The Graduate Program


The Microbiology Graduate PhD Program is an MIT-wide program that is designed to provide students with broad exposure to modern areas of microbiology and depth in the chosen area of thesis work. There are more than 50 faculty in 10 different departments and divisions that study microbes. Graduate students admitted to the program will join a vibrant, thriving microbiology community on the MIT campus and will receive training in a broad range of areas in microbiology.

The major components of the training program are described in detail below along with information on life as a graduate student at MIT.


Required course work (4):

Students with a particularly strong background in any of the below areas may have the option of placing out of the related course; approval of the Graduate Education Committee is required.

  1. Methods and Problems in Microbiology -7.492J (Same subject as 1.86J, 20.445J) (Fall) (12 units) M. Laub
    Students will read and discuss primary literature covering key areas of microbial research with emphasis on methods and approaches used to understand and manipulate microbes. Open to first-year Microbiology and Biology students; other students by permission of instructor.

  2. Microbial Genetics and Evolution -7.493J (Fall) (12 units) A. D. Grossman, O. Cordero
    Required of students in program, but open to others. Will cover aspects of microbial genetic and genomic analyses, central dogma, horizontal gene transfer, and evolution.

  3. Quantitative Biology for Graduate Students-7.57 (Spring) (12 units) J. Davis, G. W. Li Introduces the fundamental concepts and tools of quantitative approaches to molecular and cellular biology. Covers a wide range of mathematical, computational, and statistical methods, although no previous expertise in these areas is required. Focuses on understanding quantitative approaches through the analysis of particular problems and examples drawn from classical genetics, molecular biology, cell biology, genomics, and systems biology. 

  4. Biochemistry.
    of the following courses:
    Principles of Biochemical Analysis -7.51 (Fall) (12 units) A. Keating,R. T. Sauer
    Principles of biochemistry, emphasizing stucture, equilibrium studies, kinetics, informatics, single-molecule studeies, and experimental design. Topics include macromolecular binding and specificity, protein folding and unfolding, allosteric systems, transcription factors, kinases, membrane channels and transporters, and molecular machines.
    Biological Chemistry II -7.80 (Spring) (12 units) E. Nolan , R. Raines
    More advanced treatment of biochemical mechanisms that underlie biological processes. Topics include macromolecular machines such as the ribosome, the proteosome, fatty acid synthases as a paradigm for polyketide synthases and non-ribosomal polypeptide synthases, metal cluster assembly and oxidative stress. Emphasis is on experimental methods used to unravel these processes and how these processes fit into the cellular context and coordinate regulation.

 Research Rotations in Microbiology - 7.499 (Fall, IAP, Spring) (12 units) Staff
Introduction to faculty participating in the Interdepartmental Microbiology graduate program and a series of lab rotations. During the first year, students will rotate through three labs of MIT faculty that participate in the Microbiology Graduate Program. These rotations will help provide students a broad exposure to microbiology research and will be used to select a lab for their thesis research by the end of the first year. Given the interdisciplinary nature of the program and many research programs, students may be able to work jointly with more than one research supervisor. Required and limited to graduate students in the microbiology program.

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Elective course work (3):

Students must take three elective courses, totaling 36 units, from the following list. Electives can be chosen to provide depth in a specific scientific/engineering area of interest or additional breadth in training. Listed below are subjects pre-approved to fulfill the elective requirement. Courses from some other areas may also fulfill the requirement, with the approval of the Graduate Education committee.

Fall Electives:

Class information subject to change, please verify availability online in the MIT Course Listing.

Principles of Bioinorganic Chemistry5.062 (Fall) (6 units) (Part I)
Delineates principles that form the basis for understanding how metal ions function in biology. Examples chosen from recent literature on a range of topics, including the global biogeochemical cycles of the elements; choice, uptake and assembly of metal-containing units; structure, function and biosynthesis of complex metallocofactors; electron-transfer and redox chemistry; atom and group transfer chemistry; protein tuning of metal properties; metalloprotein engineering and design; and applications to diagnosis and treatment of disease. D. Suess

Advanced Biological Chemistry5.52 (Fall) (12 units)
Concepts and methods of biochemistry, with emphasis on quantitative aspects of problem analysis and fundamentals of experimental methods. Intended for first-year graduate students with a strong interest in biological chemistry.
R. Raines

Microbial Physiology7.62 (Fall) (12 units)
Biochemical properties of bacteria and other microorganisms that enable them to grow under a variety of conditions. Interaction between bacteria and bacteriophages. Genetic and metabolic regulation of enzyme action and enzyme formation. Structure and function of components of the bacterial cell envelope. Protein secretion with a special emphasis on its various roles in pathogenesis. Additional topics include bioenergetics, symbiosis, quorum sensing, global responses to DNA damage, and biofilms. Students taking the graduate version are expected to explore the subject in greater depth.  G. C. Walker, A. J. Sinskey

Systems Biology8.591J/7.81J (Fall) (12 units)
Introduction to cellular and population-level systems biology with an emphasis on synthetic biology, modeling of genetic networks, cell-cell interactions, and evolutionary dynamics. Cellular systems include genetic switches and oscillators, network motifs, genetic network evolution, and cellular decision-making. Population-level systems include models of pattern formation, cell-cell communication, and evolutionary systems biology. Students taking graduate version explore the subject in more depth.
J. Gore

Metabolic and Cell Engineering10.544 (Fall) (Spring) (12 units)
Presentation of a framework for quantitative understanding of cell functions as integrated molecular systems. Analysis of cell-level processes in terms of underlying molecular mechanisms based on thermodynamics, kinetics, mechanics, and transport principles, emphasizing an engineering, problem-oriented perspective. Objective is to rationalize target selection for genetic engineering and evaluate the physiology of recombinant cells. Topics include cell metabolism and energy production, transport across cell compartment barriers, protein synthesis and secretion, regulation of gene expression, transduction of signals from extracellular environment, cell proliferation, cell adhesion and migration.  Staff

Statistical Thermodynamics 10.546J/5.70J (Fall) (12 units)
Develops classical equilibrium statistical mechanical concepts for application to chemical physics problems. Basic concepts of ensemble theory formulated on the basis of thermodynamic fluctuations. Examples of applications include Ising models, lattice models of binding, ionic and non-ionic solutions, liquid theory, polymer and protein conformations, phase transition, and pattern formation. Introduces computational techniques with examples of liquid and polymer simulations.  A. Willard, J. Cao

Biomolecular Kinetics and Cellular Dynamics 20.420J/10.538J (Fall) (12 units)
Provides an introduction to the mechanistic analysis and engineering of biomolecules and biomolecular systems. Covers methods for measuring, modeling, and manipulating systems, including biophysical experimental tools, computational modeling approaches, and molecular design. Equips students to take systematic and quantitative approaches to the investigation of a wide variety of biological phenomena. A. Jasanoff, E. Fraenkel

Evontionary Genomics HST.508 (Fall) (12 units)
Develops deep quantitative understanding of basic forces of evolution, molecular evolution, genetic variations and their dynamics in populations, genetics of complex phenotypes, and genome-wide association studies. Applies these foundational concepts to cutting-edge studies in epigenetics, gene regulation and chromatin; cancer genomics and microbiomes. Modules consist of lectures, journal club discussions of high-impact publications, and guest lectures that provide clinical correlates. Homework assignments and final projects develop practical experience and understanding of genomic data from evolutionary principles.L. Mirny, T. Lieberman

Molecular and Cellular Pathophysiology 20.450 (Fall) (12 units)
Compares the complex molecular and cellular interactions in health and disease between commensal microbial communities, pathogens and the human or animal host. Special focus is given to current research on microbe/host interactions, infection of significant importance to public health, and chronic infectious disease. Classwork will include lecture, but emphasize critical evaluation and class discussion of recent scientific papers, and the development of new research agendas in the fields presented.
J. Niles, K. Ribbeck

Spring Electives

Class information subject to change, please verify availability online in the MIT Course Listing.

Environmental Microbiology1.89 (Spring) (12 units)
Provides a general introduction to the diverse roles of microorganisms in natural and artificial environments. Topics include cellular architecture, energetics, and growth; evolution and gene flow; population and community dynamics; water and soil microbiology; biogeochemical cycling; and microorganisms in biodeterioration and bioremediation. 7.014 recommended as prerequisite; students taking graduate version complete additional assignments.  M. Polz

Frontiers of Interdisciplinary Science in Human Health and Disease 5.64J/HST.539 (Spring) (12 units)
  Introduces major principles, concepts, and clinical applications of biophysics, biophysical chemistry, and systems biology. Emphasizes biological macromolecular interactions, biochemical reaction dynamics, and genomics. Discusses current technological frontiers and areas of active research at the interface of basic and clinical science. Provides integrated, interdisciplinary training and core experimental and computational methods in molecular biochemistry and genomics. A. Shalek

Biophysical Chemistry Techniques5.78 (6 units first half) or 7.71 (12 units whole semester) (Spring) (6 or 12 units)
Presents principles of macromolecular crystallography that are essential for structure determinations. Topics include crystallization, diffraction theory, symmetry and space groups, data collection, phase determination methods, model building, and refinement. Discussion of crystallography theory complemented with exercises such as crystallization, data processing, and model building. Meets with 7.71 when offered concurrently. Enrollment limited.  C. Drennan, T. Schwartz

Computational Systems Biology 6.874J/HST.506J (Spring) (12 units)
Presents advanced machine learning and algorithmic approaches for contemporary problems in biology drawing upon recent advances in the literature. Topics include biological discovery in heterogeneous cellular populations; single cell data analysis; regulatory factor binding; motif discovery; gene expression analysis; regulatory networks (discovery, validation, data integration, protein-protein interactions, signaling, chromatin accessibility analysis); predicting phenotype from genotype; and experimental design (model validation, interpretation of interventions). Computational methods presented include deep learning, dimensionality reduction, clustering, directed and undirected graphical models, significance testing, Dirichlet processes, and topic models. Multidisciplinary team-oriented final research project.

Molecular Biology 7.58 (Spring) (12 units)
Detailed analysis of the biochemical mechanisms that control the maintenance, expression, and evolution of prokaryotic and eukaryotic genomes. Topics covered in lecture and readings of relevant literature include: gene regulation, DNA replication, genetic recombination, and mRNA translation. Logic of experimental design and data analysis emphasized. Presentations include both lectures and group discussions of representative papers from the literature. Students taking the graduate version are expected to explore the subject in greater depth.  S. Bell, E. Calo

Immunology 7.63J/20.630J (Spring) (12 units)
Comprehensive survey of molecular, genetic, and cellular aspects of the immune system. Topics include innate and adaptive immunity; cells and organs of the immune system; hematopoiesis; immunoglobulin, T cell receptor, and major histocompatibility complex (MHC) proteins and genes; development and functions of B and T lymphocytes; immune responses to infections and tumors; hypersensitivity, autoimmunity, and immunodeficiencies. Particular attention to the development and function of the immune system as a whole, as studied by modern methods and techniques. Students taking graduate version explore the subject in greater depth, including study of recent primary literature. S. Spranger, M. Birnbaum

Molecular Basis of Infectious Disease Graduate - 7.66 (Spring) (12 units)
Focuses on the principles of host-pathogen interactions with an emphasis on infectious diseases of humans. Presents key concepts of pathogenesis through the study of various human pathogens. Includes critical analysis and discussion of assigned readings. Students taking the graduate version are expected to explore the subject in greater depth.  D. Kim, S. Lourido

Regulation of Gene Expression 7.70 (Spring) (12 units)
Seminar examines basic principles of biological regulation of gene expression. Focuses on examples that underpin these principles, as well as those that challenge certain long-held views. Topics covered may include the role of transcription factors, enhancers, DNA modifications, non-coding RNAs, and chromatin structure in the regulation of gene expression and mechanisms for epigenetic inheritance of transcriptional states. Limited to 40.  Staff, Not offered 2018-2019.

Nucleic Acids, Structure, Function, Evolution and Their Interactions with Proteins 7.77 (Spring) (12 units)
Surveys primary literature, focusing on biochemical, biophysical, genetic, and combinatorial approaches for understanding nucleic acids. Topics include the general properties, functions, and structural motifs of DNA and RNA; RNAs as catalysts and as regulators of gene expression; RNA editing and surveillance, and the interaction of nucleic acids with proteins, such as zinc-finger proteins, modification enzymes, aminoacyl-tRNA synthetases and other proteins of the translational machinery. Includes some lectures but is mostly analysis and discussion of current literature in the context of student presentations.  D. Bartel, U. RajBhandary

Foundations of Computational and Systems Biology20.490 (Spring) (12 units)
Provides an introduction to computational and systems biology. Includes units on the analysis of protein and nucleic acid sequences, protein structures, and biological networks. Presents principles and methods used for sequence alignment, motif finding, expression array analysis, structural modeling, structure design and prediction, and network analysis and modeling. Techniques include dynamic programming, Markov and hidden Markov models, Bayesian networks, clustering methods, and energy minimization approaches. Exposes students to emerging research areas. Designed for students with strong backgrounds in either molecular biology or computer science. Some foundational material covering basic programming skills, probability and statistics is provided for students with less quantitative backgrounds. Students taking graduate version complete additional assignments. Staff

Biochemical Engineering 10.542 (Spring) (12 units) Offered Alternate Years (not offered 2016-2017)
Interaction of chemical engineering, biochemistry, and microbiology. Mathematical representations of microbial systems. Kinetics of growth, death, and metabolism. Continuous fermentation, agitation, mass transfer, and scale-up in fermentation systems, enzyme technology. 

Analysis of Biological Networks 20.440 (Spring) (12 units)
Conceptual and experimental approaches to analyzing complex biological networks and systems, from molecules to human populations, focusing on human pathophysiology and disease. Moving from single component analysis to pathways and networks, combines didactic lectures with in-depth analysis of current literature. Emphasizes the chemistry and biochemistry of underlying biological processes. Topics include linking genes/SNPs to disease, defining pathways, analysis of pathways in vivo, systems-level analysis, and applications of network biology. First half of term focuses on fundamental biological processes and tools/analyses needed by biological engineers, and the second half elaborates on these fundamentals by covering complex biological processes. Students acquire skills in the fundamentals of grant preparation using an NIH format and make an oral presentation.
B. Bryson, M. Yaffe

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Rotations and thesis research

During the first year, students will rotate through three labs of MIT faculty that participate in the Microbiology Graduate Program. These rotations will help provide students broad exposure to microbiology research and will be used to select a lab for their thesis research by the end of the first year. Given the interdisciplinary nature of the program and many research programs, students may be able to work jointly with more than one research supervisor.

Teaching experience

Learning to effectively communicate scientific ideas is an important skill. Students in the Microbiology program will have an opportunity to improve their communication skills through teaching. Each student will serve as a teaching assistant for one semester in an undergraduate or graduate subject related to microbiology. This will typically take place in the second year.

Training in ethical conduct of research

All students will participate in a course on the ethical conduct of research. This will typically take place during the first year.

Qualifying exams

Students will proceed to Ph.D. candidacy after successful completion of a qualifying exam, typically during the second year. Students will submit a written research proposal in the style of a grant or fellowship application based on their planned thesis project. Students will then present and discuss the research proposal with a small committee of faculty.

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Student advising

In the first year, students will be advised by members of the graduate committee. Once students join a thesis lab, the research mentor will be the primary advisor. Early in the second year, students will form a thesis committee and meet at least annually. The committee will consist of faculty with expertise in the student's area of research and collectively provide the breadth expected by the program. The thesis committee will primarily provide advice on research. In addition, in the student's early years the thesis committee will also provide advice on course-work to ensure that students have the appropriate breadth and depth for his or her educational program. In later years, the graduate and thesis committees will also provide students with advice on career options.


All students in the program will receive a stipend/salary that is sufficient to support living in the Cambridge/Boston area. The rate-of-pay will be approximately the same as for graduate students in other MIT departments.

Financial Support and Fellowships

Students in the program will be financially supported throughout their training. This support includes tuition, stipend, and single person health insurance.

During the first year, students are supported by funds from the Provost's Office and departments in the School of Science, and the School of Engineering. These departments include the Departments of Biological Engineering, Biology, Chemical Engineering, and Civil and Environmental Engineering. In subsequent years, students will be supported as Research Assistants in their thesis lab.

Although students will be supported, they are strongly encouraged to apply for fellowships. Students applying to the Microbiology program are eligible for many of these fellowships, including those detailed on the following websites:

National Science Foundation (NSF)

National Defense Science & Engineering Graduate Fellowship (NDSEG)

Under-represented minorities should also see these websites:

Howard Hughes Medical Institute (HHMI)

Ford Foundation

Additionally, students can visit the Office of Graduate Education website for a comprehensive listing.

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Life at MIT

Living in the Boston/Cambridge area offers students a wide range of activities and opportunities outside the lab. MIT has a number of community and student groups, sponsors an extensive intramural sports program, and provides access to excellent athletic facilities. Boston and Cambridge are also rich in cultural activities, the arts, museums, theater, sports, and more. Cape Cod, New Hampshire, and Vermont are all just a couple of hours and less away, offering fantastic skiing, hiking, beach, and other outdoor activities. For more information about life at MIT, visit some of these websites:

MIT Mind & Handbook
Graduate Student Council
Community and Student Groups
MIT Athletics and Intramural Sports
Cambridge Information
Boston Information

Housing and Transportation

Graduate students have the option of living on-campus or off-campus. Upon admission to the program, students will receive housing information. In addition, see the Housing at MIT website.

Boston and Cambridge offer excellent public transportation options for getting around, commuting, and accessing Boston's Logan International Airport. The MBTA runs an extensive subway and bus system and MIT offers subsidized T-passes. For more information, see the MIT Parking and Transportation website.

Application Procedure

See this separate section for complete information on applying to the MIT Microbiology Graduate Program.

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