The Graduate Program

Overview

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 -VIRTUAL
    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. Preference to first-year Microbiology and Biology students. 

  2. Microbial Genetics and Evolution -7.493J (Fall) (12 units) A. D. Grossman, O. Cordero -VIRTUAL
    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 Analysis of Biological Data - 7.571 (Spring) ( 6 units) J. Davis
    Application of probability theory and statistical methods to analyze biological data. Topics include: descriptive and inferential statistics, an introduction to Bayesian statistics, design of quantitative experiments, and methods to analyze high-dimensional datasets. A conceptual understanding of topics is emphasized, and methods are illustrated using the Python programming language. Although a basic understanding of Python is encouraged, no programming experience is required. Students taking the graduate version are expected to explore the subject in greater depth. 

    AND: (Must complete both courses )
    Quantitative Measurements and Modeling of Biological Systems- 7.572 (Spring) ( 6 units) G. W. Li
    Quantitative experimental design, data analysis, and modeling for biological systems. Topics include absolute/relative quantification, noise and reproducibility, regression and correlation, and modeling of population growth, gene expression, cellular dynamics, feedback regulation, oscillation. Students taking the graduate version are expected to explore the subject in greater depth.

    Biochemistry.
    One
    of the following courses:
    Principles of Biochemical Analysis -7.51 (Fall) (12 units) A. Keating, R. T. Sauer - VIRTUAL
    Principles of biochemistry, emphasizing structure, equilibrium studies, kinetics, informatics, single-molecule studies, 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. 
    OR:
    Fundamentals of Chemical Biology -7.80 (Spring) (12 units) B. Imperiali,L. Kiessling, R. Raines
    Spanning the fields of biology, chemistry, and engineering, this class introduces students to the principles of chemical biology and the application of chemical and physical methods and reagents to the study and manipulation of biological systems. Topics include nucleic acid structure, recognition, and manipulation; protein folding and stability, and proteostasis; bioorthogonal reactions and activity-based protein profiling; chemical genetics and small-molecule inhibitor screening; fluorescent probes for biological analysis and imaging; and unnatural amino acid mutagenesis. The class will also discuss the logic of dynamic post-translational modification reactions with an emphasis on chemical biology approaches for studying complex processes including glycosylation, phosphorylation, and lipidation. Students taking the graduate version are expected to explore the subject in greater depth.

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) D. Suess -VIRTUAL
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. 

Tutorial in Chemical Biology5.52 (Fall) (12 units) R.Raines - VIRTAUL
Provides an overview of the core principals of chemistry that underlie biological systms. Students expore research topics and methods in chemical biology by participating in laboratory rotations, then present on experiemnts performed during each rotation. Intended for first-year graduate students with a strong interest in biological chemistry.


Microbial Physiology7.62 (Fall) (12 units) G. C. Walker, A. J. Sinskey -VIRTUAL
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. 


Systems Biology8.591J/7.81J (Fall) (12 units) J. Gore -VIRTUAL
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.


Metabolic and Cell Engineering10.544 (Fall) (Spring) (12 units) Staff
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. 


Statistical Thermodynamics 10.546J/5.70J (Fall) (12 units) J. Cao, B. Zhang - VIRTUAL
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. J. Cao, B. Zhang

Principals of Molecular Bioengineering 20.420J/10.538J (Fall) (12 units) A. Jasanoff, E. Fraenkel - VIRTUAL
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. 

Evontionary and Quantitative Genomics HST.508 (Fall) (12 units) L. Mirny, T. Lieberman - VIRTUAL
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.

Applied Microbiology 20.450 (Fall) (12 units) J. Niles, K. Ribbeck -VIRTUAL
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. Not offered 2020-2021

Spring Electives

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

Genomics and Evolution of Infectious Disease- 1.881J/HST.538J (Spring) (12 units) T. Lieberman
Provides a thorough introduction to the forces driving infectious disease evolution, practical experience with bioinformatics and computational tools, and discussions of current topics relevant to public health. Topics include mechanisms of genome variation in bacteria and viruses, population genetics, outbreak detection and tracking, strategies to impede the evolution of drug resistance, emergence of new disease, and microbiomes and metagenomics. Discusses primary literature and computational assignments. Students taking graduate version complete additional assignments. 

Earth's Microbiomes1.89 (Spring) (12 units) M. Polz
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. 

Frontiers of Interdisciplinary Science in Human Health and Disease 5.64J/HST.539 (Spring) (12 units) A. Shalek, X. Wang
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. 

Biophysical Chemistry Techniques5.78 (6 units first half) (Spring) C.Drennan
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. Not offered 2020-2021

Structural and Biophysical Analysis of Biological Macromolecules 7.71 (Spring) (12 units)T. Schwartz
Studies theory and practice of 3-D analysis of macromolecules, using X-ray crystallography and EM analysis. Covers biophysical methods to characterize molecular properties and interactions. Includes discussion of current literature and, importantly, practical exercises in crystallization, model building, and the use of shared instrumentation available at MIT. Meets with 5.78 when offered concurrently.  Not offered 2020-2021

Computational Systems Biology: Deep Learning in the Life Sciences20.490 (Spring) (12 units) D. K. Gifford
Presents innovative approaches to computational problems in the life sciences, focusing on deep learning-based approaches with comparisons to conventional methods. Topics include protein-DNA interaction, chromatin accessibility, regulatory variant interpretation, medical image understanding, medical record understanding, therapeutic design, and experiment design (the choice and interpretation of interventions). Focuses on machine learning model selection, robustness, and interpretation. Teams complete a multidisciplinary final research project using TensorFlow or other framework. Provides a comprehensive introduction to each life sciences problem, but relies upon students understanding probabilistic problem formulations. Students taking graduate version complete additional assignments.

Molecular Biology 7.58 (Spring) (12 units) S. Bell, E. Calo
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. 

Immunology 7.63J/20.630J (Spring) (12 units) S. Spranger, M. Birnbaum
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. 

Molecular Basis of Infectious Disease - 7.66 (Spring) (12 units) R. Lamason, S. Lourido
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. 

Regulation of Gene Expression 7.70 (Spring) (12 units) Staff
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. 

Nucleic Acids, Structure, Function, Evolution and Their Interactions with Proteins 7.77 (Spring) (12 units) D. Bartel, U. RajBhandary
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. 


Biochemical Engineering 10.542 (Spring) (12 units) Not offered regularly; consult department
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. 
Staff

Analysis of Biological Networks 20.440 (Spring) (12 units) B. Bryson, P. Blainey
Explores computational and experimental approaches to analyzing complex biological networks and systems. Includes genomics, transcriptomics, proteomics, metabolomics and microscopy. Stresses the practical considerations required when designing and performing experiments. Also focuses on selection and implementation of appropriate computational tools for processing, visualizing, and integrating different types of experimental data, including supervised and unsupervised machine learning methods, and multi-omics modelling. Students use statistical methods to test hypotheses and assess the validity of conclusions. In problem sets, students read current literature, develop their skills in Python and R, and interpret quantitative results in a biological manner. In the second half of term, students work in groups to complete a project in which they apply the computational approaches covered. 

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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.

Stipend

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.

For Emergencies | Accessibility

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