Core Sequence
Introduction to Synthetic Biology (Fall)
(EE400D/546A, CSE490V/599V, BIOE498D/599D)
Georg Seelig
This course is an introduction to the theory and practice of building artificial biochemical reaction networks and devices. Presently artificial biochemical devices and circuits are difficult to design, behave unpredictably, and are difficult to analyze; however new tools and approaches are emerging rapidly and promise to make engineering living systems and components broadly useful. Many of these emerging tools are based on tools in computer science (digital logic, automata theory) and electrical engineering (circuit theory, feedback control, signal processing, dynamical systems). Concepts from synthetic biology have applications in cell and tissue engineering, gene therapy, biologically derived drugs and materials, alternative fuels, biosensors, and much more.
Laboratory Methods in Synthetic Biology (Winter)
(EE425)
Eric Klavins
This course is an introduction to the theory and practice of building artificial biochemical reaction networks and devices. BioCircuits have applications in cell and tissue engineering, gene therapy, biologically derived drugs and materials, alternative fuels, biosensors, and much more. Presently artificial biochemical devices and circuits are difficult to design, behave unpredictably, and are difficult to analyze; however new tools and approaches are emerging rapidly and promise to make engineering living systems and components broadly useful. Many of these emerging tools are based on tools in computer science (digital logic, automata theory) and electrical engineering (circuit theory, feedback control, signal processing, dynamical systems). The course is open to all engineering students and does not assume any background in biology or chemistry. It will consist of a lecture and a lab. The lab will consist of about six hours a week in the lab (EE B031) and 3 hours working on lab reports and data analysis.
Advanced Systems and Synthetic Biology (Winter)
(BIOE424)
Herbert Sauro
This course offers an advanced course on system and synthetic biology. The course is designed for seniors and/or graduates who have an interest in bioengineering at the cellular network level. Topics include kinetics, modeling, stoichiometry, control theory, metabolic systems, signaling, motifs, class journal club and a one week project. All topics are set against problems in synthetic biology.
Text Books:
Uri Alon An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman and Hall/CRC; 1 edition (July 7, 2006), ISBN-10: 1584886420
Hamid Bolouri Computational Modelling Of Gene Regulatory Networks — A Primer. Imperial College Press; 1 edition (August 13, 2008), ISBN-10: 1848162219
Dennis Bray Wetware: A Computer in Every Living Cell. Yale University Press (May 26, 2009), ISBN-10: 0300141734
Edda Klipp, Wolfram Liebermeister, Christoph Wierling and Alex Kowlad, Systems Biology: A Textbook. Wiley-VCH; 1 edition (August 12, 2009), ISBN-10: 3527318747
Chris Myers Engineering Genetic Circuits. Chapman & Hall; 1 edition (July 14, 2009), ISBN-10: 1420083244
Rob Phillips, Jane Kondev and Julie Theriot Physical Biology of the Cell. Garland Science; 1 edition (November 18, 2008), ISBN-10: 0815341636
Elective Courses
Molecular Programming (Spring)
(CSE599X)
Georg Seelig
Topics: DNA in biology, chemical register machines, DNA computing, digital abstraction with chemistry, algorithmic self-assembly, digital abstraction with chemistry, DNA logic circuits, tile assembly and SAT, transcription a logic circuits, reversible computing and polymer Turing machines, smart drug state machines, formalizing DNA strand displacement cascades, how to self-assemble and electronic circuit, computational power of chemistry from a computer science point of view, molecular programs that specify shapes, making life, computational tools for nanotechnology, predicting RNA fold kinetics
Energy and Entropy (4) (Spring)
(Chem E 325)
Introduction to the basic principles of thermodynamics from both microscopic and macroscopic points of view. Emphasis on equilibrium phenomena, and the trade-off of energy and disorder in determining structure and properties. Applications of thermodynamics in process design and analysis. Prerequisite: either CHEM 142, or CHEM 145; either MATH 126 or MATH 136; PHYS 121. Offered: AWSpS
Biochemical Engineering (3) (Spring)
(Chem E 467)
Application of basic chemical engineering principles to biochemical and biological process industries such as fermentation, enzyme technology, and biological waste treatment. Rapid overview of relevant microbiology, biochemistry, and molecular genetics. Design and analysis of biological reactors and product recovery operations. Prerequisite: CHEM E 340; either CHEM 223, CHEM 237, or CHEM 335; recommended: CHEM E 465. Offered: jointly with BIOEN 467; W.
Introduction to Biological Physics (Spring)
(Physics 429 Winter)
This course aims to help students apply their physics knowledge to building models to handle biological systems in a quantitative manner. Topics: Biology by the numbers, sizes of cells and structures, energy and energy storage, mechanical and statistical mechanics, random walks, electrostatics, water, statistical view of biology, biological electricity.
Introduction to Mathematical Biology (5) (Winter)
(AMATH 422)
Modeling biological systems with differential and difference equations. Examples from: ecology (population growth, disease dynamics): biochemistry and cell biology; and neurobiology (Hodgkin-Huxley and neural networks). Methods include linear stability analyses, phase-plane analyses, and perturbation theory. Prerequisite: either MATH 307 or AMATH 351. Offered: A.
Mathematical Biology: Stochastic Models (5) (Spring)
(AMATH 423)
Focuses on stochastic modeling and analysis of biological and medical systems. Biological topics include biochemistry, population genetics, genomics, population and community ecology, and neuroscience. Mathematical topics include generating functions, the Poisson process, Markov processes and master equations, branching processes, and elementary diffusion theory. Prerequisite: either AMATH 351 or MATH 307, MATH/STAT 390. Offered: W.
Mathematical Biology: Spatiotemporal Models (3) (Spring)
(AMATH 424)
Examines partial differential equations for biological dynamics in space and time. Draws examples form molecular and cell biology, ecology, epidemiology, and neurobiology. Topics include reaction-diffusion equations for biochemical reactions, calcium wave propagation in excitable medium, and models for invading biological populations. Prerequisite: AMATH 353. Offered: Sp.
Gene Regulation (Spring)
(Genome 551)
John Stamatoyannopoulos
Course covers fundamentals of gene regulation in eukaryotes including principles of cis and trans regulation of gene expression; DNA and RNA binding proteins; role of chromatin structure in gene expression; epigenetic regulatory mechanisms; RNA-based regulatory mechanisms; and post-transcriptional regulation. The course centers on reading and discussion of landmark primary literature in the aforementioned areas.