Systems Biology
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
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 encouraged. Please refer to the GSAS Admissions Page for further information on applying. https://apply.embark.com/grad/Harvard/GSAS
Students can request information and an application from:
Office of Admissions and Financial Aid
Harvard University
Graduate School of Arts and Sciences
1350 Massachusetts Avenue
Holyoke Center 350
Cambridge, MA 02138-3654
e-mail: admiss@fas.harvard.edu
A number of candidates will be invited to interview in late January. 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.Suggested Undergraduate Preparation-
The program aims to recruit students from a variety of backgrounds including all areas of biology, physics, chemistry, computer science, engineering, and mathematics. Students who are in doubt about whether their background is appropriate are encouraged to contact the Program Administrator with a resume.Program of Study
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.
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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. -
Seminar in Systems Biology SB201
This course examines concepts and methods in Systems Biology, and follows the development of the field and current thinking through primary reading of classic and modern papers. -
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. - Special Topics in Systems Biology SB301
An exploration of new directions for the field of systems biology. This course will discuss major unsolved questions in biology and discuss the possible new approaches to these questions offered by systems biology. -
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 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 (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.
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 Harvard-affiliated teaching hospitals.
Independent Research
Acceptable modes of dissertation research will include molecular/cell biology-type experiment-based research, computer science/math/physics/engineering theoretical research, and combinations of the two. The program will not attempt to constrain students to dissertation research in the traditional formats of systems biology’s parent disciplines. Collaborative research will be encouraged.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 15 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 December 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 Systems Biology Program is comprised of 38 faculty members from the Departments of Systems Biology, Biological Chemistry and Molecular Pharmacology, Molecular and Cellular Biology, Chemistry and Chemical Biology, Cell Biology, Genetics, Physics and the Division of Engineering and Applied Sciences.
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.
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. Formalization and emergence of functional organization; genotype-phenotype mappings; distributed molecular control.
Melissa Franklin, Professor of Physics. Focuses on high energy particle physics.
Jeremy Gunawardena, Senior Lecturer on Systems Biology. Theoretical and experimental approaches to in-silico systems biology.
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, Assistant 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 post-synaptic 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.
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.
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-.
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.
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.
Brian Seed, Professor of Genetics and Health Sciences & Technology, Massachusetts General Hospital. Automation and expression analysis techniques to uncover novel relationships between proteins in cellular signaling, with a particular emphasis on signaling in the immune system. Development of new approaches to simplify the creation of experimental systems, such as gene-targeted organisms, to evaluate the in vivo significance of candidate relationships between genes uncovered by in vitro testing. Development of protein and small molecule therapeutics to treat human diseases.
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.
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.
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.
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.