About the program
Systems biology seeks to explain the relationships between parts and wholes at multiple scales of complexity through integrated empirical, computational, and theoretical approaches.
As a joint initiative of Harvard Faculty of Arts & Sciences and Harvard Medical School, the Systems, Synthetic, and Quantitative Biology PhD Program provides a foundation to tackle this challenge through training that advances our understanding of how evolved systems are organized, and to leverage this understanding for the intentional synthesis of systems. In pursuit of these goals, the training emphasizes the development and application of formal ideas from mathematics, statistics and computer science as well as the innovation of experimental techniques to acquire new kinds of quantitative data at scale.
This mission is adjacent to, but distinct from, other programs in our community. For example, students interested primarily in bioinformatics and genomics, or in physical descriptions of biological systems, will benefit from training in other programs.
Advising
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.
Systems, Synthetic, and Quantitative Biology students are required to complete an Individual Development Plan (IDP) meeting with their Dissertation Advisor (or an alternate Harvard faculty mentor of their choosing) annually. An IDP provides students with the opportunity to think about their training objectives, their progress towards them, and to set and/or refine goals for the future with their mentor. The National Institutes of Health (NIH) encourages trainees to make Individualized Development Plans to help them prepare for academic and nonacademic careers.
Curriculum
First-year students meet individually with their class advisors to discuss their background and interests, and together they design a course of study to complement the student's existing training.
Students are required to complete a minimum of 4 science courses offered at either Harvard or MIT. The number and nature of courses recommended will depend on a student's background. See a list of courses students commonly take. In addition, students will complete several professional-development workshops and mini-courses. Most courses will be taken in the G1 or G2 year.
Required courses:
SysBio200: A Systems Approach to Biology. In this introductory graduate-level course, students will develop tools and follow canonical examples of understanding biological systems. We will focus on using the language of dynamical systems theory, stochastic processes and machine learning to clarify the problems to be solved, and to approach their solution. We will use simple cases to start with, and then see how they play out in modern problems.
Two additional required SysBio courses are planned for 2025, one focused on synthetic biology and generative modeling, the other on multicellular systems biology, especially systems developmental biology and systems immunology. Information on these courses will be added in Spring 2025.
SysBio300: Research Topics in Systems, Synthetic and Quantitative Biology. This is a seminar course with talks on current research topics from individual SSQB faculty.
MedSci300qc: Conduct of Science. The course follows a discussion group format in which 8-12 second-year students meet with a faculty member who leads discussions on the ethical and responsible conduct of research.
In addition, students are required to take at least one course in the area of computational biology, machine learning or advanced statistics. Students with little background in biology will also be required to take a graduate-level biology course, e.g. in immunology, genetics, or cell biology.
Rotations
Students in the program are expected to take 3-4 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. Most rotations are expected to be 6-12 weeks long.
Teaching
Students are required to act as teaching fellows for 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 March of their second year. The examination is divided into two parts:
Part 1 focuses on an original computational or theoretical research project. Faculty will pose a broad topic or biological challenge for students to work on, and provide several papers for background reading. The topic will be related to course materials, but students will have the freedom to pursue any approach and to refine the questions as they wish. Students will be expected to spend ~2-3 weeks’ worth of work to research the topic, carry out analyses and write up a report. The report is due at the end of March of the G1 year, and oral exams will occur in April.
Part 2 focuses on the student's thesis research proposal. 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. The student will defend the proposal to a faculty committee. The exam should be taken no later than spring of the G2 year, and is often taken earlier.
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.
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.