Elective Course Work

Elective course work (3):

Students must take three graduate level 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. All courses to be offered in person and to be taken for a letter grade.

Fall Electives:

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

Principles of Bioinorganic Chemistry –5.062 (Fall) (G, 6 units) (Part I) D. Suess  
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 Biology –5.52 (Fall) (G, 12 units) R.Raines  
Provides an overview of the core principals of chemistry that underlie biological systems. 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 Physiology –7.62  (Fall) (G, 12 units) G. C. WalkerA. J. Sinskey  
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 Biology –8.591J/7.81J (Fall) (G, 12 units) J. Gore  
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 the graduate version explore the subject in more depth.

Metabolic and Cell Engineering –10.544 (Fall/Spring) (G, 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) (G, 12 units) J. Cao, B. Zhang  
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.

Principals of Molecular Bioengineering 20.420J/10.538J (Fall) (G, 12 units) A. JasanoffE. Fraenkel  
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.

Applied Microbiology – 20.450 (Not offered regularly, consult department ) (G, 12 units) J. Niles, K. Ribbeck
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.

Evontionary and Quantitative Genomics – HST.508 (Fall) (G,12 units) L. MirnyT. Lieberman  
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

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) (G, 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) (G, 12 units) O. Cordero
Provides a general introduction to the diverse roles of microorganisms in natural and artificial environments. Topics include 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. Meets with 1.089A first half of term.

Frontiers of Interdisciplinary Science in Human Health and Disease 5.64J/HST.539J (Spring) (G,12 units) A. ShalekX. 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 Techniques – 5.78 (Spring) (G, 6 units) 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.

Biophysical Technique  7.71 (Spring ) ( G, 12 units) T. Schwartz
Introduces students to modern biophysical methods to study biological systems from atomic, to molecular and cellular scales. Includes an in-depth discussion on the techniques that cover the full resolution range, including X-ray crystallography, electron-, and light microscopy. Discusses other common biophysical techniques for macromolecular characterizations. Lectures cover theoretical principles behind the techniques, and students are given practical laboratory exercises using instrumentation available at MIT. Meets with 5.78 when offered concurrently.

Computational Systems Biology: Deep Learning in the Life Sciences20.490 (Spring) (G,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) (G, 12 units) S. BellE. 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) (G, 12 units) S. SprangerM. 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) (G, 12 units) R. LamasonS. 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) (G, 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) (G, 12 units) D. BartelA. Jain
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) (G, 9 units) Not offered regularly; consult department, Staff
Explores the interactions of chemical engineering, biochemical engineering, and microbiology with particular emphasis on applications to bioprocess development. Examines mathematical representations of microbial systems, especially with regard to the kinetics of growth, death, and metabolism. Discusses the fundamentals of bioreactor design and operation, including continuous fermentation, mass transfer, and agitation. Examples encompass both enzyme and whole cell systems. Presents concepts in process development for microbial and animal cell cultures, with considerations towards production of biological products ranging from chiral specialty chemicals/pharmaceuticals to therapeutic proteins. Concludes with a discussion of aspects of cellular engineering and the role of molecular biology in addressing process development problems.

Analysis of Biological Networks – 20.440 (Spring) (12 units) B. BrysonF. White
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.