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Bioinformatics
(Bio) Courses
"Bio" Graduate-Level Courses:
| Structure & Function of Proteins -
BIOL 211 |
| |
Advanced protein
biochemistry stressing methodology and primary literature.
Topics include: properties of amino acids, peptide and proteins;
protein folding and assembly; protein interactions;
allostery and regulation; enzyme kinetics and energetics;
protein-ligand interactions; and post-translational modification
of proteins. Offered alternate fall terms.
Prereq:
BIOL 100 or cons. of instr. |
| Genomic Analysis & Bioinformatics -
BIOL 227 |
| |
The organization and evolution of
selected bacterial and eukaryotic genomes. Genomic structure as
viewed from the perspective of evolutionary rearrangements and
gene expression. Analysis of current experimental methods for
determining and modifying gene function and of computational
approaches to the identification of unique patterns in
respective protein and nucleic acid databases.
Prereq: Open to Senior undergraduates with
cons. of instr. and cons. of Graduate School. |
| Developmental Genetics & Epigenetics -
BIOL 244 |
| |
Analysis of genetic and
epigenetic influences on development, looking at specific
examples from yeast, plant and animal model organisms. Topics
include: genetics of flower development, yeast mating type
switching, DNA methylation, genomic imprinting, chromatin
remodeling, parmutation and prions. Offered alternate fall
terms. Prereq: BIOL 125
and 135 or equiv. |
| General Human Physiology -
PHYS 08202 (MCW) |
| |
Basic functions of cells, tissues, and organ systems are presented
with homeostasis and physiological reserve as the central emphasis.
Regulatory mechanisms which govern the performance of each physiological
system are covered, as are the limits of performance of these systems.
The course included lectures, laboratory and small group discussion.
The relevancy of physiological problems in clinical medicine is presented
in lectures and with audiovisual aids. |
| Physiological Genomics -
PHYS 08230 (MCW) |
| |
Fundamental strategies and principles of genetic coupled with physiological
approaches to studying the molecular genetics of disease. Genetic models,
comparison analysis and mathematical and statistical modeling in physiological
genetics will be covered. Techniques in statistical analysis of genetic
and physiological data. Modeling gene, gene-gene and gene-environment
as it pertains to disease and study design. Computational tools such
as Splus, GeneHunter and Mapmaker/QTL will be reviewed and used in simulations
and actual study data. |
| Introduction to Epidemiology -
MI-11200
(MCW) |
| |
This course will provide a
general understanding of the epidemiological approach to the
study of disease. This course is open to all students
enrolled in the Graduate School and to other qualified students
with permission of the instructor. |
| Introduction Medical Informatics I-II -
MI-13200AB
(MCW) |
| |
This
course is taught over two sequential quarters (3 credits each)
beginning in the fall. This course provides the foundation
for graduate study in Medical Informatics and is a broad
overview of the field. It is recommended that all students
begin their program of study with this course. Topics
covered include the healthcare environment and culture,
electronic medical records, clinical information systems
(hospital, outpatient, nursing, laboratory, pharmacy, radiology,
etc.), decision-support systems, clinical research and
health-assessment systems, technology assessment, and healthcare
business processes. |
| Statistical Models & Methods I -
BIOST
04231 (MCW) |
| |
Models and analysis for count
data and contingency tables, basic nonparametric methods
including sign, rank-sum and signed-ranks test, simple linear
regression model and inference, checking model assumptions,
correlation analysis, one-way and two-way analysis of variance.
Emphasis is on models, their application to data and
interpretation. |
| Statistical Genetics -
BIOST 04384 (MCW) |
| |
Fundamental elements of mathematical and population genetics, and
statistical theory of the methods of human genetic analysis. Topics
include Hardy-Weinberg equilibrium, inbreeding, selection, mutation,
models for polygenic and multifactorial inheritance, variance components
estimation for the genetic analysis of familial aggregation, linkage
and segregation analysis, and ascertainment problems. |
| Analysis of Physiological Systems -
BIEN
201 |
| |
Introduction to the use of
mathematical models in quantifying physiological systems. Model
formulation will be analyzed. Applications of analytical and
numerical solution techniques and parameter estimation methods.
Offered occasionally.
Prereq:
BIEN 152. |
| Cellular & Molecular Bioengineering -
BIEN 205 |
| |
Main topics include:
cellular biomechanics with an emphasis on the cardiovascular
system, molecular bioengineering, biotransport phenomena, and
tissue engineering with focus on artificial internal organs.
Cellular biomechanics topics covered are biomechanics of the
endothelium, endothelial-immune cell interactions, and blood
cell structural biomechanics. Topics in molecular bioengineering
include chemotaxis and chemokinesis, and modeling of
receptor-mediated endocytosis. Biotransport and tissue
engineering topics include bioreactor design and the analysis
and development of artificial internal organs like the liver and
pancreas. Offered occasionally. |
| Biomedical Instrumentation -
BIEN 240 |
| |
Relationships between
instruments for physiologic measurement and monitoring with
living systems are explored. Physiologic signals, noise, and
available sensors and transducers and their characteristics are
discussed from time and frequency domain points of view. Systems
topics include various new and conventional medical
instrumentation. Other topics include clinical and new clinical
laboratory instrumentation, instrumentation for research,
artificial organs and prostheses. Includes the use of scientific
literature, literature searches, design projects, computer
projects. Offered alternate years.
Prereq: BIEN 180; or BIEN 187; and
high level computer language or equiv. |
| Microprocessor Based Biomedical Instrumentation -
BIEN 241 |
| |
Discusses the application
of microprocessors, microcontrollers, and digital signal
processors to biomedical instrumentation. Designed to complement
BIEN 240, which covers transducers, sensors, analog signal
conditioning, and analog to digital conversion. The emphasis
will be on evaluating the memory, power, resolution, cost, and
computational requirements of a particular application, and then
selecting a type (microprocessor, microcontroller, or digital
signal processor) and particular model of processor to satisfy
the system requirements. The students will design at least two
complete processor based systems. Offered occasionally.
Prereq: Knowledge of digital electronics and microprocessors. |
| Biomedical Signal Processing -
BIEN 250 |
| |
Introduces students to
statistical processing of biomedical data. Topics include: data
acquisition, probability and estimation, signal averaging, power
spectrum analysis, windowing, digital filters and data
compression. Students will complete several computer projects
which apply these processing methods to physiologic signals.
Offered alternate years.
Prereq: MATH 83; and proficiency in C or FORTRAN. |
| Advanced Biomedical Signal Processing -
BIEN 251 |
| |
Covers modern methods of
Signal Processing encountered in the bio-medical field including
parametric modeling, modern spectral estimation, multivariate
analysis, adaptive signal processing, decimation/interpolation,
and two-dimensional signal analysis. There will be several
computer projects which apply these modern techniques to
physiologic data. Offered occasionally.
Prereq: BIEN 250 or equiv.; knowledge of
C or FORTRAN. |
| Multidimensional Biomedical Time Series
Analysis - BIEN 252 |
| |
Theory and implementation
of methods used to collect, model and analyze multidimensional
time series encountered in biomedical applications such as
functional imaging, electrophysiologic mapping and the study of
physiologic control systems. Offered occasionally.
Prereq: BIEN 250;
proficiency in C or FORTRAN. |
| Advanced Topics Biomedical Computing -
BIEN 259 |
| |
Application of signal
processing, information management, modeling and artificial
intelligence techniques in biomedical research and clinical
environments. Project approach drawing from current literature
and data from laboratories of affiliated institutions. Typical
projects include analysis of serially recorded neurophysiologic
data, development and solution of physiologic models,
application of artificial intelligence to ordering of diagnostic
terminology. Offered occasionally. |
| Mathematics of Medical Imaging -
BIEN 265 |
| |
The course will begin with
an overview of the application of linear systems theory to
radiographic imaging (pinhole imaging, transmission and emission
tomography), and will cover the mathematics of computed
tomography including the analytic theory of reconstructing from
projections and extensions to emission computed tomography and
magnetic resonance imaging. Topics may also include
three-dimensional imaging, noise analysis and image quality, and
optimization. This course will have an advanced mathematical
content. Offered occasionally. |
Other Related Courses:
- Research Tools in Physical Chemistry -
CHEM
262
- Group theory (formal theory, theory of representations, point groups,
applications to atoms and molecules), molecular orbital theory, and
computational chemistry (molecular mechanics, semiempirical and ab initio
molecular orbital calculations). Offered fall semester. Prereq: CHEM
133.
Bioinformatics (Bio) Undergraduate Courses:
| Analysis of Physiological Models -
BIEN 152 |
| |
Development of continuous
(compartmental), and distributed-in-space-and-time mathematical
models of physiological systems and molecular events. Analytical and
numerical methods for solving differential equations of the initial
and boundary value types. Simulation of model response, and
estimation of model parameters using linear and nonlinear regression
analysis. Prereq: Jr. stndg. and MATH
83; or jr. stndg. and MATH 87. |
| Biotechnology Instrumentation -
BIEN 172 |
| |
The presentation of
biotechnology instrumentation will be based on the application of
the following topics: boundary value problems (modeling of one and
two dimensional distributions of temperature and electric fields);
optics (sources, filters, cells, and sensors); control of electric
fields; heat transfer and temperature control; motor control for
mechanical and fluid movements. The molecular biology and
engineering principles will be presented for each type of instrument
or process. Students will be expected to analyze and evaluate
commercially available systems, and propose design improvements.
|
| Systems Physiology -
BIEN 180 |
| |
Analyses of the underlying
physiologic and bioengineering aspects of the major cell and organ
systems of the human from an engineer’s point of view. Classic
physiologic approaches used to introduce topics including cell
functions, nervous system, nerve, muscle, heart, circulation,
respiratory system, kidney, reproduction and biomechanics. Design
problems including models of cell-organ-system function and problems
in biomechanics illuminate topics covered. Computer techniques and
relevant instrumentation are incorporated. Experts on related topics
are invited to speak as they are available.
Prereq: Jr. stndg. |
| Biomedical Instrumentation Design -
BIEN 187 |
| |
Problems in instrumentation
relating to physiological measurements in the laboratory and clinic.
Electronic devices for stimulus as well as measurement of
physiological quantities. Design of actual instruments. Features
include mechanical design, accessory design and safety requirements.
Prereq: BIEN 100 and
BIEN 155; or
EECE 111 and EECE 113. |
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