Biosciences, Bioinformatics, and Biotechnology (IB3)

Related Catalog Entry: College of Arts and Sciences / Institute for Biosciences, Bioinformatics, and Biotechnology

Related Mason Website: IB3 Website: http://www.ib3.gmu.edu/)

510 Recombinant DNA: Techniques and Applications (2:1:3). Prerequisites: Graduate standing or permission of instructor. Laboratory-intensive course covering the current theory and practice underlying DNA procedures and methodologies. Course provides direct instruction in current recombinant DNA laboratory techniques and their applications in molecular biology. Lecture topics include molecular cloning, vectors, E. coli and other host genotypes, library construction, nucleic acid sequencing, restriction mapping, probes and PCR, and synthesis and cloning of cDNA. Laboratory sessions involve experimental protocols in characterizing and cloning DNA molecules and in constructing a genomic library. Laboratory protocols will change to reflect latest advances in techniques and domains of applicability.

511 Lab Human Mitochondrial DNA Analysis (3:1:6). Prerequisites: Graduate standing or permission of instructor. Laboratory-intensive course covering the current theory and practice underlying mitochondrial DNA procedures and methodologies. Course provides direct instruction in current mtDNA laboratory techniques and their applications. Lecture topics include mtDNA biology, genetics, and biochemistry as well as forensic science applications. Laboratory sessions involve experimental protocols in characterizing mtDNA and mtDNA sequencing and analysis. Laboratory protocols will change to reflect latest advances in techniques and domains of applicability. This course can be delivered in five intensive days and is offered during summer school and intersessions at least twice a year.

512 Human DNA Identification by STRs (3:1:6). Prerequisites: Graduate standing or permission of instructor. Laboratory-intensive course covering the science and technology of DNA polymorphism analysis. Presents current DNA polymorphism analysis techniques and applications. Lecture topics include DNA polymorphism molecular biology, molecular genetics, and biochemistry as well as forensic science, biomedical, and commercial applications. Students receive extensive hands-on laboratory training in DNA polymorphism analysis both on the ABD 310 and 377 Genetic Analyzers. Students complete a mock DNA case.

514 Advanced Analysis of Human STRs (2:2:0). Prerequisites: IB3 512 or permission of instructor. An advanced STR data analysis and interpretation course for experienced students. Course presents the theory, practice, and analysis of DNA STRs for complex forensic, clinical, and biomedical applications. Teaching will place heavy emphasis on practical examples obtained during actual case work. Students will understand the rationale of STR nomenclature, and will be able to designate alleles relative to allelic ladders in complex systems.

520 Polymerase Chain Reaction Applications in the Biosciences (2:1:3). Prerequisites: Graduate standing or permission of instructor. Laboratory-intensive course covering applications of the Polymerase Chain Reaction (PCR) to problems in the theoretical and applied biosciences. Course focus is on current applications, procedures, and problems associated with the use of this versatile technology. Lectures include, but are not limited to, PCR basics, PCR's use in determining taxonomic relationships, PCR fingerprinting, PCR in genetic and disease diagnostics, and current applications of PCR and recombinant DNA methodologies in the biosciences.

521 Advanced Methods in DNA Sequencing (2:1:3). Prerequisites: Graduate standing or permission of instructor. Laboratory-intensive course presenting the science and technology of DNA sequence determination and analysis. Provides instruction in current fluorescent automated DNA sequencing techniques and applications. Lecture topics include DNA sequencing chemistry, biochemistry, and bioinformatics used in forensic, biomedical, and biotechnology applications.

550 Introduction to Bioinformatics (3:3:0). Prerequisites: Graduate standing or permission of instructor. Provides an overview of methods and tools in bioinformatics. Internet interfaces to sequence databases; linkages between sequence databases and other relevant data sets such as metabolic pathways, regulatory networks, and molecular modeling tools; bioinformatics applications including molecular phylogeny, nucleic acid structure prediction, protein structure and function, and gene discovery.

551 Laboratory Information Management Systems (3:3:0). Prerequisites: IB3 550 or permission of instructor. Practical issues in designing and implementing a laboratory information management system for bioinformatics, biotechnology, and forensic biosciences are presented. Working in teams, students organize, manage, and develop a laboratory information management system.Various approaches are compared in the context of DNA sequencing operations.

552 DNA Sequence Analysis (3:3:0). Prerequisites: IB3 550 or permission of instructor. In-depth survey of computational methods for the analysis of DNA sequences. Objective is to enable the student to analyze the products of a DNA sequencing project by comparing the resulting DNA sequence with known sequences, and to identify structural and functional similarity with known DNA sequences.

553 Phylogenetic Analysis (3:3:0). Prerequisites: IB3 550 or permission of instructor. Issues and algorithms for inferring phylogenies, including optimality criteria; rooted and uprooted trees; character, similarity, and distance data; distance methods; parsimony methods; maximum likelihood; searching for optimal trees; reliability of inferred trees; and available software packages.

655 Data Mining for Bioinformatics (3:3:0). Prerequisites: IB3 550 or permission of instructor. Introduction to MineSet provides a highly interactive, three-dimensional (3D) visual interface for manipulating visual objects, as well as searching, filtering, and animation. Analytical data mining tools, including an association rules generator, automatic binning, cluster generator, induction and classification tools for decision tables, decision trees, bayesian evidence, option trees, and regression trees are used. Visualization tools, including cluster visualizer, decision table visualizer, statistics visualizer, and tree visualizer are presented for bioinformatics, biotechnology, and forensic biosciences applications.

658 Modeling Dynamic Biological Systems (3:3:0). Prerequisites: IB3 550 or permission of instructor. Principles of modeling dynamic biological systems; steady state, oscillation, and chaos; spatial dynamics; extensive practical use of a typical modeling system, such as STELLA; survey of biological applications including population dynamics; modeling metabolism; genetics models; and models of organisms, infectious disease, parasites, and predator-prey systems.

750 Genetic Algorithms for Bioinformatics (3:3:0). Prerequisites: IB3 550 and computer programming (C, C++, Matlab, or instructor's approval). Approaches to evolutionary algorithms, including genetic algorithms, evolution strategies, evolutionary programming, genetic programming; theoretical foundations; applications to bioinformatics, including protein structure prediction, phylogenetic reconstruction, and DNA sequence assembly.

755 Neural Networks for Bioinformatics (3:3:0). Prerequisites: IB3 550 and computer programming (C, C++, Matlab, or instructor's approval). Overview of neural network models of parallel and distributed computation. Analytical characterization of various neural network models and their relationships to radial basis functions. Application to biosciences, including image processing, pattern recognition, and classification of biomolecules.