Courses
Prerequisite Courses (6 credits)
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BI7513 Chemical Foundation for Bioinformatics (3 credits)
An intensive review of those aspects of Organic Chemistry and Biochemistry necessary to begin research in Bioinformatics and to enter graduate courses in Biology. Covalent bonding, quantum mechanical basis of bond formation, three-dimensional structure of molecules, reaction mechanisms, catalysis, polymers, enzymes, thermodynamic and kinetic foundations, metabolic pathways, sequence and structure of macromolecules. This course will make extensive use of computer approaches to convey the essential computational and visual nature of material to be covered.
Prerequisites: CM102, General chemistry, general physics, organic chemistry, and calculus.
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BI7523 Biological Foundation for Bioinformatics (3 credits)
An intensive review of those aspects of Biochemistry, Molecular Biology and Cell Biology necessary to begin research in Bioinformatics and to enter graduate courses in Biology. The areas covered will include cell structure, intracellular sorting, cellular signaling (i.e. receptors), Cytoskelton, cell cycle, DNA replication, transcription, translation. This course will make extensive use of computer approaches to convey the essential computational and visual nature of the material to be covered.
Prerequisites: General chemistry, general physics, organic chemistry, calculus, or permission of instructor.
Core Courses - All Three Required Sequences (9 credits)
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BI7533 Bioinformatics I: Sequence Analysis (3 credits)
Computer representations of nucleic acid and protein sequences, pairwise and multiple alignment methods, available databases of nucleic acid and protein sequences, database search methods, scoring functions for assessment of alignments, nucleic acid to protein sequence translation and codon usage, genomic organization and gene structure in prokaryotes and eukaryotes, introns and exons, prediction of open reading frames, alternative splicing, existing databases of mRNA, DNA, Protein, and genomic information. An overview of available programs and of resources on the web. Lab is an integral part of this course.
Prerequisites: none.
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BI7543 Bioinformatics II: Protein Structure (3 credits)
Protein folding representations, databases of protein folding classes, secondary structure prediction, tertiary structure prediction via computer folding experiments threading, and homology model building, prediction of post translation modification sites, active and binding sites in proteins, representations of contiguous and non-contiguous epitopes on protein surfaces at the sequence level, representations of functional motifs at the three dimensional an at the sequence level. Lab is an integral part of this course.
Prerequisites: BI7533.
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BI7553 Bioinformatics III: Functional Prediction (3 credits)
Functional classifications of proteins, prediction of function from sequence and structure, Orthologs and paralogs, representations of biological pathways, available systems for the analysis of whole genomes and for human-assisted and automatic functional prediction. Lab is an integral part of this course.
Prerequisites: BI7543.
Elective Courses
- BI7613 Systems Biology (3 credits)
This course explains the functioning of basic
circuit elements in transcription regulation,
signal transduction, and developmental networks
of living cells, using simplified mathematical
models. The course focuses on design
principles and information processing in biological
circuits. It discusses network motifs,
modularity, robustness, evolutional optimization
and error minimization by kinetic proofreading
in specific applications to bacterial
chemotaxis, developmental patterning, neuronal
circuits, and immune recognition in
several well-studied biological systems.
Prerequisites: Undergraduate courses in elementary
calculus and physical chemistry.
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BI7623 System Biology: -Omes & -OmicsOMICS (3 credits)
The course provides physical and chemical basis of understanding the behavior of synetic and natural polyelectrolytres in aqueous solutions, including the process of thier self-assembly into complex supermolecular structures. The course springs from discussion of fundations of Polymer science,goes through detailed examination of structure and physiological chemical properties of synthetic polyelectolytes and comes in with application of learned principles to consideration of the beahvior of biological electrolytes (nueclic acids, ploysaccharides and proteins) in aqueous media.
- BI 7843 Modeling and Simulation of Biomolecules (3 credits)
This course will introduce students to principles and applications of modern molecular modeling and simulations methods, using commercially available software packages.
Algorithms for visualization and prediction of structural and physical properties of molecules and molecular aggregates will be taught based on the principles of quantum, classical and statistical mechanics, which will be reviewed in a mathematically simplified form. Commercial software packages will be applied to illustrative problems in physical chemistry, chemical engineering, biology and medicine. Pre-requisites: Completion of core undergraduate courses in Mathematics and Science (grade C or better) in CM, CH, ME, EE, CS, PH or CE, or equivalent.
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BI7603 Research in Bioinformatics (3 credits)
Original research, which serves as basis for
master’s degree. Minimum research registration
requirements for the master’s thesis: 12
units. Registration for research required each
semester consecutively until students have
completed adequate research projects and acceptable
theses and have passed required oral
examinations. Research credits registered for
each semester realistically reflect time devoted
to research.
Prerequisites for MS candidates:
Degree status and consent of graduate
adviser and thesis director.
- BI7573 Special topics in Bioinformatics - DNA Microarrays (3 credits)
- BI7583 Guided Studies/Thesis in Bioinformatics (3 credits)
To be arranged with thesis advisor.
- CS5303 Introduction to Prog and Prob Solving (3 credits)
This course provides an introduction to discrete mathematics, computers and programming; running C/C++ programs under UNIX; algorithmic language; pseudocode; problem solving and program structure. Topics covered include constants, variable, data types, assignments, arithmetic expressions, input and output; object-oriented and top down design and procedures, selection and loops; functions; enumerated and sub-range data type; arrays, records and sets; recursion; and searching and sorting.
- CS5403 Data Structures and Algorithms (3 credits)
This course provides an introduction to data structures. Topics covered include; program specifications and design; abstract data types, stacks, queues; dynamic storage allocation; sequential and linked implementation of stacks and queues; searching methods, sequential and binary; binary trees and general trees; hashing; computational complexity; sorting algorithms - selection sort, insertion sort, heap-sort, merge-sort and quick-sort; comparison of sorting techniques and analysis.
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