Courses

This course builds on the programming skills acquired in Computer Science 134. It couples work on program design, analysis, and verification with an introduction to the study of data structures. Data structures capture common ways in which to store and manipulate data, and they are important in the construction of sophisticated computer programs. Students are introduced to some of the most important and frequently used data structures: lists, stacks, queues, trees, hash tables, graphs, and files. Students will be expected to write several programs, ranging from very short programs to more elaborate systems. Emphasis will be placed on the development of clear, modular programs that are easy to read, debug, verify, analyze, and modify. [ more ]

Genetics, classically defined as the study of heredity, is today a multidisciplinary field whose principles provide critical insight and tools to most areas of biology and medicine. This course covers the experimental basis for our current understanding of the inheritance, structures, and functions of genes. It introduces approaches used by contemporary geneticists and molecular biologists to explore questions in areas of biology ranging from evolution to medicine. A primary focus of the course is on students developing familiarity with problem solving, the logic and quantitative reasoning required to understand how genetic mechanisms lead to biological patterns. The laboratory part of the course provides an experimental introduction to modern genetic analysis as well as introductions to interpreting genetic reasoning in the primary research literature. Laboratory experiments include investigating chromosome structure using microscopy, mapping a mutation to the genome by integrating multiple streams of evidence, and determining the structure of a DNA plasmid using molecular tools. [ more ]

This course offers a critical analysis of contemporary concepts in biological evolution. We focus on the relation of evolutionary mechanisms (e.g., selection, drift, and migration) to long term evolutionary patterns (e.g., evolutionary innovations, origin of major groups, and adaptation). Topics include micro-evolutionary models, natural and sexual selection, speciation, the inference of evolutionary history, evolutionary medicine among others. [ more ]

This course examines how experimental methods in neuroscience can be used to understand the role of nature (genes) and nurture (the environment) in shaping the brain and behavior. In particular, we will explore how neuroscience informs our understanding of psychiatric disorders such as anxiety, depression, and schizophrenia. We will investigate the biological underpinning of these disorders as well as their treatments. Readings will include human studies as well as work based on animal models. Topics will include: the ways in which environmental and genetic factors shape risk and resiliency in the context of psychiatric disease, the neural circuits and peripheral systems that contribute to psychopathology, and the mechanisms through which interventions may act. In the laboratory component of the course, students will gain hands-on experience in using animal models to study complex behavior and their associated neural mechanisms. [ more ]

This course will provide an overview of Computational Biology, the application of computational, mathematical, statistical, and physical problem-solving techniques to interpret the rapidly expanding amount of biological data. Topics covered will include database searching, DNA sequence alignment, clustering, RNA structure prediction, protein structural alignment, methods of analyzing gene expression, networks, and genome assembly using techniques such as string matching, dynamic programming, hidden Markov models, and statistics. [ more ]

This course introduces the foundational concepts of biochemistry with an emphasis on the structure and function of biological macromolecules. Specifically, the structure of proteins and nucleic acids are examined in detail in order to determine how their chemical properties and their biological behavior result from those structures. Other topics covered include catalysis, enzyme kinetics, mechanism and regulation; the molecular organization of biomembranes; and the flow of information from nucleic acids to proteins. In addition, the principles and applications of the methods used to characterize macromolecules in solution and the interactions between macromolecules are discussed. The laboratory provides a hands-on opportunity to study macromolecules and to learn the fundamental experimental techniques of biochemistry including electrophoresis, chromatography, and principles of enzymatic assays. [ more ]

This lecture course provides an in-depth presentation of the complex metabolic reactions that are central to life. Emphasis is placed on the biological flow of energy including alternative modes of energy generation (aerobic, anaerobic, photosynthetic); the regulation and integration of the metabolic pathways including compartmentalization and the transport of metabolites; and biochemical reaction mechanisms including the structures and mechanisms of coenzymes. This comprehensive study also includes the biosynthesis and catabolism of small molecules (carbohydrates, lipids, amino acids, and nucleotides). Laboratory experiments introduce the principles and procedures used to study enzymatic reactions, bioenergetics, and metabolic pathways. [ more ]

RNA is known best as the message cells use to turn genes into proteins. Yet investigations of several unusual genetic phenomena over the past few decades did not find protein-coding genes, but instead uncovered non-coding RNAs with a cornucopia of functions. Today, biologists have begun to develop a framework for how RNA's non-coding functions play central roles in immune defense and genetic conflicts, in gene regulation and cancer. We will develop our own understanding of the power of small noncoding RNA to protect the genome and direct cellular processes through reading and discussion of primary scientific literature. We will learn how this emerging perspective of RNA's non-coding functions helps to resolve genetic mysteries and has opened the door to RNA-based medications. [ more ]