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Graduate Course Descriptions

BIO 500 Bioinformatics and Genome Analysis (4)
This course focuses on contemporary methods in the analysis of genetic information, including use of computerized genetic databases, sequence alignment, hypothesis testing in phylogenetics, models of sequence substitution, introductory coding for bioinformatics, secondary structure prediction and visualization, regular expression coding in biology, and tests of selection. The course includes both lectures and computer-based lab exercises, and provides first-hand experience with various analytical tools. The course is open to senior undergraduate and graduate students.

BIO 501 Advanced Biological Chemistry (4)
This course focuses on the structure and function of biological macromolecules. Topics include structure and properties of proteins and nucleic acids, enzyme kinetics, mechanisms of enzyme catalysis, and bioenergetics.

BIO 502 Advanced Cell Biology (4)
Students will acquire in-depth understanding and knowledge of a wide range of areas in cell and developmental biology. Emphasis is placed on the basic concepts and the experimental underpinnings that support these concepts. Students will further develop insight into the complexities of cell structure and function, the molecular events that mediate cellular and developmental processes, and their dynamic properties in living cells.

BIO 504 Advanced Molecular Genetics (4)
This course highlights the experimental basis for our understanding of the mechanisms of DNA replication and gene expression.  Students learn to read and analyze the primary research articles that underpin molecular genetics.  Topics include: DNA replication, chromatin and chromosome structure, the transcription process, regulation of transcription, RNA processing and decay, and translation. (Prerequisite: undergraduate genetics)

BIO 506 Signal Transduction (3)
This course discusses how cells respond to stimuli, including the mechanisms that transmit signals, “crosstalk” between signaling pathways within a cell, and how these signaling pathways generate the multitude of output responses by the cells.

BIO 507 Advanced Ecology (3)
An advanced course in the foundations of ecology emphasizing population and community ecology. Lectures in basic ecological principles are supplemented with discussions of both current and historically important issues, as well as application of ecological principles to environmental problems.

BIO 511 Marine Ecology (3)
Surveys tropical marine ecosystems, with an emphasis on coral reef communities. Examines processes controlling abundance and distribution of marine taxa using primary literature.

BIO 514 Topics in Advanced Ecology (2)
Explores a series of current topics in advanced ecological studies. Lectures and discussion may include such topics as roles of density dependent and independent population regulation; effects on coevaluation on community structure, research methods in ecology; sampling methodology and modelilng; community stability and succession; and readings in ecology. Topics vary from year to year, and may be taken for credit more than once.

BIO 517 Neurobioogy (3)
Lectures focus on the neural control of stereotypic behavior, the morphology and development of nervous systems, and the morphology and development of neuron systems, muscular systems, and cardiac systems. The recitation allows students to discuss current literature related to topics covered in lectures.  It meets six times during the semester.  It is required for MS and PhD students in Biological Sciences but optional for others.

BIO 518 Integrative Neuroscience (3)
This course examines the nervous system at the molecular, cellular, and systems levels, focusing on major functions such as perception, motor control, and development, as well as the basis for neural diseases. Second of a two-semester sequence with BIO517.
Course Director: Xu-Friedman

BIO 522/MIC 622 Protein-Nucleic Acid Interactions (3)
The interaction between proteins and nucleic acids is critical to all organisms both cellular and viral. The interaction between proteins and nucleic acids from a physical biochemical perspective will be studied. There will be significant required reading and this will be available as handouts. The format for the class (M/W/F) will consist of two lectures per week and one discussion/presentation session. These presentations will be done by students. Students will also be assigned homework problems and there will be a final exam as well. Students will be graded on the homework, final exam and presentations. (Registration by permission of instructor)

BIO 525 Special Topics: Navigating the Genome (2)
This course teaches students how to navigate in the several recent -omics datasets, including genome browsers, large multi-tissue transcriptional datasets, human genetic variation maps, as well as human disease association studies. Specifically, throughout the course, the students will learn to use several available computational tools to visualize overall genetic variation in humans, identify a subset of variants relevant to a particular disease, phenotype, or adaptation, and excavate the potential functional impact of such variation. The course is aimed at students in biological sciences and related fields with a keen interest in human genetic variation and its biomedical and evolutionary impact of human genetic variation.

BIO 525 Special Topics: Cancer Immunology  (3)
This course is designed to provide students an understanding of the interplay between tumors and the immune system, as well as current therapies that use the immune system in the setting of oncology. The course will be broken up into three main sections. The first section will cover basic immunology and tumor biology, the second will address the interplay between the immune system and tumors, and the third will discuss current immunological therapies. At the conclusion of the course, participants should understand how the immune system functions, how genesis of cancer and its progression, and the links between these two systems.

BIO 526 Special Topics: Human Genetic Diseases (3)
The aim of this class is to help students gain a sufficient understanding of human genetics so that they can appreciate the genetic basis of human diseases, and the importance of genetic considerations in the prevention and treatment of diseases. This course will use a literature-based approach to cover the fundamentals, from the chromosomal basis for hereditary to the molecular and biochemical basis of genetic diseases as well as the current molecular diagnostic and treatment methods available for genetic diseases. A combination of classic and current papers will be used.

BIO 526 Special Topics: Genes in Cancer (2)
This course will cover the functions of oncogenes and tumor suppressors in genome regulation and the pathways that lead to uncontrolled cell proliferation. Topics discussed include the cell cycle, transcription factors, signaling pathways, and metastasis.

BIO 526 Special Topics:  Genomics in Biology (3)
This course will introduce the most recent developments in DNA sequencing technology with a particular focus on “next-generation,” or massively parallel, sequencing technologies and their utilities and challenges.  With a focus on the current research literature the course will review applications of these genomics tools in studies of biodiversity and evolutionary biology, whole genome sequencing from bacteria to humans, domestication, and genomics of environmental samples (metagenomics).

BIO 549 Comparative Genomics (3)
This course will examine the structure and dynamics of the genome from a comparative perspective. Architectural relationships among genomes can be studied in the context of an organismal “family tree”. Many other themes in genome science, such gene duplication, intron-exon structure, transposable elements, and regulatory DNA, will be discussed with reference to the evolution of genome complexity.

BIO 550 Human Evolutionary Genomics  (3)
This lecture/discussion course conveys genomics approaches to tackle the questions: “What makes us human?” and “Why are we different from each other”. Specifically, this course will introduce the state­-of-­the-­art concepts and methodologies in human evolutionary genomics exploring topics such as ‘human genomic variation’, ‘ancient admixture’, ‘gene­-phenotype-­environment interactions’, ‘adaptive developmental evolution’, ‘nature vs. nurture’, ‘genetic bases of disease’, and ‘experimental and statistical approaches to associate genotype to phenotype’. The course is aimed at students in biological sciences and related fields with a strong interest in evolutionary genetics and human genomic variation. Also, this course is of relevance to advanced students in a number of disciplines, including biomedical sciences and anthropology. After taking this course, each student will have the knowledge regarding the contemporary theoretical and methodological state of human evolutionary genomics.

BIO 553 Evolutionary Biology Colloquium (1-3)
This is one of the core courses for the EEB Graduate Program, but is open to all graduate students of the College of Arts and Science with an interest in Evolution, Ecology and Behavior. 

In the fall, the course focuses on current topics in the fields of Evolution, Ecology and Behavior. Topics are briefly introduced by faculty, and students then lead discussions using recent publications. Examples of recent topics are: Symbiosis, Bioarcheology, and Evolutionary Epidemiology. The goal is to gain an overview of current science, as well as to hone your skills in discussion, argumentation, and deriving information from primary literature sources.

In the spring, the course focuses on student presentations. EEB Graduate students present their own research projects, whereas all other students present a subject of their choice. This is aimed at honing your presentation skills as well as getting feedback on research projects.

BIO 556 Evolutionary Genetics (3)
Genetic and population-level processes that underlie evolutionary change; topics include population genetics, the effects of population size and selection, population structure, molecular evolution, intragenomic conflict, molecular phylogenetics, and evolutionary development.

BIO 608 Topics in Macromolecular Structure (3)
An advanced course that considers the structural, thermodynamic, electrostatic and dynamic aspects of molecules that direct the folding of proteins and nucleic acids and govern their interactions with each other as well as with small ligands. Students will approach these topics with the aid of state-of-the-art molecular graphics and computational chemistry methods. (Prerequisites: an advanced course in biochemistry). 

BIO 611 Scientific Writing (3)
This course teaches the fundamentals of scientific writing, a critical skill for professional biologists.  Students will become familiar with stylistic elements of scientific writing and will gain experience preparing and editing three types of scientific documents – a commentary, a research paper, and a grant proposal.  This writing-intensive course is intended for second-year graduate students in biology and other life sciences.