Course Descriptions

Course Descriptions (Based on 2009-2010 Course Catalog)

Bioinformatics Core Courses

• Bioinformatics
  • CISC636: Introduction to Bioinformatics (3)
    • Term: 2009 Fall Semester
    • Introduction to concepts, methodologies, and tools in bioinformatics. Abstraction of biological problems for computational solutions. Genome sequencing and assembly, bio-sequence comparison and database search, dynamics programming, hidden Markov models, and phylogenetic trees. PREREQ: CISC220 or permission of instructor. RESTRICTIONS: Credit cannot be earned for both CISC636 and CISC436. Notes: A 600 level section meets with a 400 level section.
  • ANFS644: Bioinformatics (3)
    • Term: 2009 Fall Semester
    • Examines computer applications to biological sciences with emphasis placed upon genomics and proteomics applications. No computer programming experience required.
• Introduction to interdisciplinary domains
  • ELEG672: Cell and Molecular Biology for Engineers (3)
    • Overview of cell biology and molecular mechanisms. Covers some intercellular interactions, but main focus is on intracellular structure, organization, and function. Emphasis placed on application of cell properties to analysis of common biological data sets, including genomic, proteomic data.

    Or
    BISC665: Advanced Molecular Biology & Genetics (3)

    • Presents concepts and approaches regarding our current understanding of molecular biology and molecular genetics in eukaryotic organisms. Requires a solid background in biochemistry, cell biology and introductory molecular biology.

    ANFS670: Principles of Molecular Genetics (3)

    • Fundamentals of nucleic acid biochemistry (replication, repair, and recombination) and bacterial genetics provide the background needed for detailed study of selected topics in animal and plant molecular biology. Prerequisites: ANFS300 or permission of instructor.

    PLSC636: Advanced Plant Genetics (3)

    • Advanced survey of genetics in higher plants, including molecular methods of plant biotechnology. Topics include genome composition and evolution, disease resistance, transposable elements and retrotransposons, DNA methylation and epigenetics, quantitative traits, chromosome structure and gene expression. Prerequisites: PLSC300 and PLSC306.

    MAST616: Methods in Molecular Biology (3)

    Conceptual experience in molecular biological techniques with an emphasis on their application to marine related problems. Topics include: nucleic acid extractions, cloning, gene amplification and characterization, and expression methodologies. Prerequisites: MAST634
  • MAST667: Programming for Biologists (3)
    • N/A
• Systems Biology
  • CHEG/MATH460: Introduction to Systems Biology (3)
    • Term: 2009 Fall Semester – CANCELLED
    • Systems biology approach, mathematical modeling of biological systems; examples from biomedical and agricultural research areas, biotechnology, industrial processes, and others. Differential equations, stochastic, feedback and control, or network models are discussed. Hands-on work via PBL modules. PREREQ: CHEM527, MATH535 and one of BISC302, 305, 306, 401 or 403. Notes:   Cross-listed with MATH460050.
  • MASTxxx: Functional Genomics and Systems Biology (3)
    • N/A
• Database
  • CISC637: Database Systems (3)
    • Term: 2009 Fall Semester
    • Physical and logical organization of databases. Data retrieval languages, relational database languages, security and integrity, concurrency, distributed databases. PREREQ: CISC220 and CISC304 or equivalent RESTRICTIONS: Credit cannot be received for both CISC637 and CISC437. Notes: A 600 level section meets with a 400 level section.
• Biostatistics
  • STAT656: Biostatistics (3)
    • An introduction to statistics focused toward applications in biological, medical and other life sciences. Topics include graphical and numerical techniques, random variables and their distribution, estimation and inference. Prerequisites: MATH201

    Or
    STAT617: Multivariate Methods (3)

    • Term: 2009 Fall Semester
    • Multivariate analysis of variance and covariance; classification and discrimination; canonical correlation; principal components; factor analysis. PREREQ: STAT371. Notes: Requires permission from the instruction.
• Ethics
  • CISC355: Computers, Ethics and Society (3)
    • Term: 2009 Fall Semester
    • Explains relationships among information technology, society and ethics by examining issues raised by increasingly widespread use of computers. Topics include ethics for computer professionals, computer impact on factory work, office work, personal privacy and social power distribution. RESTRICTIONS: Cannot be used as a technical elective for CISC majors or minors.

    Or
    NURS413: Biomedical Research Ethics (3)

    • Critically examines scientific integrity and responsible conduct in biomedical and translational research within theoretical and social context of research ethics using case examples and previous experiences. Topics include: individual and institutional responsibilities for promoting scientific integrity; protection of the rights of the researcher and human and animal subjects; data issues; collaboration; authorship practices; intellectual property; and impact of future developments in science. Students write case analyses, reflections and critiques about field experiences to ethical review boards and research laboratories and discuss the culmination of their experiences specific to research ethics.

    Or
    BIOL631: Practice of Science (3)

    • Uses historical, philosophical, and sociological perspectives to better understand the nature of modern science and its practice. Examines "science misconduct," and satisfies the NIH mandate requiring graduate training in "the responsible conduct of research."

Elective Courses – Computational Sciences

• CISC841: Algorithms in Bioinformatics (3)
  • Advanced topics in current bioinformatics research, such as hidden Markov models, kernel based methods, and bayesian based analysis with applications to functional annotation, structural prediction, and biological networks inferences. Prerequisites: CISC436 or CISC636 or permission of instructor.
• CISC621: Algorithm Design and Analysis (3)
  • Term: 2009 Fall Semester
  • Emphasis on developing expertise in the design and analysis of algorithms. Equal importance given to techniques and specific algorithms. Particular topics include advanced data structures, graph algorithms, disjoint set manipulation, sorting and selection, amortized analysis, NP-completeness, and matrix and polynomial multiplication. PREREQ: Undergraduate algorithms and discrete math courses.
• CISC640: Computer Graphics (3)
  • Term: 2009 Fall Semester
  • Computer graphics technology, two- and three-dimensional systems, graphics software systems, modeling and object hierarchy, and animation. PREREQ: CISC220 or equivalent COREQ: CISC320 recommended RESTRICTIONS: Credit cannot be received for both CISC640 and CISC440. Notes: A 600 level section meets with a 400 level section.
• CISC659: Topics in Communications, Distributed Computing and Networks (3)
  • Contents vary to coincide with the interests of students and faculty. Prerequisites:   CISC650
• CISC675: Object Oriented Software Engineering (3)
  • Understand and apply a complete modern software engineering process. Topics include requirements analysis, specification, design, implementation, verification, and project management. Real-life team projects cover all aspects of software development lifecycle, from requirements to acceptance testing. Use of formal methods in the specification, design, and verification of software will be explored.
• CISC681: Artificial Intelligence (3)
  • Term: 2009 Fall Semester
  • Programming techniques for problems not amenable to algorithmic solutions. Problem formulation, search strategies, state spaces, applications of logic, knowledge representation, planning and application areas. PREREQ: CISC220 and CISC304 or equivalent. RESTRICTIONS: Credit cannot be received for both CISC681 and CISC481. Notes: A 600 level section meets with a 400 level section. Cross-listed with CGSC681010.
• CISC683: Introduction to Data mining (3)
  • Concepts, techniques, and algorithms for mining large data sets to discover structural patterns that can be used to make subsequent predictions. Emphasis on practical approaches and empirical evaluation. Use of a workbench of data mining tools, such as the Weka toolkit.
• CISC882: Natural Language Processing (3)
  • Term: 2009 Fall Semester
  • Introduction to computational models of syntax, semantics and pragmatics for natural language understanding. Emphasis on design of English interfaces to data bases and ill-formed input. PREREQ: CISC681
• CISC886: Multi-Agent Systems (3)
  • Introduction to the field of Multi-Agent Systems, examining issues that arise when groups of self-interested or cooperating autonomous agents interact to solve shared problems. Issues include reasoning about the knowledge and beliefs of other agents, communication and negotiation, computational organization, coordination and control. Prerequisites: CISC681 or equivalent
• CISC887: Internet Information Gathering (3)
  • Approaches to information gathering, filtering, and integration including work in the heterogeneous database, information retrieval and agent-oriented communities. Text indexing, vector-based and probabilistic retrieval, semantic web technologies, wrappers and mediators, query planning and optimization, collaborative filtering, information agents, applications. Prerequisites: CISC681 or equivalent
• CISC888: Machine Learning (3)
  • Concepts and algorithms underlying computer programs that learn from data to solve a task will be discussed. A range of modern machine learning algorithms will be covered.
• MATH607: Survey of Scientific Computing (3)
  • Term: 2009 Fall Semester
  • Numerical solution of linear systems; interpolation; differentiation and quadrature; transforms/FFT; nonlinear equations; initial value problems; boundary value problems; Monte Carlo methods; finite difference methods for partial differential equations. Additional topics at the discretion of the instructor. PREREQ: Linear algebra, differential equations, multivariable calculus. RESTRICTIONS: This course may not be taken for credit toward degree programs in Mathematical Sciences. Notes: See course catalog for prereq/coreq.
• MATH611: Introduction to Numerical Analysis and Scientific Computing (3)
  • Term: 2009 Fall Semester
  • Introduction to numerical computing, analysis and solution of systems of linear equations, linear least-squares, eigenvalue problems, methods for unconstrained optimization, solution of systems of nonlinear equations. Experience with standard computer packages, code development and simulations of applied problems. PREREQ: Linear algebra and multivariate calculus. Notes:   See course catalog for prereq/coreq.
• STAT608: Statistical Research Methods (3)
  • Term: 2009 Fall Semester
  • Experimental design and plot plans, collection, analysis and presentation of data in agricultural and biological research. Notes:  Open to graduate students only. Cross-listed with FREC608010.
• STAT615: Design and Analysis of Experiments (3)
  • Term: 2009 Fall Semester
  • Fundamental principles of design, randomized designs, Latin squares, sources of error, components of error. Factorial designs, response surfaces, models for design. PREREQ: STAT371
• STAT619: Time Series Analysis (3)
  • Fundamental topics in time series analysis – features the Box and Jenkins techniques of fitting time series data. Includes an introduction to appropriate statistical packages.
• STAT674: Applied Data Base Management (3)
  • Term: 2009 Fall Semester
  • Provides an in-depth understanding of using computers to manage data using programs such as SAS and Microsoft/Access. Notes: RESTRICTIONS: Requires permission of instructor. Cross-listed with FREC674040.
• STAT840: Statistical Computing (3)
  • Computer organization. Error in floating point computation. Approximating probabilities. Random numbers: generating and testing. Simulation. Computational linear algebra. Optimization methods appropriate for maximum likelihood computation. Fast Fourier transforms. Prerequisites: STAT602 and CISC105
• ELEG633: Image Processing (3)
  • Review of concepts of linear systems and spectral analysis, human visual response, scanning and display of images, Fourier optics, image enhancement and feature extraction, design of digital filters for image processing, 2D fast Fourier transform algorithms and computed tomography.
• ELEG652: Principles of Parallel Computer Architectures (3)
  • Provides an introduction to the principles of parallel computer architecture. Begins at a level that assumes experience in introductory undergraduate courses such as digital system design, computer architecture, and microprocessor based systems.
• CPEG/ELEG655: High-Performance Computing with Commodity Hardware (3)
  • Term: 2009 Fall Semester
  • New commodity computing devices, e.g., GPUs, bring the originally elite high performance computing into the reach of general public. Principles of program optimization, GPU and IBM Cell architecture, along with concepts and techniques for optimizing general purpose computing on the new hardware. Notes: A 600 level section meets with a 400 level section. Cross listed with ELEG655010.
• ELEG673: Signal Processing in Neural Systems (3)
  • Signal processing in real neural systems, with emphasis on mammalian/human sensory systems. Stimulus transduction, complex receptive fields, encoding, feature binding, and experimental techniques in visual, somatosensory, auditory and olfactory systems. Prerequisites:   ELEG471/671 or instructor’s permission
• ELEG674: Nonlinear Dynamics in Neural Systems (3)
  • Introducion to the mathematical tools, theory, and experimental observations that concern nonlinear dynamics of biological nervous systems. Classical methods are employed to develop a unified approach to the study and understanding of nonlinear dynamics, chaos, synchronicity, bifurcation, and self-organization. Prerequisites:  MATH243
• ELEG675: Image Processing with Biomedical Applications (3)
  • Fundamentals of digital image processing, including image formation, acquisition, transforms, enhancement, restoration, coding, and reconstruction from projections. Attention given to biomedical imaging modalities, including X-ray, computed tomography (CT), magnetic resonance (MR) imaging, and ultrasound. Prerequisites: ELEG305 or equivalent.
• ELEG677: Biosignal Processing (3)
  • Biomedical signal characteristics, biomedical systems and models, applications of Fourier transform, wavelet transforms, and joint-time frequency analysis of biomedical signals. Systems studies include ultrasounds, EKG’s, CAT scans, MRI’s, X-rays, and others. Prerequisites: ELEG305, ELEG310, or equivalent
• ELEG679: Introduction to Medical Imaging Systems (3)
  • Physics, instrumentation, system design, and image reconstruction algorithms will be covered for the following modalities: radiography, x-ray computed tomography (CT), single photon emission computed tomography (SPECT), positron emission tomography (PET), magnetic resonance imaging (MRI), and real-time ultrasound.
• CHEG620: Biochemical Engineering (3)
  • Term: 2009 Fall Semester
  • Application of chemical engineering principles to analyze different molecular engineering approaches, evaluate bioreactors and product recovery processes, analyze cellular engineering approaches and critically evaluate primary bioengineering data from literature and laboratory experiments. PREREQ: MATH243 and CHEM527 or CHEM641 and CHEM642
• CHEG621: Metabolic Engineering (3)
  • Focuses on design and control of cellular metabolism and includes analysis of metabolic function using systems engineering and molecular biology tools. Goals are to learn computational approaches for analyzing metabolic behavior, and experimental techniques to measure cellular components, metabolites, proteins and nucleic acids. Prerequisites: CHEM527 or CHEM641; MATH305. Open only to graduate students, seniors and juniors.

Elective Courses – Life Sciences

• BISC600: Biotechnology and Molecular Medicine (3)
  • Application of molecular and cellular biology techniques and principles to the field of biotechnology. Stresses the applied side of science and focuses on the practical side of molecular biology and how scientists and companies reduce the basic knowledge to practice. Emphasis on product formation and the skills required to meet such goals. Covers tangential issues of biotechnology and the ethical choices made in developing clinical trial protocols. Prerequisites:   Undergraduate course in biology or chemistry or permission of the instructor.
• BISC602: Molecular Biology of Animal Cells (3)
  • Term: 2009 Fall Semester
  • Examination of eucaryotic genes, synthesis and processing of messenger RNA and control of protein synthesis with emphasis on regulation of normal cellular growth and differentiation and the process of cancer cell transformation. Emphasis on recombinant DNA technology, monoclonal antibody production and tissue culture. PREREQ: BISC401 and BISC403. Notes:   See course catalog for prereq/coreq. Requires permission from the instructor.
• BISC612: Advanced Cell Biology (3)
  • Four major sections: (1) cell structure/function; (2) signaling mechanisms and cell fate; (3) protein biosynthesis and trafficking and (4) integrative cell biology. Requires interpreting and evaluating data from primary scientific literature. Meets literature requirement for biology majors.
• BICS625: Cancer Biology (3)
  • Provides an integrated lecture series summarizing current knowledge in cancer biology. Topics include: statistics of incidence/survival, pathology, the process of chemical carcinogenesis and sources of carcinogens, genetic and epigenetic mechanisms and consequences, viral and hormonal carcinogenesis as well as current treatment options. Prerequisites: BISC207, BISC401, CHEM103, CHEM104, CHEM321.
• BISC641: Microbial Ecology (3)
  • Principles of microbial interactions in natural environments, including applications to industrial microbiology and certain types of pollution. Prerequisites:   BISC300
• BISC645: Bacterial Evolution (3)
  • Term: 2009 Fall Semester
  • Explores the development of the enormous bacterial diversity beginning with current theories on the origin of life. Examines the evolution of viruses and the "directed evolution" controversy which concerns mechanisms of bacterial evolution. PREREQ: BISC300 or equivalent
• BISC654: Biochemical Genetics (3)
  • Covers the use of genetic model organisms to answer biological questions, including mapping and cloning of human disease genes and the creation of animal models for human genetic diseases. There is an emphasis on examples from the recent scientific literature and building scientific writing skills. Prerequisites:   BISC403 and BISC401; or permission of instructor
• BISC656: Evolutionary Genetics (3)
  • Exploration of the theory, methods and experiments underlying current research in evolutionary processes determining genetic variation within and between species, estimation of population structure from genetic data, and the genetics of speciation. Prerequisites:   BISC403
• BISC665: Advanced Molecular Biology & Genetics (3)
  • Presents concepts and approaches regarding our current understanding of molecular biology and molecular genetics in eukaryotic organisms. Requires a solid background in biochemistry, cell biology and introductory molecular biology.
• BISC671: Cellular and Molecular Immunology (3)
  • Term: 2009 Fall Semester
  • Introduces the basic concepts of immunology and describes how different immune responses can either protect the body from infection or lead to immunological based diseases. Focuses on cellular interactions and the resultant molecular responses that lead to immune protection. PREREQ: BISC401 or BISC305 or BISC300. RESTRICTIONS: Requires permission of instructor.     Notes:   Requires permission from the instructor. A 600 level section meets with a 400 level section.
• BISC679: Virology (3)
  • Molecular biology of animal viruses. Virus structure and organization; mechanisms of penetration, replication, maturation and transformation. Prerequisites:   BISC401 or biochemistry
• BISC682: Bacterial Pathogens: Molecular Mechanisms (3)
  • Explore the molecular mechanisms of infectious diseases. Disease transmission and infection, horizontal gene transfer and pathogenomics are reviewed using primary research literature. Topics include water and food borne, airborne, vector borne and human borne pathogens, their molecular mechanisms of invasion, colonization, virulence and immune avoidance.
• BISC693: Human Genetics (3)
  • Emphasis on the medical and social implications of our knowledge of human genetics. Discusses theoretical and practical principles of genetics useful in studying human variation such as cytogenetics and cell genetics, biochemical genetics, developmental genetics and teratology, principles of genetic counseling, multi-factoral inheritance and the genetics of cancer. Prerequisites:  BISC403
• CHEM641: Biochemistry (3)
  • Term: 2009 Fall Semester
  • Structure and function of proteins, enzymes and coenzymes; kinetics and mechanisms; carbohydrate metabolism and its regulation; and citric acid cycle. PREREQ: CHEM322 or CHEM332.
• CHEM645: Protein Structure and Function (3)
  • Term: 2009 Fall Semester
  • Overview of structural biology, including how x-ray crystallography, NMR spectroscopy, homology modeling and other techniques are used to solve or model structures of macromolecules. Representative proteins discussed in terms of how a protein’s structure relates to its function. PREREQ: CHEM641
• CHEM646: DNA-Protein Interactions (3)
  • Term: 2009 Fall Semester
  • Current topics of DNA-protein interactions which focus on DNA replication, DNA recombination, DNA damage repair, transcription and translation processes. PREREQ: CHEM642
• CHEM/CHEG649: Molecular Biophysics (3)
  • Biophysical principles and methods: thermodynamic and kinetic analysis of folding; protein-nucleic acid interactions; ligand binding; spectroscopy; structural methods; modeling; calorimetry; ultracentrifugation; SPR. Problem solving in macromolecular interactions: protein refolding; altering ligand affinity; increasing protein stability; drug design and HTS; protein expression and solubility; protein engineering. Prerequisites: Introductory-level courses in chemistry, physics biochemistry.
• CHEM624: Principles of Mass Spectrometry (3)
  • Principles of mass spectral measurements for the elucidation of molecular structure; applications to biomolecular materials and topics from the current literature. Prerequisites:   CHEM437
• ANFS670: Principles of Molecular Genetics (3)
  • Fundamentals of nucleic acid biochemistry (replication, repair, and recombination) and bacterial genetics provide the background needed for detailed study of selected topics in animal and plant molecular biology. Prerequisites:   ANFS300 or permission of instructor.
• MAST616: Methods in Molecular Biology (3)
  • Conceptual experience in molecular biological techniques with an emphasis on their application to marine related problems. Topics include: nucleic acid extractions, cloning, gene amplification and characterization, and expression methodologies. Prerequisites:   MAST634
• MAST618: Marine Microbial Ecology (3)
  • Examines role of microbes in the oceans and their impact on oceanographic processes and biogeochemical cycles in marine environments. Emphasis is on bacteria and their interactions with other marine organisms. Introduces use of molecular tools to examine uncultivated microbes.
• MAST623: Physiology of Marine Organisms (3)
  • Processes and mechanisms of adaptation of organisms to marine environments. Examines how environmental factors affect physiological processes in marine organisms. Lectures address physiological processes at cellular, whole organism and habitat levels. Prerequisites: MAST634 or equivalent. Requires permission of instructor
• MAST625: Microbial Physiology and Diversity (3)
  • Emphasis on diversity of physiological strategies developed by prokaryotic microbes and some simple eukaryotes. Approach is to examine and dissect specific metabolic pathways both in isolation and in how they integrate with central metabolism. Prerequisites:  BISC 207/208, CHEM 321 or CHEM 331, or permission of instructor. Juniors, Seniors, and Graduate Students
• MAST634: Marine Molecular Sciences (3)
  • Term: 2009 Fall Semester
  • This course surveys the dominant molecular processes in marine organisms that are essential for survival. Students are introduced to metabolic pathways, protein structure and function, DNA replication and repair, gene transcription and translation, and mitochondiral and chloroplast organelle function.
• PLSC636: Advanced Plant Genetics (3)
  • Advanced survey of genetics in higher plants, including molecular methods of plant biotechnology. Topics include genome composition and evolution, disease resistance, transposable elements and retrotransposons, DNA methylation and epigenetics, quantitative traits, chromosome structure and gene expression. Prerequisites:   PLSC300 and PLSC306.
• PLSC644: Physiology of Plant Stress (3)
  • Angiosperms’ response to biotic and abiotic environmental stresses; mineral nutrients, salt, drought, cold, heat, light, pathogens and herbivores at the physiological and molecular levels. Prerequisites: PLSC410.
• PLSC804: Plant Molecular Biology (3)
  • Fundamental and applied aspects of plant molecular biology, including organization of plant genes, genomes, gene expression, gene transfer and genetic engineering. Prerequisites:   ANFS670 or BISC653.
• HESC654: Medical Physiology (3)
  • Survey of medical physiology, including discussion of major body systems with emphasis on system interaction, homeostasis, and pathophysiology. Prerequisites: A previous course in mammalian, applied, cell, or exercise physiology.
• PHYT632: Applied Physiology I (3)
  • Description: In-depth analysis of the physiological mechanisms of the cardio-pulmonary system. Lectures in normal and abnormal function of this system. Emphasis on cardiopulmonary testing and rehabilitation techniques including stress tests and pulmonary function tests. Prerequisites: PHYT622
• HESC602: Data Analysis and Interpretation in Health Sciences (3)
  • Overview of statistical practice in health sciences research, particularly experimental research. Topics include experimental design, regression, analysis of variance including repeated measures designs and nonparametric tests.