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Introduction to Program

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.

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. Students will be introduced to the tools that are now available, and to important unsolved problems in biology that may now be possible to address using quantitative and theoretical approaches.

For more information, please visit http://sysbio.harvard.edu/phd.

Admissions Reqiurements

The typical student has a strong background in one of the disciplines relevant to Systems Biology (such as biology, mathematics, engi­neering, physics, chemistry and computer science) and a strong interest in interdisci­plinary research. Although cross training is not required, many of the students admitted have had some experience in biology and some exposure to quantitative or theoretical approaches.

Students considering graduate work should request an application from the Office of Admissions and Financial Aid Harvard Graduate School of Arts and Sciences. Online submission of the application is required. Please refer to the GSAS Admissions Page for further information on applying.

Students can request information from:

Office of Admissions and Financial Aid
Harvard University
Graduate School of Arts and Sciences
Holyoke Center 350
1350 Massachusetts Avenue
Cambridge, MA 02138-3654
e-mail: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

A number of candidates will be invited to interview in late January or early February. Final decisions concerning admission are made by the dean of the Graduate School of Arts and Sciences, and the candidates are notified by letter from the Admissions Office.

Combined MD-PhD Program

Students admitted to Harvard Medical School as candidates for the MD degree may also apply for admission to the Systems Biology program in order to earn a PhD degree in systems biology.

This program may be of particular interest to prospective medical students with a strong theoretical background and to students enrolled in the Harvard-MIT Division of Health Sciences and Technology. 

Financial Aid

All students accepted into the program are awarded full support, including a stipend, full tuition, and health fees. Students are encour­aged to apply for external fellowships, such as those administered by the National Science Foundation, National Defense Science and Engineering Fellowship, and National Insti­tutes of Health.

Degree Requirements

Each student’s program of graduate study is planned in consultation with faculty advi­sors. The degree program is designed to be completed in a maximum of six years. The program consists of three parts:

Coursework

Incoming students are assigned to two advi­sors, generally from different disciplines, who are available to help plan the student’s initial program of graduate study. 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. Five formal courses are currently offered by Program faculty and a wide variety of courses taught at Harvard and MIT are available. Additionally, an informal summer course is offered for incoming students during the month of August that introduces a range of experimental techniques, theoretical/computa­tional tools and programming languages.

(1) A Systems Approach to Biology SB200
Introduces theoretical tools and computational approaches from mathematics, physics, computer science and engineering in the context of biological problems and situations.

(2) Seminar in Systems Biology SB201
This course will examine concepts and methods in systems biology. We will follow the development of the field and the current thinking through paper reading, discussion, and lecture.

(3) Synthetic Biology SB202
This course will cover the design and synthesis of new genetic circuits, construction of novel genomes and the chemical basis for building self-replicating systems.

(4) Fundamentals of Quantitative and Systems Biology SB203
Cell tissue biology from molecular, dynamical systems and information theoretic perspectives. Approaches to modeling biological pathways, collecting quantitative data and deriving mechanistic insight will be presented through weekly lectures, workshops and literature analysis.

(5) Introduction to Systems Biology Research SB300
Introductory lectures by Systems Biology Program members. Weekly one-hour lectures introduce the research areas of faculty performing research in systems biology.

(6) Biologists at the Computer SB302
This course provides an introduction to the field of computer science for biology students.

Lab Rotations

Students in the program are expected to take two to four 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 (both experimental and theoretical), rather than to accomplish a research project. The program does not set time limits on rotations, but most rotations are expected to be 4-12 weeks long.

Independent Research

After the first year students may choose a single faculty member as their dissertation advisor, or may elect to initiate a collaboration between two or more labs. Subject to Program approval, students may choose advisors from any science department at Harvard, including the research departments of the 11 Harvard­affiliated teaching hospitals.

Preliminary Qualifying Examination

The purpose of the examination is to ensure that the student is prepared to embark on dissertation research. The examination is given in two phases. The first phase must be completed by June 1 of the student’s first year, and is intended to evaluate the student’s prog­ress in acquiring competence in mathematical and/or computational approaches. Students will formulate a question related to any problem in biology and devise a mathematical or computational approach to addressing it. Results of the project will be presented in a short written summary and orally. Phase two must be completed by the end of January of the student’s second year. Students will prepare and defend an original research proposal related to the student’s proposed dissertation research.

Dissertation

After completing the Qualifying Exam, 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 DAC and the student will meet and discuss the proposal, and the student will receive feedback, advice and suggestions from Committee members. This should help refine the student’s ideas about their dissertation project and define the scope, direction and overall soundness of the idea.

Acceptable modes of dissertation research will include experiment-based research, theo­retical research, and combinations of the two. We do not attempt to constrain students to dissertation research in the traditional formats of systems biology’s parent disciplines. We encourage collaborative research, and especially situations in which the student is bringing a new question or a new tool to their dissertation lab(s).

A completed dissertation will ordinarily include at least three chapters comprising original research, of which at least two could be (or have been) submitted for peer-reviewed publication. Alternative forms of publication (for example, a useful computer program or a Website/database that required significant original research and intellectual input) may be acceptable. The Dissertation Examina­tion will involve a public seminar describing the dissertation research, followed by an oral examination by the DAC. We expect that students will complete their dissertation by their fifth or sixth year of study. 

Participating Faculty

The 47 faculty members of the Systems Biology Program are from the Departments of Systems Biology, Biological Chemistry and Molecular Pharmacology, Molecular and Cellular Biology, Chemistry and Chemical Biology, Cell Biology, Genetics, and Physics, and from the School of Engineering and Applied Sciences. 

Edoardo Airoldi, Assistant Professor of Statistics. We develop and apply statistics, methods for analyzing complex dynamical systems. We are broadly interested in characterizing mecha­nisms of regulation in bacteria, yeast, and cancer systems, quantitatively. Our focus is on cellular proliferation, metabolism, signaling pathways, and protein-mRNA regulation.

Debra Auguste, Assistant Professor of Biomed­ical Engineering. Developing novel biomate­rials for drug delivery and tissue engineering.

Michael Brenner, Gordon McKay Professor of Applied Mathematics and Applied Physics. Quantitative modeling of complex phenomena in science and engineering.

Martha Bulyk, Assistant Professor of Medicine, Pathology, and Health Sciences & Technology; Associate Member of Broad Institute of MIT and Harvard. Functional and computational genomics studies of transcription factors and Cis regulatory elements.

Lewis Cantley, Professor of Medicine, Professor of Systems Biology. The biochemical pathways that regulate normal mammalian cell growth and the defects that cause cell transformation.

George Church, Professor of Genetics. Synthetic biology design of 3D, multicell, & new trans­lational codes; stem-cell, aging & cancer epige­netics, ecosystem models, personal genomics.

Philippe Cluzel, Professor of Molecular and Cellular Biology and Gordon McKay Professor of Applied Physics.

Angela DePace, Assistant Professor of Systems Biology. Mechanism and evolution of gene regulation.

Catherine Dulac, Professor of Molecular and Cellular Biology. Molecular and developmental biology of olfactory and pheromone sensing.

Daniel Fisher, Professor of Physics and Professor of Applied Physics. Condensed matter theory, geophysics, biology.

Walter Fontana, Professor of Systems Biology. Experimental and theoretical approaches to address fundamental problems in systems biology as they relate to aging (C.elegans), plasticity in molecular signaling, and the evolvability of phenotype.

Jeremy Gunawardena, Senior Lecturer on Systems Biology. Theoretical and experimental approaches to in-silico systems biology.

John Higgins, Assistant Professor of Systems Bilogy.

Marc Kirschner, Professor of Systems Biology, Chair of the Department of Systems Biology. Regulation of the cell cycle, the role of cytoskeleton in cell morphogenesis, and mech­anisms of establishing the basic vertebrate body plan.

Roy Kishony, Associate Professor of Systems Biology. Combining theoretical and experi­mental approaches to understand how biolog­ical function emerges in complex genetic and chemical networks. Using population genetics approaches to understand the interplay between biological design and the evolutionary process.

Galit Lahav, Assistant Professor of Systems Biology. The dynamics of conserved network motifs in diverse signaling systems in human cells, studied by stimulating the proteins of interest and accurately monitoring their expression level and localization in individual living cells.

Richard Losick, Professor in the Department of Molecular and Cellular Biology. Gene regula­tion and development in microorganisms.

Gavin MacBeath, Assistant Professor of Chem­istry and Chemical Biology. Systems-level investigation of protein-protein interactions in intracellular signaling networks using protein microarrays; emphasis on receptor tyrosine kinase mediated signaling and pre- and post­synaptic signaling.

Lakshminarayanan Mahadevan, Gordon McKay Professor of Applied Mathematics and Mechanics. The applications of mathematics to understand the mechanical behavior of matter in all its forms, but with a particular emphasis on soft materials and biological systems.

Christopher Marx, Assistant Professor of Organ­ismic and Evolutionary Biology. Experimental evolution of microbes to address broad evolu­tionary and ecological questions and explore the systems-level function and optimization of complex biological networks.

Sean Megason, Assistant Professor of Systems Biology. Studies how the program contained in the genome is executed during develop­ment to turn and egg into an embryo, using confocal/2-photon imaging of living, trans­genic zebrafish embryos to watch biological circuits function in vivo and use these data in cell-based, quantitative modeling.

Melissa Franklin, Professor of Physics. Focuses on high energy particle physics.

Timothy Mitchison, Hasib Sabbagh Professor of Systems Biology, Deputy Chairman of the Department of Systems Biology. Cytoskeleton dynamics, in particular the mechanism of mitosis and the mechanism of cell motility dependent on actin polymerization.

Vamsi Mootha, Assistant Professor of Systems Biology. Biochemical adaptation at the level of the mitochondrion, assessed through physiology, functional genomics (microarrays, proteomics), and computation; integration of genome-scale datasets to discover gene networks underlying rare and common human metabolic diseases biology.

Andrew Murray, Professor of Molecular and Cellular Biology; Co-director of the Bauer Center for Genomics Research. Mitosis, meiosis, experi­mental evolution, and signal transduction .

Radhika Nagpal, Assistant Professor of Computer Science, Instructor in Systems Biology. Developing programming paradigms for robust collective behavior, inspired by biology; understanding robust collective behavior in biological systems.

Dan Needleman, Assistant Professor of Applied Physics and of Molecular and Cellular Biology. Combining quantitative experiments and theory to understand the architecture and dynamics of self-organizing, subcellular struc­tures, particularly the metaphase spindle.

Martin Nowak, Professor of Mathematics and of Biology. Theoretical biology, somatic evolution of cancer.

Erin O’Shea, Professor of Molecular and Cellular Biology; Co-Director of the Bauer Center for Genomics Research. Systems level and molecular analysis of signaling pathways, transcriptional regulation, and developing methods for expressing and assaying the entire complement of proteins derived from an organism.

Kevin Parker, Assistant Professor of Biomedical Engineering. Cellular mechanotransduction in the heart.

Johan Paulsson, Assistant Professor of Systems Biology. Mathematical theory for noise in intracellular networks and the development of new experimental techniques for counting molecules in single cells. Combining theory and experiments in the study of e.g. stochastic gene expression, homeostatic control, near-critical metabolism and intracellular selfishness .

Sharad Ramanathan, Assistant Professor of Molecular and Cellular Biology and of Applied Physics. Studies how cells and organisms process signals from their environment and how underlying molecular pathways evolve.

Tom Rapoport, Professor of Cell Biology. Getting proteins across membranes.

Aviv Regev, Assistant Professor of Biology at MIT and Member of the Broad Institute of Harvard/MIT. Understanding the mechanisms by which molecular networks accommodate changes at different time scales.

Fritz Roth, Assistant Professor of Biological Chemistry & Molecular Pharmacology. Using large-scale experiments to understand pheno­type and human disease.

Pardis Sabeti, Assistant Professor of Organismic and Evolutionary Biology. Studying the effect of natural selection on the human genome and on the genomes of other organisms and uncovering the traits that have emerged to shape these species, and to understand mecha­nisms of evolutionary adaptation in humans and pathogens.

Alan Saghatelian, Assistant Professor of Chem­istry and Chemical Biology. The development and application of LC-MS based metabo­lomics approaches to study basic as well as biomedical problems in biology.

Alex Schier, Professor of Molecular and Cellular Biology. Developmental genetics and neurobi­ology.

Jagesh Shah, Assistant Professor of Systems Biology. Scaling molecular events into cell behavior. Using molecular techniques and modern biophysical tools they are piecing together quantitative models of endogenous and synthetic cellular networks.

William Shih, Assistant Professor of Biological Chemistry and Molecular Pharmacology. Explores the principles of self-assembling molecular machine design and evolution, using DNA nanostructures as model systems. Also develop DNA nanostructures as tools for molecular and structural biology.

Pamela Silver, Professor of Systems Biology. Systems analysis of genomes, RNA and nuclear organization; designing biological systems; synthetic biology.

Michael Springer, Assistant Professor of Systems Biology.

Peter Sorger, Professor of Systems Biology. The application of experimental and computa­tional approaches to the analysis of chromo­some segregation, genomic stability and programmed cell death in yeast, mice and human cells.

Jack Szostak, Professor of Genetics. Directed evolution; information content and molecular function; self-replicating systems.

Antoine Van Oijen, Assistant Professor of Biological Chemistry and Molecular Pharma­cology. Single-molecule studies of complex multi-protein machineries. Current interests: DNA replication, viral fusion.

Ralph Weissleder, Professor of Systems Biology. Development of novel imaging tools and their application to understanding complex diseases.

David Weitz, Professor of Applied Physics and Physics. Studies soft condensed matter physics, and applies physical methods to study the elastic properties of cell, both by creating in vitro model systems, and by developing tech­niques for in vivo studies of cells. The goal of the work is to understand the origin of the force transduction in cells.

Xiaoliang Sunney Xie, Professor of Chemistry and Chemical Biology. Single molecule spec­troscopy and dynamics; molecular interaction and chemical dynamics in biological systems.

Xiaowei Zhuang, Assistant Professor of Chem­istry and Chemical Biology and of Physics. Study of complex biological processes at the single molecule (or single working unit) level; devel­opment of new imaging techniques.