About

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 course offered at either Harvard or MIT, which include 3 required courses. Most courses are taken in the G1 or G2 year.

Required courses:

SSQB200: Modern Systems Biology. This graduate-level course prepares students for research in modern systems biology by providing mathematical foundations and computational tools needed for systems-level understanding. It does so by introducing problems spanning different scales of biological organization, which emphasize different approaches. In taking this course, you will bridge dynamical system modeling, stochastic processes and contemporary computational inference (machine learning) methods.

SSQB 300: Research Topics in Systems, Synthetic and Quantitative Biology. This is a seminar course with talks on current research topics from individual SSQB faculty. This is a year-long G1 course.

SSQB 240: Scientific Writing and Analysis. This course trains Systems Biology PhD students in the skills of scientific writing, critical analysis of papers, and research proposal development. Anchored around the Department’s weekly seminar series, the class provides structured opportunities to analyze recent high-impact papers from leading systems biology labs and to practice writing and defending independent research proposals. Students learn to identify the core narrative of a scientific story, evaluate methodological rigor and impact, and formulate creative, testable hypotheses that could serve as the basis for future fellowship and grant applications, and for their qualifying exams. This is taken with SB300 in the G1 year.

SSQB 250: Synthetic Biology Practicum. This is a quarter course that seeks to apply engineering principles to biological systems in order to solve real-world problems in health, environment, and industry. This design-focused practicum integrates conceptual foundations with practical design exercises using current computational and experimental tools. This is taken in late spring of your G1 year.

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. This is taken in the fall of your G2 year.

SB212: Scientific Presentation. Students will work collaboratively with faculty and one another on critical science communication skills and giving oral presentations.

Rotations

Students in the program are expected to take 3-4 laboratory rotations before selecting a dissertation project. Rotations must be with HILS faculty and at least one with SSQB faculty. 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.