Course Descriptions

BIOL 7994 - Independent Study in Biology

This course is for graduate students participating in graded, graduate-level courses offered at MLBS during summer sessions. Students enroll in this course during the fall semester following completion of the MLBS summer course. Credits earned are the same as the number of credits designated for the MLBS course. Upon completion of the course, the instructor of record provides a grade and a written evaluation of each student’s work in the course.



Credits: 1-4

BIOL 8010 - Colloquium in Developmental Biology

A weekly conference in which students present reports covering various aspects of development. May be repeated for credit.
Prerequisite: Instructor permission.



Credits: 2

BIOL 8020 - Colloquium in Physiology

A weekly conference in which students present reports covering various aspects of physiology. May be repeated for credit. Prerequisite: Instructor permission.



Credits: 2

BIOL 8030 - Colloquium in Genetics

A weekly conference in which students present reports covering aspects of genetics. May be repeated for credit.
Prerequisite: Instructor permission.



Credits: 2

BIOL 8040 - Colloquium in Biology

A weekly conference in which students present reports covering various topics that cross development, genetics, and physiology. May be repeated for credit.
Prerequisite: Instructor permission.



Credits: 2

BIOL 8050 - Advanced Evolutionary Biology

This course will cover a range of evolutionary concepts and approaches, including levels of selection, the role of evolution in structuring ecological communities, game theoretical models of adaptation, frequency-dependence, neutral processes and drift, the evolution of sex, the evolution of virulence, the molecular basis of adaptation, population and quantitative genetics, and the evolution of genome structure.



Credits: 2

BIOL 8060 - Colloquium in Circadian Biology

Readings and two-hour student seminar preparations focusing on recent research and primary literature in circadian biology.
Prerequisites: Instructor Permission



Credits: 2

BIOL 8070 - Colloquium in Population Biology

BIOL 8140 - Developmental Genetics

Analyzes the role of genes in development and an examination of the idea of differential gene action during development.



Credits: 2

BIOL 8200 - Structure and Regulation of Eukaryotic Genes

Studies the structure, regulation, and evolution of eukaryotic genes, reviewing current literature and ideas in this field.
Prerequisite: Instructor permission.



Credits: 3

BIOL 8250 - Communicating in Science

This course will supplement the “7 Habits for Highly Effective Grad Students” course with hands-on practice in presenting scientific data and communicating effectively in scientific writing and oral presentations. Students will meet weekly to practice and critique oral presentations, scientific manuscripts, figures and tables, statistical results, grant proposals, etc. Req. of all first-year graduate students in biology.



Credits: 1

BIOL 8270 - Seven Habits of Highly Effective Graduate Students

Weekly discussion to acclimate new graduate students to rigors of academic research in the Department of Biology. There will be an emphasis on time management, scientific writing, presentations, and work-life balance. A rotation of Biology faculty, students, and staff will contribute to the weekly discussion.



Credits: 2

BIOL 8490 - Advanced Drosophila Genetics

Examines genetic techniques available in Drosophila: segregation and use of translocation heterozygotes in the generation of segmental anueploids; segregation and use of compound chromosomes, including their use in the half-tetrad analysis of gene conversion events; methods for making mosaics; methods for P-element induced mutagenesis, including site directed mutagenesis; P-element mediated transformation; and using enhancer traps.
Prerequisite: BIOL 3010 or equivalent.



Credits: 2

BIOL 8510 - Field Biology at Mountain Lake Biological Station

Field experiential courses in evolution, ecology, behavior and biology taught at the Biology Department’s Mountain Lake Biological Station (MLBS), a field research and teaching facility located in southwestern Virginia. Students may enroll for more than one section as each section is a specialized topic.



Credits: 1 to 4

BIOL 8559 - New Course in Biology

BIOL 8800 - Selected Topics in Genetics

BIOL 8810 - Selected Topics in Evolution

BIOL 8820 - Selected Topics in Developmental Biology

BIOL 8840 - Selected Topics in Physiology

BIOL 8850 - Selected Topics in Molecular Genetics

BIOL 8860 - Selected Topics in Cell Biology

BIOL 8870 - Selected Topics in Developmental Genetics

BIOL 8880 - Selected Topics in Biochemistry

BIOL 8900 - Selected Topics in Developmental Botany

BIOL 8998 - Non-Topical Research, Preparation for Research

BIOL 8999 - Non-Topical Research

BIOL 9010 - Research in Genetic Development

BIOL 9030 - Research in Yeast Genetics

BIOL 9040 - Research in Yeast Genetics

BIOL 9070 - Research in Molecular Genetics

BIOL 9090 - Research in Developmental Biology

BIOL 9110 - Research on Protein Structure

BIOL 9150 - Research in Biochemistry

BIOL 9230 - Research in Neuroethology of Electric Fish

BIOL 9250 - Research in Population Biology

BIOL 9270 - Research in Plant Physiology

BIOL 9290 - Research in Plant Biology

BIOL 9330 - Research in the Circadian Organization of Vertebrates

BIOL 9350 - Research in Cell Structure and Function

BIOL 9370 - Research in Gene Expression during Development

BIOL 9390 - Research in Behavior Neuroendocrinology

BIOL 9410 - Yeast Morphogenesis

BIOL 9450 - Research in Evolutionary Biology

BIOL 9470 - Research in Neurophysiology and Developmental Neurobiology

BIOL 9559 - New Course in Biology

BIOL 9600 - Research in Cell Structure and Function

BIOL 9630 - Research in Drosophila Neurobiology

BIOL 9650 - Research in Ecological Genetics

BIOL 9670 - Research in Animal Cell Growth

BIOL 9770 - Research in Molecular Aspects of Development

BIOL 9790 - Research in Development and Function of Neuronal Networks

BIOL 9810 - Research in Developmental Genetics and Morphogenesis

BIOL 9830 - Research in the Neurophysiological Basis of Circadian Rhythms

BIOL 9910 - Rotation Research

An exposure to the working techniques and interactions of the modern Biological Laboratory. Required of all first-year biology graduate students.



Credits: 3

BIOL 9920 - Rotation Research

An exposure to the working techniques and interactions of the modern Biological Laboratory. Required of all first-year biology graduate students.



Credits: 3

BIOL 9995 - Topical Research in Biology

BIOL 9998 - Non-Topical Research, Preparation for Doctoral Research

BIOL 9999 - Non-Topical Research

BME 6026 - Quantitative Models of Human Perceptual Information Processing

An introduction to the measurement and modeling of human perceptual information processing, with approaches from neurophysiology to psychophysics, for the purposes of system design. Measurement includes classical psychophysics, EEG field potentials, and single-neuron recordings. Modeling includes signal detection theory, neuronal models (leaky integrate-and-fire, Hodgkin-Huxley, and models utilizing regression, probability, and ODEs).
Prerequisite: Graduate standing; background courses in ordinary differential equations, statistics and probability; or consent of instructor.



Credits: 3

BME 6060 - Biomedical Innovation

BME 6101 - Physiology I for Engineers

Introduces fundamental concepts of cellular physiology; applies quantitative engineering analysis to intra- and intercellular signaling and mechanical systems relevant to organ physiology and pathology; teaches students to learn to think critically about the physiology and cell biology literature.
Prerequisite: BME 2104 or equivalent; proficiency with ODEs.



Credits: 3

BME 6102 - Engineering Physiology II

Second part of physiology sequence for engineering students; focuses on physiology of the cardiovascular, pulmonary, renal, and nervous systems; emphasizes quantitative analysis of organ function, particularly the use of mathematical models to identify and understand key underlying mechanisms.
Prerequisite: BME 6101



Credits: 3

BME 6103 - Physiology I

We learn how excitable tissue, nerves and muscle, and the cardiovascular and respiratory systems function. You will develop an understanding of mechanisms, with an introduction to structure, an emphasis on quantitative analysis, and integration of hormonal and neural regulation and control.
Prerequisites: introductory undergraduate courses in biology, chemistry, physics and calculus or instructor permission.



Credits: 3

BME 6104 - Physiology and Pathophysiology

BME 6280 - Motion Biomechanics

Focuses on the study of forces (and their effects) that act on the musculoskeletal structures of the human body. Based on the foundations of functional anatomy and engineering mechanics (rigid body and deformable approaches); students are exposed to clinical problems in orthopedics and rehabilitation.
Cross-listed as AM 6280.
Prerequisite: BME 6103.



Credits: 3

BME 6310 - Mathematics, Modeling, and Computation in Biomedical Engineering

The principle objective of this course is to instruct graduate students on fundamental mathematical, modeling, and computational principles of relevance in biomedical engineering. The course is structured to provide lecture material, biomedical examples that use modeling and computation, and homework/exams that strengthen the mathematical and computational foundation of the graduate students.
Prerequisites: 1. BME 6101: Physiology I (or equivalent) 2. SEAS grad student status 3. Some previous exposure to probability-statistics, Fourier analysis, and linear systems 4. Or instructor permission



Credits: 3

BME 6311 - BME Measurement Principles

Students will gain a fundamental understanding of the theoretical principles underlying biomedical measurements. Topics are organized sequentially from signal initiation through signal processing to downstream statistical analysis of measurements. Students will be exposed to the practical implementation of general principles through homework assignments that involve the analysis and evaluation of molecular, cellular, and clinical measurements.
Prerequisites: 1. BME 6101: Physiology I (or equivalent) 2. SEAS graduate student status 3. Some previous exposure to probability-statistics, Fourier analysis, and linear systems 4. Or Instructor Permission



Credits: 3

BME 6550 - Special Topics in Biomedical Engineering

Applies engineering science, design methods, and system analysis to developing areas and current problems in biomedical engineering. Topics vary by semester.



Credits: 3

BME 7003 - Biomedical Engineering Seminar

A seminar course in which selected topics in biomedical engineering are presented by students, faculty and guest investigators.



Credits: 0

BME 7370 - Quantitative Biological Reasonsing

Provides students with a quantitative framework for identifying and addressing important biological questions at the molecular, cell, and tissue levels. Focuses on the interplay between methods and logic, with an emphasis on the themes that emerge repeatedly in quantitative experiments.
Prerequisites: BME 6101 (or equivalent), SEAS graduate student status, or instructor permission.



Credits: 3

BME 7641 - Bioelectricity

Studies the biophysical mechanisms governing production and transmission of bioelectric signals, measurement of these signals and their analysis in basic and clinical electrophysiology. Introduces the principles of design and operation of therapeutic medical devices used in the cardiovascular and nervous systems.
Prerequisite: BME 6310 or instructor permission.



Credits: 3

BME 7782 - Medical Imaging Systems Theory

Develops an intuitive understanding of the mathematical systems theory needed to understand and design biomedical imaging systems, including ultrasound, magnetic resonance imaging and computed tomography. Topics will include multidimensional Fourier transform theory, image reconstruction techniques, diffraction theory, and Fourier optics.
Prerequisite: BME 6310 or equivalent exposure to linear systems theory or instructor permission.



Credits: 3

BME 7784 - Medical Image Analysis

Comprehensive overview of medical image analysis and visualization. Focuses on the processing and analysis of these images for the purpose of quantitation and visualization to increase the usefulness of modern medical image data. Topics covered involve image formation and perception, enhancement and artifact reduction, tissue and structure segmentation, classification and 3-D visualization techniques as well as pictures archiving, communication and storage systems. Involves ‘hands-on’ experience with homework programming assignments.
Prerequisite: BIOM 6310 and ECE 6782 or instructor permission.



Credits: 3

BME 7806 - Biomedical Applications of Genetic Engineering

Provides biomedical engineers with a grounding in molecular biology and a working knowledge of recombinant DNA technology, thus establishing a basis for the evaluation and application of genetic engineering in whole animal systems. Beginning with the basic principles of genetics, this course examines the use of molecular methods to study gene expression and its critical role in health and disease. Topics include DNA replication, transcription, translation, recombinant DNA methodology, methods for analyzing gene expression (including microarray and genechip analysis), methods for creating genetically-engineered mice, and methods for accomplishing gene therapy by direct in vivo gene transfer.
Prerequisite: BME 6103, undergraduate-level cell and/or molecular biology course. (e.g., BME 2104) or instructor permission. Suggested preparation: biochemistry, cell biology, genetics, and physiology.



Credits: 3

BME 8315 - Computational Systems Bioengineering

In this course students will gain working knowledge of constructing mathematical and computational models of biological processes at many levels of organizational scale from genome to whole-tissue. Students will rotate through several modules where they will hear lectures, read literature, and participate in discussions focused on the various modeling techniques.
Prerequisites: BME 6101/6102: Physiology (or equivalent); 2. One of the following courses in cellular and/or molecular biology: BME 2104: Cell and Molecular Biology for Engineers, BME 7806: Genetic Engineer.



Credits: 3

BME 8550 - Advanced Topics in Biomed Engineering

Applies engineering science, design methods, and system analysis to developing areas and current problems in biomedical engineering. Topics vary by semester.



Credits: 3

BME 8730 - Diagnostic Ultrasound Imaging

Underlying principles of array based ultrasound imaging. Physics and modeling techniques used in ultrasound transducers. Brief review of ID circuit transducer models. Use of Finite Element techniques in transducer design. Design considerations for 1.5D and 2D arrays will be reviewed. Diffraction and beamforming will be introduced starting from Huygen’s principle. FIELD propagation model will form an important part of the class. In depth discussion of various beamforming and imaging issues such as sidelobes, apodization, grating lobes, resolution, contrast, etc. The course addresses attenuation, time-gain-compensation and refraction. Finally, speckle statistics and K-Space techniques will be introduced. Laboratories will involve measuring ultrasound image metrics, examining the effect of various beamforming parameters and simulating these on a computer using Matlab.
Prerequisite: instructor permission, BIOM 6310 and BIOM 6311. Preparation: Undergraduate Physics, Electronic circuit analysis, Differential Equations, Fourier and Laplace Transforms, Sampling Theorems.



Credits: 3

BME 8782 - Magnetic Resonance Imaging

The course covers the physical principles of nuclear magnetic resonance, the biological and medical problems addressed using MRI, the analysis and design of MRI pulse sequences from a signal processing perspective, and MR image reconstruction techniques. It will introduce various advanced topics, such as cardiac MRI and spectroscopic imaging. The course will include laboratory sessions working with an MRI scanner.
Prerequisites: BME 7782 Biomedical Imaging Systems Theory, or knowledge of 2D Fourier transforms and linear systems theory.



Credits: 3

BME 8783 - Advanced Magnetic Resonance Imaging

Advanced physics and applications of magnetic resonance imaging and spectroscopy will be covered. Upon completion of this course, the student will understand the factors that affect the MRI signal, and will know how these factors can be exploited to image or measure various aspects of physiology with MR.
Prerequisites: BME 8782 Magnetic Resonance Imaing and MATLAB experience.



Credits: 3

BME 8823 - Cell Mechanics, Adhesion, and Locomotion

Biomechanics and structural biology of cell structure and function, focusing on quantitative description and measurements of cell deformability, adhesion, and locomotion. Cell deformability: erythrocyte properties, membrane mechanics, shear, bending, and area elasticity. Leukocyte structure and deformability. Structural basis of plasma membrane, lipid bilayer, surface structures, nucleus, organelles, cell junctions, cytoskeleton, membrane transport, active cytoskeletal functions, specific and non-specific forces between molecules, protein structure, molecular graphics. Cell adhesion molecules: families of adhesion molecules, cell-cell and cell-matrix binding, biochemical characteristics, regulation of expression, regulation of binding avidity, functional role. Cell adhesion assays: detachment assays, aggregation of leukocytes and platelets, controlled shear systems, flow chambers. Mechanics of cell adhesion: equilibrium analysis of cell adhesion, models of cell rolling, adhesion bond mechanics. Liposomes, microbubbles, and applications to targeted adhesion. Cell motility: measurement of active forces and motility in cells, molecular motors. Effects of mechanical stress and strain on cell function.
Prerequisite: Instructor permission.



Credits: 3

BME 8890 - Biomolecular Engineering

In this class, students design treatment strategies for cancer and cardiovascular disease based on molecular bioengineering principles. Special topics will include design of nanoparticle drug and gene delivery platforms, materials biocompatibility, cancer immunotherapy, and molecular imaging.
Prerequisites: Undergraduate coursework in cell and molecular biology and biomechanics. Recommended undergraduate course in transport processes.



Credits: 3

BME 8900 - Graduate Teaching Instruction

BME 8995 - M.E. Supervised Project Research (M.E. STUDENTS ONLY)

FOR M.E. STUDENTS ONLY. A research project in biomedical engineering conducted in consultation with a faculty advisor. Includes the design, execution, and analysis of experimental laboratory work and computational or theoretical computer analysis of a problem. Fulfills the project requirement for the Biomedical Engineering Masters of Engineering degree.
Prerequisites: Instructor Permission Required.



Credits: 1 to 6

BME 8999 - Master’s Research

BME 9000 - Graduate Teaching Instruction

BME 9999 - Dissertation

Formal record of student commitment to doctoral research under the guidance of a faculty advisor. May be repeated as necessary.



Credits: 1 to 12

BIMS 5012 - Cell Structure and Function

A beginning graduate course in molecular cell biology examining the functional organization of eukaryotic cells and the interactions of cells with their surroundings. General and specialized forms of cell signaling are discussed, and events involved in regulating cell proliferation and differentiation are emphasized.



Credits: 5

BIMS 5030 - Macromolecular Structure and Function

This integrated course provides the necessary background at the professional level for careers in a variety of biological and physical sciences.
Prerequisites: Calculus, organic chemistry, physical chemistry. Some introductory knowledge assumed.



Credits: 4

BIMS 5410 - Computational Methods in Diabetes and Endocrinology

A focused introduction to contemporary quantitative methods applied to basic and clinical diabetes and endocrine research. Topics may include the clinical blood glucose optimization problems of diabetes, history of quantifying characteristics of T1DM and T2DM, error-grid analysis, behavioral determinants of T1DM control, risk analysis of blood glucose data, use of self-monitoring blood glucose data for evaluation of patients’ glycemic control, stochastic modeling of blood glucose fluctuations, network modeling of blood glucose dynamics, and analysis of continuous monitoring data.
Prerequisites: consent of advisor.



Credits: 4

BIMS 5550 - Neural Development and Regeneration

This course will cover basic principles and current research topics concerning neural development and regeneration. Sections will focus on gene regulatory and signal transduction networks involved in early neural development and later events refining regional specificity within the brain. Topics will include neuronal plasticity, neural stem cells, developmentally-based neuronal diseases, and issues concerning regeneration of the nervous system.



Credits: 2

BIMS 5559 - New Course in Biomedical Sciences

BIMS 6000 - Core Course in Integrative Biosciences

This course is designed to equip students with core concepts and fundamental skill sets needed for biomedical research. It combines traditional didactic lectures with small group and individual learning activities, problem solving exercises, workshops, and hands-on analyses of data sets. The course emphasizes the integration of topics spanning the fields of biochemistry, cell and molecular biology, and genetics.



Credits: 10

BIMS 6559 - New Course in Biomedical Sciences

BIMS 7100 - Research Ethics

Beginning in 1989, the National Institutes of Health introduced a requirement that institutions provide a program of instruction in the responsible conduct of research (NIH Guide for Grants and Contracts, Volume 18, Number 45, 1989). This was later expanded to require that all fellows on NIH training grants should receive instruction in the responsible conduct of research. The requirement does not specify a particular format or curriculum. However, recommendations are made that several areas should be covered in the instruction: conflict of interest, responsible authorship, policies for handling misconduct, policies regarding the use of human and animal subjects, and data management. This course is designed to help student consider each of these areas and therein formulate an understanding of responsible conduct in research.



Credits: 1

BIMS 7559 - New Course in Biomedical Sciences

BIMS 8010 - Gene Structure, Expression and Regulation

Study of the molecular biology of bacterial and eukaryotic cells, emphasizing the application of recombinant DNA for elucidation of gene structure, the mechanism of gene expression, and its regulation. Five lecture hours.



Credits: 5

BIMS 8030 - Current Topics in Genome Sciences

Each week, a UVA faculty member or guest lecturer will summarize current work in their area of research. The emphasis in these lectures will be on high-throughput genomic and bio-informatic approaches to elucidating the mechanisms of pathogenesis in human disease and disease models.



Credits: 1

BIMS 8050 - Explorations in Human Disease

BIMS 8051 - Cell & Molecular Biology Proj

BIMS 8052 - Cell & Molecular Biol Projects