University Catalog 2005-2006

Bioinformatics (BINF)

School of Computational Sciences

354 Foundations in Mathematical Biology (3:3:0) Prerequisites: completion or concurrent enrollment in all other required general education courses; chemistry and integral calculus; or permission of instructor. Interdisciplinary course designed as an introduction to life sciences for physicists, chemists, engineers, and mathematicians. Combines knowledge from the core General Education areas of natural sciences, social and behavioral sciences, quantitative reasoning, and information technology. Covers selected topics in ecology, physiology, biochemistry, and behavior. May include biochemical reaction kinetics, Hodgkin Huxley model for cellular electrical activity, continuous and discrete population interactions, and neural network models of learning. Techniques utilized include ordinary differential equations, difference equations, algebraic equations, and computer simulations.

630 Bioinformatics Methods (3:3:0) Prerequisites: graduate standing or permission of instructor. Introduction to bioinformatics methods and tools for pairwise sequence comparison, multiple sequence alignment, phylogenetic analysis, protein structure prediction and comparison, database similarity searches, and discovery of conserved patterns in protein sequence and structures.

631 Molecular Cell Biology for Bioinformatics (3:3:0) Prerequisites: undergraduate background in biochemistry or cell biology, or permission of instructor. Intensive review of aspects of biochemistry, molecular biology, and cell biology necessary to begin research in bioinformatics. Topics include cell structure and cell cycle; DNA replication, transcription, and translation; molecular structure of genes and chromosomes.

633 Molecular Biotechnology (3:3:0) Prerequisites: graduate standing or permission of instructor. Laboratory intensive introduction to theory and practice of modern biotechnology. Includes study of recombinant DNA, gene expression, and genetic analysis and associated methods. Lab exercises reflect more recent advances in the field.

634 Bioinformatics Programming (3:3:0) Prerequisites: graduate standing and computer programming experience, or permission of instructor. Data representation, control structures, file input/output, subroutines, regular expressions, debugging, introduction to relational databases. Emphasizes bioinformatics applications including DNA sequence analysis, parsing FASTA and GenBank files, processing BLAST output files, SQL, or equivalent query language.

636 Microarray Methodology and Analysis (3:3:0) Prerequisite: BINF 633 or permission of instructor. Theory and practice of genome analysis including the genetics, biochemistry, and tools for analyzing global gene expression, and detection and quantification of genes and gene products.

637 Forensic DNA Sciences (3:3:0) Prerequisites: graduate standing or permission of instructor. Laboratory intensive introduction to theory and practice of modern forensic DNA science, including biochemistry, chemistry, genetics, statistics, instrumentation, software, and wetware required for applications of DNA science to forensic science.

639 Introduction to Biometrics (3:3:0) Prerequisites: programming experience (such as CSI 603 and 604) or permission of instructor. Introduction to methods for measuring humans. Topics include face, speaker, fingerprint, and shoeprint recognition; and handwriting analysis. Students will develop computer programs to perform many of these tasks.

690 Numerical Methods for Bioinformatics (3:3:0) Prerequisites: calculus and knowledge of a programming language, such as CS 112 and MATH 113, or permission of the instructor. Computational techniques for solving scientific problems focusing on applications in bioinformatics and computational biology. Students will develop the ability to convert a quantitative problem into computer programs to solve the problem. Emphasizes efficiency and readability of code.

701/BIOS 701 Biochemical Systematics (Biochemistry) Core for Doctoral Studies in Biosciences and Bioin-formatics (3:3:0) Prerequisite: admission to PhD program in biosciences or bioinformatics, CHEM 663, or equivalent. Introduction to biochemical systems now in use to investigate complex, multicomponent, dynamic functions of cellular systems. Such studies employ myriad conceptual and technical approaches in their application. Articles from current literature are basis of course offering. The application of molecular techniques within biosciences is now universal. The cell: What is its structure and how does it function? This is the underlying question of course.

702/BIOS 702 Research Methods (3:3:0) Prerequisite: admission to PhD program in bioinformatics or biosciences. Trains students in research methodologies for life sciences. Covers the three phases of biological research projects: experimental design, data collection, and data analysis.

703 Bioinformatics Lab Rotation (1:0:1) Prerequisite: permission of instructor. Short-term introductory research on a specific topic in computational sciences and infor-matics under direction of faculty member. May be repeated as necessary.

704 Seminar in Bioinformatics (1:1:0) Prerequisite: graduate standing. Seminar presentations in a variety of areas of bioinformatics and computational biology by SCS faculty, staff, advanced PhD students, and professional visitors. May be repeated for credit.

705 Research Ethics (1:1:0) Prerequisite: permission of instructor. Examines ethical issues in scientific research, beginning with a reflection on its purpose and a review of foundational principles for evaluating ethical issues. Provides skills for survival in scientific research through training in moral reasoning, and teaching of responsible conduct. Students learn to apply critical thinking skills to the design, execution, and analysis of experiments and analysis of current ethical issues in research, including use of animals and humans, ethical standards in the computer community, and research fraud. Currently accepted guidelines for data ownership, manuscript preparation, and conduct of people in authority may be presented and discussed in terms of relevant ethical issues.

730 Biological Sequence Analysis (3:3:0) Prerequisites: BINF 702 or previous courses in programming, molecular biology, and probability, or permission of instructor. Fundamental methods for analyzing nucleic acid and protein sequences, including pairwise and multiple alignment, database search methods, profile searches, and phylogenetic inference. Development of probabilistic tools, including hidden Markov models and optimization algorithms. Survey of current software tools.

731 Protein Structure Analysis (3:3:0) Prerequisite: permission of instructor, or previous courses in molecular biology, biochemistry, and computer programming. Computational methods for analyzing, classifying, and predicting three-dimensional protein structures. Covers theoretical approaches, techniques, and computational tools for protein structure analysis.

732 Genomics (3:3:0)Prerequisites: BINF 730 or previous courses in biology, numerical methods, and programming; or permission of instructor. Surveys computational tools and techniques to study whole genomes, and explores biological basis of genome analysis algorithms. Lecture topics include genome mapping, comparative genomics, and functional genomics.

733 Gene Expression Analysis (3:3:0) Prerequisites: programming experience and a course in molecular biology, or permission of instructor; S-Plus or Matlab experience may also be helpful. Focuses on analyzing gene expression data. Topics include cluster analysis and visualization of expression data, inference of genetic regulatory networks, and theoretical models of genetic networks.

734 Advanced Bioinformatics Programming (3:3:0) Prerequisites: BINF 634 or permission of instructor. Selected topics including algorithm design, complex data structures, object oriented programming, relational databases, designing modules, and graphics and web programming. Students will complete a bioinformatics programming project.

739 Topics in Bioinformatics (3:3:0) Prerequisite: permission of instructor. Selected topics in bioinformatics not covered in fixed-content bioinformatics courses. May be repeated for credit as needed.

796 Directed Reading and Research (3:3:0) Reading and research on a specific topic in computational sciences and informatics under direction of faculty member. May be repeated as necessary.

798 Research Project (3:0:0) Prerequisites: 12 graduate credits and permission of instructor. Project chosen and completed under guidance of graduate faculty member that results in acceptable technical report.

799 MasterÕs Thesis (1-6:0:0) Prerequisites: 12 graduate credits and permission of instructor. Project chosen and completed under guidance of graduate faculty member that results in acceptable technical report (masterÕs thesis) and oral defense. Graded S/IP.

996 Doctoral Reading and Research (1-12:0:0) Prerequisites: admission to doctoral program and permission of instructor. Reading and research on specific topic in computational sciences and informatics under direction of faculty member. May be repeated as needed.

998 Doctoral Dissertation Proposal (1-12:0:0) Prerequisite: permission of advisor. Covers development of research proposal, which forms basis for doctoral dissertation, under guidance of dissertation director and doctoral committee. May be repeated, but no more than 12 credits of BINF 998 may be applied to doctoral degree requirements.

999 Doctoral Dissertation (1-12:0:0) Prerequisite: admission to doctoral candidacy. Doctoral dissertation research under direction of dissertation director. May be repeated, but no more than 24 credits in BINF 998 and 999 may be applied to doctoral degree requirements.