These courses are designed specifically for graduate students. In addition to the courses in Biology that are listed below, students may take courses in other departments at MIT or at other universities in the area. See the Biology Education Office, 68-120, for more information.

All classes have materials and further information on Stellar course websites. See also the MIT Course Catalog online.

Required Courses
Method & Logic in Molecular Biology – 7.50 Fall
(Leonard Guarante , Michael Hemann, David Housman, Richard Hynes, Jackie Lees, David Sabatini)
Logic and experimental design: an in-depth discussion and assessment of biochemical, physical, genetic, and cell biological methods employed in testing hypotheses. Limited to Course 7 graduate students.

Principles of Biochemical Analysis - 7.51 Fall
(Bob Sauer, Frank Solomon)
Fundamental principles of biochemistry. Analysis of the structure and mechanism of catalytic and regulatory macromolecules.

Genetics for Graduate Students - 7.52 Fall
(Bob Horvitz, David Housman, Angelika Amon)
Principles and approaches of genetic analysis, including Mendelian inheritance and prokaryotic genetics, developmental genetics, neurogenetics, population genetics, human genetics, genomics, and epigenetics. Recitations and problem sets supplement lectures.

Elective courses
(grad students typically choose four, based on their interests).

Principles and Practice of Drug Development - 7.547J Fall
(T. J Allen, C.L. Cooney, S.N. Finkelstein, Gokaraju K Raju, R. H. Rubin & Anthony Sinskey)
Description and critical assessment of the major issues and stages of developing a pharmaceutical or biopharmaceutical. Drug discovery, preclinical development, clinical investigation, manufacturing and regulatory issues considered for small and large molecules. Economic and financial considerations of the drug development process. Multidisciplinary perspective from faculty in clinical; life; and management sciences; as well as industry guests.

Perspectives in Biological Engineering - 7.548J Spring
(Ernest Fraenkel, Forest White)
An in-depth presentation of how engineering and biological approaches can be combined to solve problems in science and technology, emphasizing integration of biological information and methodologies with engineering analysis, synthesis, and design. Emphasis on molecular mechanisms underlying cellular processes, including signal transduction, gene expression networks, and functional responses. Enrollment restricted to Biological Engineering and Biology graduate students.

Case Studies and Strategies in Drug Discovery and Development - 7.549J Spring
(S. R. Tannenbaum, E. Berndt, Anthony Sinskey) (not offered 08-09)
The stages in drug discovery and development begin with target identification and end with the submission of preclinical and clinical data to the regulatory authorities. Following identification of a lead compound, there is optimization of structures for pharmaceutical properties, bioavailability, and safety. Subject relies on actual cases presented by the scientist(s) involved in discovery and drug development. A major goal is to analyze the cases and determine how the discovery and development process might be influenced by new and future technologies.

Foundations of Cell Biology - 7.56 Spring
(Frank Solomon & Steve Bell)
Designed for graduate students interested in understanding biological processes at the cellular level, this course serves biologists working in a wide range of areas and provides the foundation to approach the current literature. The goals are to discuss fundamental topics in cell and molecular biology; demonstrate how the major questions have been approached, technically and intellectually; analyze how one interprets the data produced by those approaches; and identify the questions that remain. Topics include macromolecular synthesis, assembly of cellular complexes and structures, control of cell division, and cell signaling. Familiarity with the basics of biochemistry and genetics is assumed.

Quantitative Biology for Graduate Students - 7.57 Spring
(Michael Laub & Aviv Regev)
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

Molecular Biology - 7.58 Spring
(Tania Baker & Steve Bell)
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.

Teaching College-Level Science - 7.59J Spring
(S. Mahajan)
Participatory seminar focuses on the knowledge and skills necessary for teaching science and engineering in higher education. Topics include: theories of adult learning; course development; promoting active learning, problem solving, and critical thinking in students; communicating with a diverse student body; using educational technology to further learning; lecturing; creating effective tests and assignments; and assessment and evaluation. Students research and present a relevant topic of particular interest. Subject is appropriate for both novices and those with teaching experience.

Cell Biology: Structure and Functions of the Nucleus - 7.60 Spring
(Phil Sharp & Richard Young)
Eukaryotic genome structure, function, and expression, processing of RNA, and regulation of the cell cycle. Emphasis on the techniques and logic used to address important problems in nuclear cell biology. Lectures on broad topic areas in nuclear cell biology and discussions on representative recent papers.

Eukaryotic Cell Biology: Principles and Practice - 7.61 Fall
(Richard Hynes, Monty Krieger)
Emphasizes methods and logic used to analyze eukaryotic cells in diverse systems (e.g., yeast, fly, worm, mouse, human; development, neurons). Subject combines lectures and in-depth roundtable discussions of literature readings with active participation of faculty experts. Focuses on membranes, organelles, the cell surface, cytoskeleton and extracellular matrix. Topics include membrane protein structure, cell surface receptors and transporters; signal transduction pathways; membrane trafficking/sorting/secretion; adhesion and its effects on organization, migration and polarity of cells; regulation of the cell cycle; integration of cells into tissues and organs. Ranges from basic studies to applications to human disease, while emphasizing critical analysis of experimental approaches. Limited enrollment.

Microbial Physiology - 7.62 Fall (meets with 7.21)
(Graham Walker, Boris Magasanik, Dianne Newman)
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 symbiosis, quorum sensing, global responses to DNA damage, and biofilms. Students taking the graduate version are expected to explore the subject in greater depth.

Immunology - 7.63 Spring (meets with 7.23)
(Lisa Steiner, Jianzhu Chen, Hidde Ploegh)
A 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; immunoglobulin, T cell receptor, and major histocompatibility complex (MHC) genes and structure; development and functions of B and T lymphocytes; immune responses to infections and tumors; hypersensitivity, autoimmunity, and immunodeficiencies. Particular attention is paid to the development and function of the immune system as a whole as studied by modern methods and techniques.

Genetic Neurobiology - 7.67J Fall
(William (Chip) Quinn & Troy Littleton)
Specific functions of neurons, the interactions of neurons in development, and the organization of neuronal ensembles to produce behavior, by functional analysis of mutations and molecular analysis of their genes. Concentrates on work with nematodes, fruit flies, mice, and humans.

Cellular and Molecular Neurobiology - 7.68J Spring
(Morgan Sheng, Martha Constantine-Paton & William (Chip) Quinn)
Major areas of cellular and molecular neurobiology including excitable cells and membranes, ion channels and receptors, synaptic transmission, cell-type determination, axon guidance, neuronal cell biology, neurotrophin signaling and cell survival, synapse formation and neural plasticity. Includes lectures and exams, and involves presentation and discussion of primary literature. Focuses on major concepts and recent advances in experimental neuroscience.

Developmental Neurobiology - 7.69J Spring (not offered 08-09)
(Elly Nedivi)
Considers molecular control of neural specification, formation of neuronal connections, construction of neural systems, and the contributions of experience to shaping brain structure and function. Topics include: neural induction and pattern formation, cell lineage and fate determination, neuronal migration, axon guidance, synapse formation and stabilization, activity-dependent development and critical periods, development of behavior. In addition to final exam, analysis and presentation of research papers required for final grade. Additional readings required for graduate credit. Offered alternate years. Meets w/9.18.

Regulation of Gene Expression - 7.70 Spring
(Gerald Fink, Richard Young, Laurie Boyer)
Cells utilize a variety of mechanisms to regulate gene expression, growth, development, and behavior in response to both external and internal conditions. Seminar examines basic principles of biological regulation and focuses on examples that underpin the principles, as well as those that challenge certain long-held views. Enrollment limited to 40.

Biophysical Chemistry Techniques - 7.71 Spring (not offered 08-09)
(Thomas Schwartz, Catherine Drennan)
For students who want to understand the benefits and caveats of biophysical techniques used to ascertain the structure of macromolecules, especially on the 3-D level. The first half of the course focuses on X-ray crystallography, the single most important technique used in determining the 3-D structure of macromolecules. Discussion of crystallographic theory is complemented with exercises such as crystallization, data processing, and model building. In the second half of the course, biophysical techniques are covered that supplement the 3-D characterization of biological macromolecules. Topics include CD spectroscopy, isothermal calorimetry, analytical ultracentrifugation, dynamic light and small-angle X-ray scattering. Theoretical principles behind the techniques are covered, and students are given practical exercise using instrumentation available at MIT. Meets with 5.78.

Development and Evolution - 7.72 Fall
(Hazel Sive & Terry Orr-Weaver)
Graduate level lecture and literature discussion subject covering animal development and evolution. Focus on molecular mechanisms, experimental approaches, and relevant disorders. Comparison of vertebrate (mouse, chick, frog, fish) and invertebrate (fly, worm) models. Topics include the early body plan, cell type determination and diversity, organogenesis, morphogenesis, stem cells, cloning, and issues in human development.

Topics in Metabolic Biochemistry - 7.75J Fall
(Gene Brown)
Special topics include major metabolic pathways for the biosynthesis of certain cellular constituents and oxidative metabolism. Emphasis is on enzymology and methods used to understand metabolism and enzymatic processes. Meets w/7.35.

Topics in Protein Biochemistry - 7.76 Spring
(Bob Sauer & Amy Keating)
In-depth analysis and discussion of classic and current literature, with an emphasis on protein structure and function. Topics include binding specificity; cooperativity and allostery; protein folding and misfolding; macromolecular assembly; sequence homology and prediction of structure; and protein engineering and design. Undergraduates should have taken 7.71 or 5.64.

Nucleic Acids, Structure, Function, Evolution and Their Interactions 7.77 Spring
(Tom RajBhandary & David Bartel)
Lectures, analysis, and discussion of current literature, student presentations. Biochemical, biophysical, and genetic approaches to understanding nucleic acids. General properties, functions, and structural motifs of DNA and RNA. DNAs and RNAs as catalysts. Interaction of nucleic acids with proteins such as repressors, restriction and modification enzymes, aminoacyl-tRNA synthetases and other proteins of the translational machinery. RNA protein recognition. Selection and engineering approaches for generating nucleic acid molecules with novel catalytic and binding properties.

Biological Chemistry II 7.80 Spring
(Alice Ting)
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, and polymerases. Emphasis is on experimental methods used to unravel these processes and how these processes fit into the cellular context and coordinate regulation. Students taking the graduate version are expected to explore the subject in greater depth.

Systems Biology - 7.81J Fall (not offered 08-09)
(A. van Oudenaarden)
Introduction to mathematical modeling techniques to address key questions in modern biology. Overview of modeling techniques in molecular biology and genetics, cell biology and developmental biology. Description of key experiments that validate mathematical models. Topics include molecular systems biology — constructing and modeling of genetic networks, control theory and genetic networks, lambda phage as a genetic switch, synthetic genetic switches, bacterial chemotaxis, genetic oscillators, and circadian rhythms; cellular systems biology — reaction diffusion equations, local activation and global inhibition models, gradient sensing systems, and center-finding networks; developmental systems biology — general pattern formation models, modeling cell-cell communication, quorum sensing, and models for Drosophila development.

Topics of Mammalian Development and Genetics - 7.82 Spring
(Rudolf Jaenisch & David Page)
Seminar covering embryologic, molecular, and genetic approaches to development in mice and humans. Topics include preimplantation development; gastrulation; embryonic stem cells, gene targeting and nuclear cloning; genomic imprinting; X-inactivation; sex determination; germ cells; association and linkage analysis.

The Protein Folding Problem - 7.88J Spring
(Jon King, Susan Lindquist)
Many chronic human diseases are associated with misfolding or aggregation of particular proteins or their fragments. Notable examples include Alzheimer's disease, Parkinson's disease, Huntington's disease, bovine spongiform encephalopathy (mad cow disease), human prion diseases, and light chain amyloidosis. Covers the underlying protein and cell biochemistry, including folding of newly synthesized polypeptide chains within cells; unfolding and refolding of proteins in vitro; folding intermediates, aggregation, and competing off-pathway reactions; amyloid fibril structure and polymerization; amyloids that produce biofilms, pigments, and other functional structures; roles of chaperonins, isomerases, and other helper proteins. Examines key model systems, including yeast, nematodes, flies and mice, as well as human pathologies and phenotypes.

Topics in Computational and Systems Biology 7.89J Fall
(Chris Burge)
Seminar based on research literature. Papers covered are selected to illustrate important problems and different approaches in the field of computational and systems biology, and provide students a framework from which to evaluate new developments. Required of, and restricted to, first-year CSBi PhD students.

Foundations 7.91J Spring
(Amy Keating, Chris Burge)
Introduction to computational and systems biology emphasizing fundamentals of nucleic acid, protein sequence, and structural analysis, as well as the analysis of complex biological systems. 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, dead-end elimination and energy minimization approaches. Exposure to emerging research areas. Designed for graduate students and advanced undergraduates 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. Enrollment limited to 90.

Neurology, Neuropsychology, and Neurobiology of Aging - 7.92J Spring
(S. Corkin, L-H. Tsai)
Lectures and discussions explore the clinical, cognitive, and cellular-molecular aspects of brain aging processes. Topics include loss of memory and other cognitive capacities in normal aging and neurodegenerative conditions, with an emphasis on Alzheimer's disease and associated mouse models. Other topics include neurodegenerative movement disorders, such as Parkinson's and Huntington's diseases. Based on lectures, readings from the primary literature, and discussions. Students are expected to present topics based on their readings. One written midterm test and one final examination.

Cancer Biology - 7.95 Spring
(Jackie Lees & Bob Weinberg)
Intensive analysis of historical and current developments in cancer biology. Topics include principles of transformation, viral and cellular oncogenes, tumor suppressor genes, tumor-cell growth, apoptosis, principles of cancer biology, and cancer genetics. Detailed analyses of the current research literature including important research reports published in recent years. Limited enrollment.

Neural Plasticity in Learning and Development - 7.98J Spring
(Susumu Tonegawa, Chip Quinn, Matt Wilson & Mark Bear )
Examination of the role of neural plasticity during learning and memory of invertebrates and mammals. Detailed critical analysis of the current literature of molecular, cellular, genetic, electrophysiological, and behavioral studies. Student-directed presentations and discussions of original papers supplemented by introductory lectures. Juniors and seniors require instructor's permission.