Special Topics Courses (489 & 689)

• *ECEN 689-601 (Fall 2009): Statistical Computation in Genomic Signal Processing. Instructor: Dr. Ulisses Braga-Neto
• *PLPA 689-600 (Fall 2009): Cyberinfrastructure for Biological and Biomedical Research. Instructor: Joshua S. Yuan
• *POSC 689-600 (Fall 2009). Current Topics in Genomics. Instructors: Huaijun Zhou and Mike Bailey
• BICH 489-501 (Spring 2009): Computational Techniques for Evolutionary Analysis Instructor: Dr. Sing-Hoi Sze
• CPSC 689-609 (Spring 2009): Structural Bioinformatics Instructor: Dr. Thomas Ioerger
• CPSC 689-606 (Spring 2009): Algorithmic Techniques for Biology Instructor: Dr. Sing-Hoi Sze
• STAT 689-601 (Spring 2009): Statistical Bioinformatics Instructor: Dr. Alan Dabney
• ECEN 689-612 (Spring 2008): Statistical Models & Algorithms for Biological Sequence Analysis. Instructor: Dr. Byung-Jun Yoon
• POSC 489-501, 689-602 (Fall 2008). Current Genomics Topics. Instructor: Huaijun Zhou
• VTPP 489-500, 689-600 (Spring 2008): Analysis of Genomic Signals. Instructor: Ivan V. Ivanov
  

Courses

• ANSC 624 Mammalian Developmental Genetics. (3-0). Credit 3. Genetic control of developmental pathways responsible for pattern formation and morphogenesis in mammals; genetic networks and genome organization; significance of genetic regulatory networks in developmental processes. Prerequisites: GENE 301 or 320; BICH 410/411 or equivalent.
• ANSC 629 Applied Animal Genomics. (3-0). Credit 3. Theory and application of genomics by livestock industries; consideration of genetic markers, gene mapping methods, genome analysis, and emerging technologies such as microarrays, transgenesis, cloning and marker assisted selection; exposure to bioinformatic tools for genomics. Prerequisites: GENE 603.
  
• *BICH/BIOL 450 Introduction to Genomics. (3-0). Credit 3.
  Introductory genomics course designed to provide a basic understanding of the science of genomics, the study of genome data; major emphasis placed on the logic behind genomic approaches and the capabilities and limitations of these approaches to investigate biological processes; discussion of genomics as another extension of the science of genetics. Prerequisite: Junior or senior classification in Biology, Genetics or Biochemistry.
• *BICH/BIOL 650 Genomics. (3-0). Credit 3.
  Modern genomics as a tool for understanding biological systems, gene structure, and organization as well as the history of sequencing technologies; focus on transcriptional, translational and functional genomics. Prerequisite: Graduate classification or approval of instructor.
• *BICH/CSCE 628. Computational Biology. (3-0). Credit 3. Introduction to computational biology; formulations of biology problems as computational problems; computational approaches to solve problems in genomics and proteomics. Prerequisite: Graduate classification or approval of instructor.
• BIOL 451 Bioinformatics. (3-0). Credit 3.
  Introduction to the entire field of bioinformatics; theoretical background of computational algorithms, with an emphasis on application of computational tools related to modern molecular biological research. Prerequisite: Junior or senior classification, or approval of instructor.
• BIOL 651 Bioinformatics. (3-0). Credit 3.
  Introduction to applications related to information processing in biological research with practical training exercises; includes internet databases, sequence alignment, motif prediction, gene and prometer prediction, phylogenetic analysis, protein structure classification, analysis and prediction, genome annotation, assembly and comparative analysis, and proteomics analysis. Prerequisite: Graduate classification or approval of instructor.
• BMEN 431/631 Thermodynamics of Biomolecular Systems. (3-0). Credit 3.
  Introduces equilibrium and non-equilibrium statistical mechanics and applies them to understand various biomolecular systems; including ensemble theory, reaction kinetics, nonlinear dynamics and stochastic processes; applied examples such as enzyme-ligand binding kinetics, conformational dynamic of proteins and nucleic acids, population dynamics, and noise in biological signals. Prerequisites: BMEN 240, PHYS 208 and MATH 308.
• BMEN 432/632 Molecular and Cellular Biomechanics. (3-0). Credit 3.
  Introduces biomolecules and their assemblies that play structural and dynamical roles in subcellular to cellular level mechanics, with emphasis on quantitative/theoretical descriptions, and discussions of the relevant experiment approaches to probe these nano to micro-scale phenomena; including topics in (1) self-assembly of cytoskeleton and biomembranes, (2) molecular motors, (3) cell motility, and mechanotransduction. Prerequisites: BMEN 240 and MATH 308.
• MATH 469. Introduction to Mathematical Biology. (3-0). Credit 3. Introduction to mathematical modeling techniques in the biological sciences; continuous versus discrete models; deterministic versus stochastic models; includes population dynamics and ecology, spread of infectious diseases, population genetics and evolution, spatial pattern formation. Prerequisites: MATH 304, 308 or equivalent.
• *MATH 648. Computational Algebraic Geometry. (3-0). Credit 3. Broad introduction to algorithmic algebraic geometry, including numerical and complexity theoretic aspects; theory behind the most efficient modern algorithms for polynomial system solving and the best current quantitative/geometric estimates on algebraic sets over various rings is derived. Prerequisite: MATH 653 or approval of instructor.
• MATH 664. Seminar in Applied Mathematics. (3-0). Credit 3. Problems, methods and recent developments in applied mathematics. This course may be taken five times for credit as content varies. Prerequisite: Approval of instructor.
  
• MATH 664-601 (Fall 2008). Mathematical Methods of Computerized Tomography. Instructor: Peter Kuchment
• MATH 669. Seminar in Mathematical Biology. (3-0). Credit 3. Problems, methods and recent developments in Mathematical Biology. Prerequisite: Approval of instructor.
• STAT 606. Design of Experiments. (3-0). Credit 3. Fundamental concepts in the design of experiments, justification of linear models, randomization, principles of blocking and the use of concomitant observations; construction and analysis of basic designs including confounding, fractional replication, composite designs and incomplete block designs. Prerequisite: STAT 642 or 653 or approval of instructor.
• STAT 632. Statistical Decision Theory (3-0). Credit 3. Fundamentals of Bayesian inference, single and multi-parameter models, Bayesian regression and linear models, posterier simulation, MCMC, hierarchical models. Prerequisite: STAT 611 or approval of instructor.
• STAT 643. Biostatistics I. (3-0). Credit 3. Bio-assay for quantitative and quantal responses: statistical analysis of contingency, including effect estimates, matched samples and misclassification. Prerequisites: STAT 608 and 642.
• STAT 644. Biostatistics II (3-0). Credit 3. Generalized linear models; survival analysis with emphasis on nonparametric models and methods. Prerequisite: STAT 643 or approval of instructor.
• STAT 661. Statistical Genetics (3-0). Credit 3. Basic concepts in human genetics, sampling designs, gene frequency estimation, Hardy-Weinberg equilibrium, linkage disequilibrium, association and transmission disequilibrium test studies, linkage and pedigree analysis, segregation analysis, polygenic models, DNA sequence analysis. Prerequisites: STAT 610 and 611.

Journal Clubs

• BICH/MBCH 674. Protein Folding and Stability. (1-0). Credit 1. Selected topics from recent literature in the general areas of protein folding, structure, and stability. Prerequisite: Approval of instructor. Meets Thursdays from 4-5pm.
• GENE 681-602. Genome Structure and Function. (1-0). Credit 1. Selected topics from recent literature in the general areas of functional genomics, system-wide characterization of gene or protein expression, and functional analysis of genes and gene variants. Meets Tuesdays 11am-12pm.