but not exclusive) preparation for the midterm and exams. For those interested in more detail about particular topics, optional additional readings will occasionally be provided.

1.S993 Syllabus for Web