Bi 192. Introduction to Systems Biology
6 units (2-0-4); first term. Prerequisite: graduate standing; or Ma1abc and either Bi8, CS1, or ACM95; or instructor’s permission. The course will explore how to analyze biology from a systems-level point of view. Given what biological systems do and the constraints they face, what general properties might biological systems have? Students will explore design principles in biology, including plasticity, exploratory behavior, weak-linkage, constraints that deconstrain, robustness, (non)optimality, and evolvability. The class will read the equivalent of 2-3 scientific papers every week. The format will be a seminar with active discussion from all students. Class size will be limited to a maximum of 15. Students from all backgrounds are welcome.
Instructor: Goentoro

Bi 250 b. Topics in Systems Biology. 9 units (3-0-6); second term. Prerequisite: graduate standing. The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale. Instructor: Murray, Elowitz.

Reading Systems Biology
Seminar; Staff

Bi/Ch 132. Biophysics of Macromolecules. 9 units (3-0-6); first term. Recommended prerequisite: Bi/Ch 110. Structural and functional aspects of nucleic acids and proteins, including hybridization; electrophoretic behavior of nucleic acids; principles and energetics of folding of polypeptide chains in proteins; allostery and cooperativity in protein action; enzyme kinetics and mechanisms; and methods of structure determination, such as X-ray diffraction and magnetic resonance. Structure and function of metalloenzymes. Instructors: Beauchamp, Cai.

CDS 140 ab. Introduction to Dynamics. 9 units (3-0-6); second, third terms. Prerequisites: ACM 95/100 ab or equivalent. Basics topics in dynamics in Euclidean space, including equilibria, stability, Lyapunov functions, periodic solutions, Poincaré-Bendixon theory, Poincaré maps. Attractors and structural stability. Introduction to simple bifurcations and eigenvalue crossing conditions. Discussion of bifurcations in applications, invariant manifolds, the method of averaging and singular perturbation theory. Additional topics may include Hamiltonian and Lagrangian systems. Instructors: Murray, MacMynowski, Staff.

BE/APh 161. Physical Biology of the Cell. 12 units (3-0-9); second term. Prerequisites: Ph 2ab and ACM 95abc, or background in differential equations and statistical and quantum mechanics, or instructor's written permission. Physical models applied to the analysis of biological structures ranging from individual proteins and DNA to entire cells. Topics include the force response of proteins and DNA, models of molecular motors, DNA packing in viruses and eukaryotes, mechanics of membranes, and membrane proteins and cell motility. Instructor: Phillips.

Bi 182. Gene Regulation Systems and the Control of Embryonic Development. 6 units (2-0-4); second term. Prerequisites: Bi 8 and at least one of the following: Bi 111, Bi 114, or Bi 122 (or equivalents). This course will cover the principles of developmental gene regulation in animals with emphasis on causal mechanism; theory, solution, and explanatory power of gene regulatory networks and how they are directly encoded in the genome; regulatory mechanisms underlying embryonic and postembryonic processes of development. Specific examples will be drawn mainly from sea urchin and Drosophila, but comparative treatment of other modes of development will be included. Given in alternate years. Instructors: Davidson, Stathopoulos.

Bi 188. Human Genetics and Genomics. 6 units (2-0-4); third term. Prerequisite: Bi 122; or graduate standing and instructor’s permission. Introduction to the genetics of humans. Subjects covered include human genome structure, genetic diseases and predispositions, the human genome project, forensic use of human genetic markers, human variability, and human evolution. Instructor: Wold.

Bi 190. Systems Genetics. 6 units (2-0-4); third term. Prerequisites: Bi 122. Lectures and discussions covering how genetic analysis is used to solve biological problems. Emphasis is on genetic and genome-scale approaches used in model organisms such as yeast, flies, worms, and mice to elucidate the function of genes, genetic pathways and genetic networks. Instructor: Sternberg.

BE/CS/CNS/Bi 191 ab. Biomolecular Computation. 9 units (3-0-6) second term; (2-4-3) third term. Prerequisite: none. Recommended: ChE/BE 163, CS 21, CS 129 ab, or equivalent. This course investigates computation by molecular systems, emphasizing models of computation based on the underlying physics, chemistry, and organization of biological cells. We will explore programmability, complexity, simulation of and reasoning about abstract models of chemical reaction networks, molecular folding, molecular self-assembly, and molecular motors, with an emphasis on universal architectures for computation, control, and construction within molecular systems. If time permits, we will also discuss biological example systems such as signal transduction, genetic regulatory networks, and the cytoskeleton; physical limits of computation, reversibility, reliability, and the role of noise, DNA-based computers and DNA nanotechnology. Part a develops fundamental results; part b is a reading and research course: classic and current papers will be discussed, and students will do projects on current research topics. Instructor: Winfree.

Bi 199. Introduction to MATLAB for Biologists. 6 units (3-0-3); second term. This hands-on course provides an introduction to MATLAB's structure and syntax, writing of functions and scripts, image analysis, and data visualization. Instructor: Kennedy

Bi 214. Hematopoiesis: A Developmental System. 6 units (2-0-4); third term. Prerequisite: Bi 114, or Bi 182, or Bi 117 plus Bi/Ch 111, or graduate standing. An advanced course with lectures and seminar presentations, based on reading from the current literature. The characteristics of blood cells offer unique insights into the molecular basis of lineage commitment and the mechanisms that control the production of diverse cell types from pluripotent precursors. The course will cover the nature of stem cells, the lineage relationships among differentiated cell types, the role of cytokines and cytokine receptors, apoptosis and lineage-specific proliferation, and how differentiation works at the level of gene regulation and regulatory networks. Roles of prominent regulatory molecules in hematopoietic development will be compared with their roles in other developmental systems. Emphasis will be on explanation of cellular and system-level phenomena in terms of molecular mechanisms. Instructor: Rothenberg.

Gene Regulatory Networks Instructor: Davidson.