Bioinformatics and Computational Biology
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 introduction to life sciences for physicists, chemists, engineers, and mathematicians. Combines knowledge from 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.
401 Bioinformatics and Computational Biology I (3:3:0) Prerequisites: BIO 231, IT 108, IT 208, or CS 112 (instead of IT 108 and IT 208), STAT 344, or STAT 250. Topics are presented as three-week units: protein sequence, structure prediction, and modeling methods; nucleic acid sequence and structure prediction, and evolutionary models; gene structure prediction in prokaryotes and eukaryotes; image analysis, and biomedical applications.
402 Bioinformatics and Computational Biology II (3:3:0) Prerequisites: BINF 401 and BINF 403. Topics are presented as three-week units: the design and use of parallel genomics platforms, mapping the measurements to biomolecules; approaches for inferring biological pathways; simulation methods for the dynamics of biomolecules; systems approaches to biology.
403 Bioinformatics and Computational Biology Lab I (1:0:3). Corequisite: BINF 401. Laboratories will introduce students to bioinformatics tools designed to answer research problems in the topics covered in lectures, such as sequence alignment, sequence pattern recognition, structural conformation modeling, phylogenetic analysis methods and image comparisons.
404 Bioinformatics and Computational Biology Lab II (1:0:3) Prerequisites: concurrent enrollment in BINF 402 and passing grades in BINF 401 and 403. Laboratories will introduce students to research bioinformatics tools relevant to lecture topics such as: the correspondence of measured fragments to parent biomolecules, inference methods for gene and protein networks, predicting system outputs given specified inputs.
491 Senior Thesis in Bioinformatics (1:1:3) Prerequisites: the bioinformatics minor core classes. A project is chosen and completed under the guidance of a Bioinformatics Department faculty member. An oral progress report with a poster at the fall semester Bioinformatics Student Research Day is required.
492 Senior Thesis in Bioinformatics (1:1:3) Prerequisite: BINF 491. A project is chosen and completed under the guidance of a Bioinformatics Department faculty member. A written thesis in standard format is required.
630 Bioinformatics Methods (3:3:0) Prerequisites: graduate standing, or permission of instructor. Introduction to 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 biochemistry, molecular biology, and cell biology necessary to begin research in bioinformatics. Topics include cell structure and cell cycle; DNA replication, transcription, and translation; and 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. 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 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. Intensive introduction to parameters affecting data QC and analysis, including factors arising from biochemistry, chemistry, genetics, statistics, instrumentation, and software.
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 develop computer programs to perform many of these tasks.
650 Introduction to Bioinformatics Database Design (3:3:0) Prerequisites: BINF 634 or equivalent, or permission of the instructor. Students will acquire skills needed to exploit public biological databases, and establish and maintain personal databases that support their own research; such skills include learning underlying data models and the basics of DBMS and SQL.
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 instructor. Computational techniques for solving scientific problems focusing on applications in bioinformatics and computational biology. Students 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 Bioinformatics (3:3:0) Prerequisite: admission to PhD program in biosciences or bioinformatics, CHEM 663, or equivalent. Introduction to biochemical systems 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 informatics under direction of faculty member. May be repeated.
704 Colloquium 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, reflecting on purpose and reviewing 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 design, execution, and analysis of experiments and analysis of ethical issues in research, including use of animals and humans, standards in computer community, and research fraud. Guidelines for data ownership, manuscript preparation, and conduct of people in authority may be presented and discussed.
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. Topics include genome mapping, comparative genomics, and functional genomics.
733 Gene Expression Analysis (3:3:0) Prerequisites: programming experience and course in molecular biology, or permission of instructor; S-Plus or Matlab experience may be helpful. Analyzes 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. Topics include algorithm design, complex data structures, object oriented programming, relational databases, designing modules, and graphics and web programming. Students 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.
740 Introduction to Biophysics (3:3:0). Prerequisites: undergraduate courses in general physics, calculus, and biology. Introduces biophysics, focusing on physical and chemical concepts and their relation to rapidly expanding interdisciplinary interfaces among biology, chemistry, and physics. Reveals multiscale nature of biophysics, and includes exploration of macroscopic and microscopic applications.
741 Introduction to Computer Simulations of Biomolecules (3:3:0). Prerequisites: BINF 690 and 701, and knowledge of computer programming language; or permission of instructor. Details computational methods in biomolecular simulations, such as molecular dynamics and Monte Carlo algorithms. Special emphasis given to practical applications. Reviews most recent advances in biomolecular simulations.
751 Biochemical and Cellular Systems Modeling (3:3:0). Prerequisites: calculus and knowledge of a computer programming language; and BINF 690 and 701; or permission of instructor. Course in differential equations is recommended. Mathematical and computational methods for analysis of cellular and subcellular processes. Topics may include ion channels, whole cell models, intracellular signaling, biochemical oscillations, pathway modeling, parameter estimation, and sensitivity analysis.
796 Directed Reading and Research (3:3:0) Reading and research on specific topic in computational sciences and informatics under direction of faculty member. May be repeated.
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 Master's 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 (master's thesis) and oral defense. Graded S/IP.
820 Advanced Topics in Molecular Cell Biology (3:3:0). Prerequisites: BINF 631 or equivalent. Advanced molecular and cellular biology foundation for BINF students. Topics may include biomembranes and cell architecture, cell signaling, receptor activation, gene control, protein targeting and trafficking, and cell cycle regulation.
831 Structural Genomics Project (3:3:0). Prerequisite: BINF 731, or permission of instructor. Covers knowledge-based, large-scale protein structure analysis; classification and prediction of protein structure and function; and other current research topics in structural genomics. Projects address entire research enterprise from developing and defending proposal to peer-reviewed publication.
841 Research Topics in Biomolecular Simulations (3:3:0). Prerequisite: BINF 741, or permission of instructor. Research-oriented course combining lectures and work on individual projects in biomolecular simulations. Topics include protein and peptide aggregation, binding, and unfolding and folding.
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.
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.
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.