Graduate Course Descriptions

BIO 500 Bioinformatics and Genome Analysis (4) (Sp)
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. This 4-credit 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) (F)
Structure and function of biological macromolecules discussed. Topics: structure and properties of proteins, nucleic acids, carbohydrates, mechanisms of enzyme catalysis, energy transduction and metabolic regulation. LEC

BIO 502 Advanced Cell & Developmental Biology (4) (F)
Major topics in cell and developmental biology are covered at the advanced textbook level. Emphasis is placed on the experimental basis underpinning our current knowledge. LEC (Prerequisite: a course in cell biology)

BIO 504 Advanced Molecular Genetics (4) (Sp)
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) (F)
This course discusses how cells respond to stimuli, which encompasses 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 ecolgy. 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. LEC (Prerequisite: a basic course in ecology)

BIO 511 Ocean Shallow Water Ecosystem (3)
Consideration of basic ecological forces at work in controlling creation and maintenance of ecological niches in the ocean. Implies an understanding of both physical and biological aspects of these ecosystems. Course describes interaction between major physical environmental forces (such as light, salinity, wave activity, etc.) and various marine organisms. Emphasizes more detailed study of interactions in organisms. Emphasizes more detailed study of interactions in selected ecological niches. LEC (Prerequisite: basic ecology and invertebrate zoology).

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. SEM (Prerequisite: permission of instructor).

BIO 515 Virology (2)
Surveys bacterial, plant, and animal viruses. Examines viral strategies for existence as simple life forms and covers medical and research importance of viruses. This is a basic undergraduate/graduate course for individuals interested in research or careers related to medicine. LEC (Prerequisite: BIO 200, 201, 202 or equivalent, or permission of instructor).

BIO 517 Neurobiology (4) (F)
This course examines basic concepts of Neurobiology.  Lectures primarily concern cellular aspects of the nervous system, including electrophysiology, neurochemistry, signalling, synaptic transmission, neuroanatomy, and sensory function.

BIO 518 Integrative Neuroscience (3) (Sp)
Prerequisite: BIO 517

This course examines the nervous system at the molecular, cellular, and systems levels, focussing 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 BIO417.

BIO 519 Introduction to Bioinformatics and Computational Biology (3 cr) (S)
Introduces graduate students to the concepts and practices of bioinformatics, including computational analysis of DNA and protein sequences, analysis of large-scale DNA and protein datasets, statistical analysis of sequence alignments and gene array datasets, proteomics, and RNA and protein structure prediction.

BIO 522/Mic 522: Protein-Nucleic Acid Interactions
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.

BIO 425/525 Cancer Immunology
Undergraduate Prerequisite: BIO 319 Genetics

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.
Note about prerequisites: Not required but strongly recommended for undergraduates are previous courses in cellular biology and biochemistry. For graduate students there are no formal prerequisites, but students should possess a comfortable understanding of genetics, biochemistry, and cellular biology

BIO 525 Microbial Genomes: Symbionts, Epidemiology, Disease (1) (S 2014)
Prerequisite: BIO 200, Instructor: Dr. Dittmar
This is a lecture course based on cutting edge publications in the field of microbiology. This course is about the latest conceptual and computational developments in microbial genomics and epidemiology. The topics will touch on lateral gene transfer, microbial ecological transitions and microbial epidemiology. While it will be advantageous for students already familiar with the microbial world, it can be taken by any undergraduate (or graduate) student in our department, especially with those interested in: evolution, medicine (pre-med/ pre-vet), microbiology, microbial ecology, public health.

BIO 525 Special Topics: mRNA Export (1) (S)
Required: BIO367 or permission of instructor
This is a literature-based, seminar-type course on the topic of mRNA export. It gives a historical perspective on this field, and the latest advances in our understanding on how mRNA export is regulated and how it affects different aspects of RNA metabolism and gene expression.

BIO 525 Special Topics: Development and Evolution (3) (F)
Required: BIO367 or permission of instructor

This course will explore how evolutionary biology informs developmental biology, and how developmental biology is important for the study of evolution. LEC

BIO 525 (LIN) Special Topics In Modern Biology: Genomics in Biology (3 cr) (F)
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 525 Human Genetic Diseases (2) (Sp)
Prerequisite: BIO 319

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) (S)
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(BRY) – Special Topics In Modern Biology: Advances in Plant-Pathogen Interactions (2 cr) (F)
This new course covered topics relating to plant-pathogen interactions, with a strong focus on molecular and cellular processes. Topics covered included basic plant defense mechanisms (hypersensitive response and systemic acquired resistance), plant virology, mechanisms and uses of RNAi/RNA silencing (viral cross protection in plants, silencing of specific genes, modification of developmental processes), and microRNAs in plant development and viral diseases. Course runs part semester.

BIO 532 Microbial Genomics and Metagenomics (3) (Sp)
This is a lecture-based course dealing with basic findings and approaches in the field of microbial genomics and metagenomics using bacteria and viruses as examples. Conceptual aspects, as well as methodology and technical advances used to obtain and explore genome sequences will be covered. Some of the areas that will be explored include bacterial and viral genome structure and evolution, genomic variation, and impact of horizontal gene transfer on genome evolution. Topics such as human and animal microbiomes, as well as environmental metagenomics will also be covered.

BIO 540 Experimental Endocrinology (2)
Study of cellular integration of peptide hormone influences and molecular mechanisms which mediate these influences. This includes: 1) role of hormones in cellular function; 2) surface membrane receptor-transduction mechanisms; 3) nonmembrane receptor-transduction mechanisms; 4) role of the “state” of the cell in cellular response to hormone and 5) cellular integration of multiple hormone influences.  

BIO 548 Seminar in Ecology and Liminology (1)
Evaluation and review of selected topics in ecology and limnology with emphasis on aquatic interrelation. May be taken more than once for credit. SEM (Prerequisite: permission of instructor).

BIO 549 Comparative Genomics (3) (Sp)
Prerequisite: BIO 319, or permission of instructor

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. SEM

BIO 550 Human Evolutionary Genetics (3) (F)
This 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’.

BIO 553 Evolutionary Biology Colloquium (1-3)
Colloquium for Evolution, Ecology, and Behavior: one of the core courses for the EEB Graduate Program; OPEN to all graduate students of the College of Arts and Science with an interest in Evolution, Ecology and Behavior (MS, MA, PhD). Advanced undergraduate students are welcome, but should ask permission from Dr. Dittmar, the EEB Director (
In the Fall semester, this seminar discusses current topics in the fields of Evolution, Ecology and Behavior (~ last 2 years). Topics are briefly introduced by faculty, and students then lead discussions using recent publications. Examples of recent topics (2013) touched on are: Symbiosis, Bioarcheology, Evolutionary Epidemiology, to name a few. The goal is to gain an overview of current science, as well as hone your skills in discussion and argumentation, and deriving information from primary literature sources. In the Spring semester, the course focusses 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 (EEB Students). The Spring course does not count toward course credit totals for BIO PhD, MA, or MS students. This course can be taken for 1-3 credits, and is taught by multiple faculty instructors from the Departments of Biological Sciences, Geology, Anthropology, Psychology, and Geography. This course can be taken in consecutive semesters or as single course units.

BIO 556 Evolutionary Genetics (F)
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. LEC

BIO 558 Molecular Ecology(3) (Sp)
This course focuses on the use of molecular markers to study the ecological causes and consequences of population structure as well as phenomena as diverse as life history strategies and symbiosis. This course will give students a strong foundation in the ecological questions and issues that can be addressed with a molecular approach, and a working knowledge of the molecular tools necessary to address those issues.

BIO 561 Basic Radiation Science (4)

Introduction to production, properties, interactions, dosimetry, detection, and instrumentation of radiations from radioisotopes, radiation producing equipment, and nuclear reactors. Safe handling procedures and survey methods appropriate for biological, health, and engineering sciences included. This is a basic introduction to theory and instrumentation for radioisotope techniques and radiobiology and is a prerequisite to all other courses in this area of science. LEC/LAB

BIO 563 Radiation Protection (4)
Prerequisite: BIO 561 and 565

Theory and practice of radiation safety programs including site, area, and personnel monitoring of various types of installations, including dental, medical diagnostic and therapy, industrial research, and nuclear reactors. Translation of guides and regulations into working procedures for facility design and survey emphasized. LEC/LAB

BIO 565 Radiation Biology (3)
Prerequisite: BIO 561

Effects of ultraviolet and ionizing radiations on biological systems. Molecular, physiological, genetic, and lethal responses considered at the level of molecules, cells, organs, and organisms with implications of risk to human population. LEC

BIO 599 Supervised Teaching (1-3)
Teaching assistants (TA) enroll with permission of department chair. Members of faculty supervise instructional efforts of TAs assisting their courses. Credit up to three hours dependent on type and amount of instructional duties. May be taken more than once for credit.

BIO 600 Problems in the Biological Sciences (1-8)
Research performed under the guidance of individual faculty members.

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. LEC/LAB (Prerequisites: an advanced course in biochemistry).

BIO 610 Graduate Student Seminar (1)
All graduate students required to attend this seminar during the first four semesters of residence. M.S. students will present one seminar, and Ph.D. students will present two. Seminars normally will be presented by second year students. SEM

BIO 610 Graduate Student Seminar for M.A. Students (1)
All MA students are required to attend this seminar during their spring semesters of residence. Each student will present one seminar, normally in their second year. SEM

BIO 614 Departmental Seminar (1)
Required of all graduate students every semester. Seminars on current topics in cell and molecular biology by invited speakers. SEM

BIO 615 Advanced Research Topics (1)
Multiple sections of this course are offered each semester, with each section taught by a different instructor. Each section will review the most recent research results occurring in the instructor’s own field. Since each student in a section will either be doing research in the field or interested in doing research in the field, permission of the instructor is required for each student registering for each section. May be taken more than once for credit. SEM

BIO 680 Graduate Research (1-12)
An original investigation to be pursued under sponsorship of one or more faculty members.

BIO 700 Thesis (1-12)
Upon satisfactory completion of original investigation (Graduate Research), M.S. and Ph.D. students shall be the results of their research to their committee, and upon their approval, the results will be documented in thesis form. M.S. and Ph.D. students must take this class once.