Graduate Courses


402. Molecular Biology

This course deals with the molecular mechanisms of gene replication, gene expression, and the control of gene expression in both prokaryotic and eukaryotic cells. Topics include enzymatic mechanisms of DNA replication, recombination and repair; transposable elements; DNA transcription; RNA splicing; RNA translation; repressors, activators, and attenuators; recombinant DNA and genetic engineering. (Fall)


405. Evolution

Fundamentals of evolution and population genetics. Topics include origin of biological variation, natural selection and its ecological basis, population genetics including selection and drift. Molecular evolution and speciation are also covered. (Fall)


IND 408. Biochemistry

This course is designed primarily for graduate students. One-hour lectures cover selected topics in modern biochemistry including analysis of protein and domain structure by classical and modern methods; protein-ligand and protein-protein interactions; enzyme kinetics and catalytic mechanisms; and a discussion of selected examples of biochemical circuits and regulatory systems. These include protein kinases, protein phosphatases, and G proteins, and their biochemical roles in signal transduction and the regulation of metabolic pathways; biochemistry of glycosylation and protein sorting; nucleic acid protein interactions; and the biochemistry and regulation of protein synthesis, folding, and degradation. In addition to the lectures, workshops are held once a week, during which time additional examples from the literature are discussed. (Fall)


IND 409. Cell Biology

This course is designed primarily for graduate students. One-hour lectures include discussion of specific modern topics including: membrane structure and transport; intracellular compartments and protein sorting; cytoskeleton; signal transduction and cell-cell communication; cell cycle and its breakdown during cancer; and apoptosis. In addition to the lectures, workshops are held weekly to emphasize particular points with examples from the literature. (Fall)


IND 410. Molecular Biology and Genetics

This course is designed primarily for graduate students. One-hour lectures cover modern topics of interest, including DNA replication; DNA repair and mutagenesis, recombination and transposable elements; regulation of gene expression on prokaryotes; and regulation of eukaryotic transcription and RNA processing. Emphasis is placed on both biochemical and genetic approaches to the study of these problems. Special additional topics include genomics as an approach to regulation and mammalian genetic techniques of analysis. In addition to the lectures, workshops are held once a week to study further examples from the literature. (Spring)


420. Advanced Cell Biology

An advanced course focusing on a mechanistic understanding of cellular organization and function. This course relies heavily on the primary research literature, classic and recent, and the design and interpretation of experiments, drawn from biochemistry, microscopy and genetics. Topics include the cytoskeleton, membrane traffic, cell-cell signaling and the cell cycle. Oral and written student presentations and active participation in classroom discussions are essential features of the course. (Fall)


422. Biology of Aging

This course focuses on molecular mechanisms of aging. We will discuss popular theories of aging, model organisms used in aging research, evolution of aging, relation between aging and cancer, human progeroid syndromes, and interventions to slow aging. (Fall)


426. Developmental Biology

This course deals with the cellular and molecular aspects of animal development, with emphasis on processes and underlying mechanisms. Topics include: embryonic cleavage, gastrulation, early development of model vertebrates and invertebrates, patterning of cell fates along embryonic axes of Drosophila and vertebrates, organogenesis, and stem cells. (Fall)


443. Eukaryotic Gene Regulation

This course systematically examines the organization of the eukaryotic genome and its role in the regulation of gene expression. Topics discussed include structure of chromosomes, mechanisms of gene activation and transcription, epigenetic gene regulation, regulatory networks, and functional genomics. Lectures and readings draw heavily on current and classic primary literature. (Spring)


453. Computational Biology

An introduction to the history, theory, and practice of using computers to conduct biological research. Topics include the fundamentals of Linux-based computing and perl programming, accessing and storing biological data, alignment of molecular sequences, and computer-based analysis of data. (Spring)


460. Animal Behavior

Examines animal behavior from an ecological and evolutionary perspective. Topics include social organization, mating systems, foraging, animal learning, and aggression. Students learn quantitative techniques in behavioral biology. (Fall)


463. Ecology

A survey of adaptations to the physical environment, dynamics of natural populations, interactions between species, and human impacts on the environment. (Fall)


465. Molecular Evolution

This course explores evolution at the molecular level. We use evolutionary principles to infer history from DNA sequences, to determine what forces have shaped the evolution of genes and genomes, to understand the relationship between molecular evolution and phenotypic evolution, and to address applied problems, like assigning biological function to genome sequences, finding the sources of epidemics, and finding the genes involved in human diseases. (Spring)


468. Laboratory in Molecular, Cell and Developmental Biology

This course is designed to provide (1) introduction to model organisms (2) training in specific methods used in molecular, cell and developmental biology research, with emphasis on data acquisition and analysis (3) experience in the design and execution of experiments, reading and writing scientific reports, and public scientific presentation. (Spring)


471/472/473/474. Advanced Ecology and Evolutionary Biology A-D

A four-course sequence that provides comprehensive coverage of advanced topics in ecology and evolutionary biology. Areas covered include: population and community ecology; population and quantitative genetics; molecular evolution; evolutionary genomics; evo-devo; phylogenetics; and speciation. This course is intended for graduate students; exceptional undergraduate students can enroll by permission of the course coordinator. (Fall and Spring)


480. Graduate Laboratory Rotation

An introduction to research in the laboratories of individual faculty members. (Fall and Spring)


IND 501. Ethics and Professional Integrity

This course aims to bring to light some of the issues related to ethics and responsible conduct in clinical and basic science biomedical research arenas. A required course for Ph.D. students. (Fall)


GEN 508. Genomics and Systems Biology

This is a graduate level course aimed at providing students with the up-to-date scientific information and background knowledge behind the biomedical research into functional genomics and molecular mechanisms of development and of disease pathogenesis. The lectures are in modular format with homework for each module. Six modules are currently included, each by an instructor(s) most familiar with the topics. The modules include (1) overview of mammalian development and genomics; (2) hematopoiesis and blood cell diseases; (3) CNS development, stem cells and systems biology; (4) genomics of cardiovascular development and diseases; (5) chromatin biology and epigenomics; and (6) genomic and systems biology approaches to cancer. (Spring)


516. Cell/Developmental/Molecular Biology Seminar

This one credit course examines current topics in cell, developmental and molecular biology. Student-led seminars and discussions based on representative publications in the recent literature. One or several broad topics, drawn from active fields of cell, developmental and molecular biology, will be covered each semester. (Fall)


517. Graduate Research Seminar

Ph.D. students prepare and present their research findings to the Department. This course carries one credit. (Spring)


580. Journal Club in Ecology and Evolution

Current topics in ecology and evolutionary biology are explored by reading research and review papers. Students choose topics for reading and lead discussions of their chosen topics. This course carries one credit. (Fall and Spring)


581. Topics in Cell, Development and Molecular Biology

This two-credit course will be taught by all faculty members of the Biology Department that conduct research in the areas of Cellular, Developmental and Molecular Biology. Each week one faculty will provide a general introduction to his/her field of interest and a comprehensive overview of their own research efforts. Short (1-2 page) papers will be assigned throughout the course, critiqued and returned for rewriting. Grades will be determined by participation in class discussions and the assigned writings. (Fall)


584. Seminar in Evolution

Biology Colloquium. Members of the staff and advanced students in the biological sciences meet on regularly announced dates for presentation and discussion of research by members of the department or invited guests. These seminars are open to all. (Fall and Spring)