Instructor: Rebecca Schulman
Time: Monday / Wednesday 3-4:15
Location: Hackerman 320
Office Hours: By appointment (rschulm3 at jhu dot edu)

News

October 24 Final project descriptions
October 31 Here is the full reading list for the course: reading list.

Course summary

Inside every cell, decisions are constantly being made. Should genes be turned on or off? Should the cell grow, divide or die? These decisions are made autonomously by the cells components and usually take into account information gained from sensing the cell's environment, like the concentration of metabolites or the type of neighboring cells.

This course considers how cells, and molecules in general, make decisions, and how we can in turn decision biomolecular systems that similar make decisions and control processes via chemical reactions.

Sample course reading

Book

Michael A. Savageau. Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology.

Articles

Jacques Monod, Jean-Pierre Changeux and François Jacob. Allosteric proteins and cellular control systems. Journal of Molecular Biology 6 (4), 306-329, 1963. Download Original Link


Jesse Stricker, Scott Cookson, Matthew R. Bennett, William H. Mather, Lev S. Tsimring and Jeff Hasty. A fast, robust and tunable synthetic gene oscillator. Nature 456, 516-519, 2008. Download Original link


Keller Rinaudo, Leonidas Bleris, Rohan Maddamsetti, Sairam Subramanian, Ron Weiss and Yaakov Benenson. A universal RNAi-based logic evaluator that operates in mammalian cells. Nature Biotechnology 25, 795-801, 2007. Download Original link

Sergi Regot, Javier Macia, Núria Conde, Kentaro Furukawa, Jimmy Kjellén, Tom Peeters, Stefan Hohmann, Eulàlia de Nadal, Francesca Posas, Ricard Solé. Distributed biological computation with multicellular engineered networks. Nature 469, 207-211, 2011. Download Original link


Timothy S. Gardner, Charles R. Cantor and James J. Collins. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339-342, 2000. Download Original link


Tomas Helikar, John Konvalina, Jack Heidel, and Jim A. Rogers. Emergent decision-making in biological signal transduction networks. PNAS 105 (6) 1913-1918, 2008. Download


David Soloveichik, Georg Seelig and Erik Winfree. DNA as a universal substrate for chemical kinetics. PNAS 107 (12), 5393-5398, 2010. Download Original link


A. Prasanna de Silva and Seiichi Uchiyama. Molecular logic and computing. Nature Nanotechnology 2, 399-410, 2007. Download Original link


Phil Senum and Marc Riedel. Rate-Independent Constructs for Chemical Computation. PLoS ONE, 6 (6), 2011. Download Original link


Yuri Lazebnik. Can a biologist fix a radio?—Or, what I learned while studying apoptosis. Cancer Cell 2 (3) 179-182, 2002. Download Original link


J. J. Hopfield. Kinetic Proofreading: A New Mechanism for Reducing Errors in Biosynthetic Processes Requiring High Specificity. PNAS 71 (10), 4135-4139, 1974. Download Original link

Course philosophy

This course is designed to cover the state of the art in the area of understanding and designing autonomous decision-making and computing systems for biology and biomolecular systems. The course covers what is still a new area of research and it lies at the intersection of biomolecular engineering, synthetic biology, computer science and control theory. It is not intended to be a comprehensive course, as there is no comprehensive body of knowledge yet! Instead we will cover interdisciplinary foundational material and read and discuss seminal and recent literature. Since this is also a fertile research area, some of the course will be devoted to a final project where a research question will be proposed.

Course structure

Each class will cover either a research paper or reading from a book which will be available to download online. For each reading, you are expected to write a paragraph or two response. The response should summarize the contributions of the paper, evaluate the results of the work and make suggestions for extensions or variation on the work. The goal of the summary is to prepare points for discussion in class. The first half of each class will be a discussion of the assigned reading. The second half of each class will be a lecture in which new material that is relevant to the next reading is presented. There will be a break. The other major component to the course will be a final project, which will present an idea for building upon the readings we cover in class. Example ideas for final projects include

• A genetic coin-flipping device
• A low-noise signal-transduction system
• A reaction-diffusion program that builds a bulls eye pattern

We will discuss ideas for final projects around the middle of the term. These projects will consist of a writeup and presentation. The last couple of weeks of the term will be dedicated to project presentations.

Assignments and Grading

The goal of the course is for you to develop a familiarity with the research field of molecular control and decision making and to be able to integrate concepts from the field into your own work. Grades will reflect

1. Paper and reading write-ups (30%)
2. Class discussion (30%)
3. Final project write-up and presentation (40%)