Introduction

Systems biology aims to explain how higher level properties of complex biological systems arise from the interactions among their parts. This new field requires a fusion of concepts from many disciplines, including biology, computer science, applied mathematics, physics and engineering. Students with backgrounds in any of these disciplines are encouraged to apply.

Through coursework and collaborative research, we aim to enable students to combine experimental and theoretical approaches to develop physical and quantitative models of biological processes. The Program aims to introduce students to the tools that are now available, and to help them select important unsolved problems in biology that may now be possible to address using quantitative and theoretical approaches.

This is a small and friendly Program with many opportunities to meet and interact with faculty. Program activities include seminars, a retreat, and a weekly discussion session known as Theory Lunch.

How the program works

Incoming students will meet with the class advisors individually at the beginning of each semester to plan their initial program of graduate study. Class advisors will be available to meet with students at any time during their graduate career.

The class advisors will lead a week long orientation for incoming students at the end of August. The orientation will include a set of lectures and campus tours that will introduce students to the many resources at and around Harvard and will answer their questions regarding research, academics and the graduate program.  Students will also be paired with a senior graduate student mentor during the orientation.

After the first year a student will either choose a single faculty member as their dissertation advisor, or initiate a collaboration between two or more labs. Students may choose dissertation advisors from any science department at Harvard, including the research departments of the 11 Harvard-affiliated teaching hospitals.

Coursework

Students are required to take SB300 Introduction to Systems Biology, MedSci300 Conduct of Science, and four additional courses chosen in consultation with their faculty advisors. A current list of courses students commonly take is provided to students at the beginning of the year. 

Four formal courses are currently offered by the Systems Biology Department. In addition, a wide variety of courses taught at Harvard and MIT are available.

  1. Dynamic and Stochastic Processes in Cells SB200 Rigorous introduction to (i)dynamical systems theory as a tool to understand molecular and cellular biology (ii) stochastic processes in single cells, using tools from statistical and physics and infomration theory.
  2. Principles of Animal Development from a Systems Perspective SB 201 Intensive and critical analysis of systems approaches to circuits and principles controlling pattern formation and morphogenesis in animals.
  3. Synthetic Biology SB205 A course covering the design and synthesis of new genetic circuits, construction of novel genomes and the chemical basis for building self-replicating systems.
  4. Introduction to Systems Biology Research SB300 Introductory lectures by Systems Biology Program members. Weekly one and a half hour lectures will introduce the research areas of faculty performing research in systems biology.

Rotations

Students in the program are expected to take 2-4 laboratory rotations before selecting a dissertation project. This is to allow the student to explore different research areas, identify potential collaborators, and experience the environment in different research groups. The program does not set time limits on rotations, but most rotations are expected to be 4-12 weeks long.

Teaching

Students are required to act as teaching fellows in at least one course. We recommend that students complete this requirement by the end of their second year if possible.

Preliminary Qualifying Examination

Students will be expected to complete the Preliminary Qualifying Exam by the end of December of their second year. The examination is divided into two parts:

Part 1 must be completed no later than June 1 of the first year. Students will formulate a question related to any problem in biology (on any scale) and develop a simple set of equations and/or a computer program designed to address the question in a quantitative way. Students are encouraged to discuss possible questions and models with each other and with faculty in preparing for the exam, but the final project should be their own original work. Students will prepare a short written summary and an oral presentation on their project.

Part 2 must be completed no later than the end of March of the student’s second year. Students will prepare and defend an original research proposal derived from the student’s proposed dissertation research. The proposal should define the important questions to be addressed, provide adequate background and describe some details of experiments, computation and/or theoretical work to be undertaken.

Dissertation

After completing the PQE, students will be required to meet once a year with a Dissertation Advisory Committee (DAC) consisting of their advisor(s) and three additional faculty. This should help refine the student’s ideas about their dissertation project and define the scope, direction and overall soundness of the idea.

The role of the DAC is to assist the student in defining the dissertation project, review scientific progress, offer critical evaluation, suggesting extension or modification of objectives, arbitrate differences of opinion between the student and the advisor if they arise, and decide when the work accomplished constitutes a dissertation.  We expect that students will complete their dissertation by their fifth or sixth year of study.