Bioinformatics Course Descriptions

Core Courses

Bioinformatics I (Genomics), BI450

This upper-level undergraduate or graduate elective course is designed to introduce students to the field of bioinformatics and genomics. An examination of the genomic organization of viral, bacterial, plant, animal, and human organism will be performed. The central role of bioinformatics in managing and mining the vast amounts of biological information generated from the genome projects will be emphasized. This course is designed to be project-oriented with hands-on experience using DNA/protein analysis software and molecular databases a major objective.

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Bioinformatics II (Methods and Applications), BI451

The second semester of the introductory bioinformatics sequence focuses on the algorithmic approaches most important for solving computational problems in bioinformatics. Topics include recursive and combinatorial algorithms and dynamic programming. The C programming language is used in implementing algorithms, with a secondary focus on PERL as an important scripting and prototyping language.
(Prerequisites: CS202 Computer Programming II, BI290 Molecular Biology, and BI450)

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Molecular Evolution & Phylogenetics, BI745

This course will present fundamental concepts of molecular evolution, and a survey of the computational algorithms that are employed to construct phylogenetic trees and to estimate pertinent biological data from phylogenetic reconstruction.
(Prerequisites: BI450 and BI451, or permission of instructor)

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Advanced Probability for Bioinformatics, BI755

This course will present concepts and methods of advanced probability theory with application to problems in Bioinformatics. Topics will include Bayesian probability and statistics, stochastic methods, information theory, and a variety of probabilistic inference methods.
(Prerequisites: ST310 and BI450, or permission of instructor)

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Microarray Technology, BI765

This course will cover a variety of topics concerning microarray technology. Fundamental and advanced concepts in microarray design, construction, utilization and analysis will be addressed. The course will be taught as a combination of lecture and computer-based data analysis.
(Prerequisite: BI450 or permission of instructor)

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Advanced Systems Analysis and Design for Bioinformatics, BI780

This course will provide theory and practical training in the development of data processing systems for use in genomic/sequence analysis and database design. Topics covered include construction of compute pipelines using UNIX tools and PERL, the BioPERL toolkit, fundamentals of relational databases and SQL, integrating databases with custom applications, and construction of client/server applications.
(Prerequisite: BI451 or permission of instructor)

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Advanced Algorithms for Bioinformatics, BI785

This course will cover advanced theory in the areas of chemical and biological informatics. Specific topics covered will depend on the interests of the instructor; for example, in previous semesters application of neural networks, Hidden Markov models, and Support Vector Machines in data mining and sequence analysis have been discussed. Students will work in teams to implement real-world projects using Java as the primary language.
(Prerequisite: BI780 or permission of instructor)

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Master's Project in Bioinformatics, BI790

In this course, the student will select a real-world bioinformatics problem to solve in collaboration with a mentor in industry or academia. The student will devise a solution in cooperation with the mentor and independently implement it. The student will be encouraged to develop a contemporary approach using Web-based tools. May be taken for two semesters.
(Prerequisites: status as a matriculating student in the graduate bioinformatics program and permission of instructor)

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Graduate Seminar, BI898

Current literature topics and research in bioinformatics will be analyzed in writing and presented orally.

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Biotechnology, BS764

This course offers an in-depth study of the techniques and applications of recombinant DNA technology with emphasis on current literature. Students will learn about techniques of recombinant DNA technology, develop an understanding of biotechnology industry product development, and examine ethical issues concerning biotechnology.
(Prerequisites: one semester each of genetics and biochemistry, or permission of instructor)

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Biotechnology Laboratory, BS765

This laboratory course will provide students with the opportunity to gain hands-on experience in recombinant DNA technology, experimental design principles, and data analysis.
(Pre- or corequisites: BS764 and permission of instructor)

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Elective Courses

Bioinformatic Computing, BI425

This course will cover a variety of topics concerning computing and computer programming in modern bioinformatics research. The focus will be on the UNIX operating system, along with fundamentals of procedural and object-oriented programming in C/C++ and Perl.

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Proteomics, BI775

This course will cover a variety of proteomic topics with a special focus on protein structure determination and prediction. Widely used experimental techniques such as mass spectrometry, NMR and X-ray as well as computational techniques will be presented. The course will be taught as a combination of lecture, demonstration and hands-on exercise.

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Plant Biochemistry, BS724

This course covers the biosynthetic mechanisms of the plant and biogenesis of alkaloids, steroids, glycosides, volatile oils, tannins, flavonoids, and other plant principles.
(Prerequisite: one semester of biochemistry or permission of instructor)

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Virology, BS750

The focus of this course will be the study of bacteria and plant and animal viruses with an emphasis on viral genetics and animal virology. Students will develop and understanding of virion struction, viral taxonomy, mechanisms of viral reproduction and replication, the pathology of selected viral families, and the nature of the viral/host relationship.
(Prerequisite: one semester of biochemistry or permission of instructor)

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Advanced Immunology, BS752

The principles of immunology will be presented with emphasis on cellular and molecular interactions. The genetic factors that govern immune mechanisms will be described. Application of immunological principles to tissue implantation, hypersensitivity, tumor development and therapy, AIDS, psycho-neuro influences on the immune system, and aging will be discussed.
(Prerequisites: one semester each of microbiology, genetics, and biochemistry, or permission of instructor)

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Advanced Cell Biology, BS761

This course is designed to give the student a working knowledge of the most recent advances in "hot" topics in cell biology through critical analysis of the current literature. The course will be presented in a lecture/seminar format.
(Prerequisite: one semester of cell biology, biochemistry, or genetics, or permission of instructor)

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Cell Biology Methods, BS763

This course covers the theory of methodologies and techniques commonly used in modern cell biology and biochemistry laboratory settings. Each student will be required to develop an understanding of the theory and current practice of separations and analysis of biochemical and cellular systems, including cell cultures, SDS-PAGE, affinity chromatography, HPLC analysis, cell manipulation, ELISAs, and fluorescence microscopy. The course is complementary to BS767, Cell Biology Methods Laboratory.
(Prerequisites: one semester each of cell biology and biochemistry, or permission of instructor)

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Special Topics in Cell Biology and Biotechnology, BS860

This course is designed to allow in-depth exploration of one of a variety of topics of current interest in the field. The general topic will be designated by the instructor. A variety of formats may be used, including lecture, presentations, papers, and discussion.
(Prerequisite: permission of instructor)

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Structure-Activity Relationships, CH714

Selected classes of medicinal agents are examined, stressing general structures, synthesis, and, in particular, the relationships between structure and pharmacological activity.
(Prerequisites: CH212 and permission of instructor)

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Physical Biochemistry, CH727

Course covers the application of the principles of thermodynamics, kinetics, and quantum chemistry to biochemical systems.
(Prerequisite: CH321)

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Advanced Biochemistry, CH728

Selected topics in protein structure and function, especially enzymology, will be discussed.
(Prerequisite: two semesters of undergraduate biochemistry)

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Computer-Aided Drug Design, CH748

This hands-on course will provide a broad survey of computational chemistry, with special focus on applications to drug design and "virtual screening" of bioactive compounds. Students will have the opportunity to learn to use several commercial software packages for molecular modeling and drug design, including SYBYL, UNITY, SPARTAN, and Gaussian98.

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Analytical Separations Chemistry, CH762

Theory, instrumentation, and practical aspects of analytical and preparative methods of separations, including gas, liquid, and supercritical fluid chromatography; capillary electrophoresis; and separation techniques coupled with mass spectrometry.
(Prerequisite: CH361 or permission of instructor)

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Peptide Biochemistry, CH843

Course is a consideration of the structure, synthesis, purification, characterization, and bioassay of peptides.
(Prerequisite: CH728 or permission of instructor)

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Special Topics in Physical Chemistry, CH892

Topics of current interest in physical chemistry are discussed, with detailed treatment of topics not ordinarily included in a classical course. Students are expected to keep abreast of current literature.
(Prerequisite: permission of instructor)

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Statistics for Research, ST704

This course covers statistical inference on two samples, design of experiments, repeated measures, analysis of covariance, multiple regression, categorical data analysis, and factor analysis.
(Prerequisite: ST310 or permission of instructor)

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Regression Analysis, ST720

Course includes basic statistics, straight line regression analysis, the correlation coefficient, analysis of variance, multiple regression analysis, testing hypothesis in multiple partial, regression diagnostics, and selecting the best regression equation.
(Prerequisite: ST310)

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