Protein Fundamentals (BCMB/HGEN/MGCB 30400). The course covers the physical chemical phenomena that define protein structure and function. Topics include: the principles of protein folding, molecular motion and molecular recognition; protein evolution, design and engineering; enzyme catalysis; regulation of protein function and molecular machines; proteomics and systems biology. Koide, Keenan. Autumn.
Structure and Function of Membrane Proteins (BCMB/MGCB 32300). This course will be an in depth assessment of the structure and function of biological membranes. In addition to lectures, directed discussions of papers from the literature will be used. The main topics of the courses are: (1) Energetic and thermodynamic principles associated with membrane formation, stability and solute transport (2) membrane protein structure, (3) lipid-protein interactions, (4) bioenergetics and transmembrane transportmechanisms, and (5) specific examples of membrane protein systems and their function (channels, transporters, pumps, receptors). Emphasis will be placed on biophysical approaches in these areas. The primary literature will be the main source of reading. Perozo.. Autumn.
Cell Biology 1 (MGCB/BCMB/HGEN 31600). Eukaryotic protein traffic and related topics, including molecular motors and cytoskeletal dynamics, organelle architecture and biogenesis, protein translocation and sorting, compartmentalization in the secretory pathway, endocytosis and exocytosis,and mechanisms and regulation of membrane fusion. Turkewitz, Glick. Autumn.
Cell Biology 2 (MGCB/BCMB 31700). This course covers the mechanisms with which cells execute fundamental behaviors. Topics include signal transduction, cell cycle progression, mitosis, checkpoints, cytoskeletal polymers and motors, cell motility, cytoskeletal diseases, and cell polarity. Each lecture will conclude with a dissection of primary literature with input from the students. Students will write and present a short research proposal, providing excellent preparation for preliminary exams. Cell Bio I 31600 is not a prerequisite. Glotzer, Kovar. Winter
Quantitative Analysis of Cellular Dynamics (DVBI 32000). This course covers quantitative approaches to understanding biological organization and dynamics at molecular, sub-cellular and cellular levels. A key emphasis is on the use of simple mathematical models to gain insights into complex biological dynamics. We also will cover modern approaches to quantitative imaging and image analysis, and methods for comparing models to experimental data. A series of weekly computer labs will introduce students to scientific programming using Matlab and exercise basic concepts covered in the lectures. Rust, Munro. Spring
Stem Cells and Regeneration (DVBI 36200). The course will focus on the basic biology of stem cells and regeneration, highlighting biomedically relevant findings that have the potential to translate to the clinic. We will cover embryonic and induced pluripotent stem cells, as well as adult stem cells from a variety of systems, both invertebrate and vertebrates. Ferguson, Prince, Cunningham, De Jong, Wu. Autumn
Genetics and Systems Approaches
Human Genetics 1: Human Genetics (HGEN 47000). This course covers classical and modern approaches to studying cytogenic, Mendelian, and complex diseases. Topics include chromosome biology, single gene and complex disease, non-Mendelian inheritance, cancer genetics, human population genetics, and genomics. The format includes lectures and student presentations. Ober, Waggoner, Nobrega. Autumn.
Genetic Analysis of Model Organisms (BCMB/HGEN/MGCB 31400). Fundamental principles of genetics discussed in the context of current approaches to mapping and functional characterization of genes. The relative strengths and weaknesses of leading model organisms are emphasized via problem-solving and critical reading of original literature. Bishop, Moskowitz, Ferguson, Malamy. Autumn.
Genomics and Systems Biology (IMMU/HGEN 47300). This lecture course explores the technologies that enable high-throughput collection of genomic-scale data, including sequencing, genotyping, gene expression profiling, assays of copy number variation, protein expression and protein-protein interaction. We also cover study design and statistical analysis of large data sets, as well as how data from different sources can be used to understand regulatory networks (i.e., systems). Statistical tools introduced include linear models, likelihood-based inference, supervised and unsupervised learning techniques, methods for assessing quality of data, hidden Markov models, and controlling for false discovery rates in large data sets. Readings are drawn from the primary literature. Gilad. Spring
Statistical Inference and Stochastic Models for Computational Biologists (HGEN 48600). Covers key principles in probability and statistics that are used to model and understand biological data. There will be a strong emphasis on stochastic processes and inference in complex hierarchical statistical models. Topics will vary but the typical content would include: Likelihood-based and Bayesian inference, Poisson processes, Markov models, Hidden Markov models, Gaussian Processes, Brownian motion, Birth-death processes, the Coalescent, Graphical models, Markov processes on trees and graphs, Markov Chain Monte Carlo. Prereq: STAT 244 or equivalent and comfort with programming, or consent of instructor. Novembre, Stephens. Spring.
Molecular Biology 1 (MGCB/BCMB 31200). Nucleic acid structure and DNA topology; methodology; nucleic-acid protein interactions; mechanisms and regulation of transcription, replication and genome stability and dynamics. Rothman-Denes, Bishop. Winter.
Molecular Biology 2 (MGCB/BCMB/DVBI 31300). The content of this course will cover the mechanisms and regulation of eukaryotic gene expression at the transcriptional and post-transcriptional levels. Our goal is to explore research frontiers and evolving methodologies. Rather than focusing on the elemental aspects of a topic, the lectures and discussions highlight the most significant recent developments, their implications and future directions. Enrollment requires the equivalent of an undergraduate molecular biology course or consent from the instructors. Staley, Ruthenburg. Spring.