Duke University | Howard Hughes Undergraduate Program

Department of Biology

• BIOLOGY 117: Structure-Function Relationships in Biology: Molecules to Organisms

  This course focuses on the biochemical and physical principles underlying physiological processes and includes the description and investigation of three themes: key biological systems, especially bioenergetics and movement; perception and integration of information about environmental or internal states (signals); and the molecular, structural and behavioral mechanisms by which organisms respond to signals (networks).  Lectures include sections on how quantitative and experimental data can be used to estimate or validate models of pathways.  The material covered in lectures is expanded on in "quantitative laboratory" sections over the course of the semester.  These lab sections emphasize model building and data analysis such as modeling biochemical pathways and using concept maps to facilitate the modeling process.  Each of the modeling labs incorporates both physiological and molecular mechanisms and concepts.

• BIOLOGY 147: Introduction to Systems Biology

  This course is intended for students majoring in computer science, mathematics, physics, statistics or engineering, but who would like to work on problems originating in biology.  The course includes a sufficient amount of biology so that students will be able to tackle problems in the area of systems biology.  The course covers the following topics: cells and cellular states; DNA—how the cell stores information; gene expression—how the cell processes information; proteins and signaling—how a cell controls information flow; networks controlling the cell cycle; transcriptional networks in development; networks and cancer biology; and network evolution.  This course will be paired with Introduction to Computer Modeling, a course that presents the basics of modeling to students with strong backgrounds in other sciences.  Students from both courses will engage in joint projects in systems biology.
  

• BIOLOGY 25L: Principles of Biology

  A systems perspective has been integrated into our introductory biology course to engage students with current questions in biology and to prepare them for advanced courses. Integrated lecture and laboratory sessions illustrate how mathematical models can elucidate gaps in our current understanding of biological systems as well as suggest areas of additional experimentation and promote systems-level thinking.
  

• BIOLOGY 205L: Experimental Development and Molecular Genetics

  BIOLOGY 205L is an upper level stand-alone laboratory course created in 1994 with funding from an HHMI grant to Duke University. In this course students study up to six different model organisms using experimental methods ranging from classical embryology to molecular genetics.  The course is inquiry driven, with students planning and executing experiments of their own design. With new HHMI funding, the course now incorporates several modules that introduce systems biology, including gene disruption in Caenorhabditis elegans, gene regulatory networks in sea urchins, and transcriptional changes induced in nutrient-deprived Arabidopsis plants.

Departments of Mathematics and Computer Sciences

• MBS XXX: Shared Perspectives in Research Modeling

  This new course, to be first offered in 2009-10, will serve as the capstone experience for students who complete the Undergraduate Certificate in Modeling Biological Systems (MBS).
  
  MBS provides rigorous biological, mathematical, and computational training and an intensive independent research experience for Duke students. The overarching mission of the MBS program is to facilitate intellectual growth in our undergraduates by mentoring the development of sound reasoning skills towards complex biological models.  
  
  The introductory seminar for the certificate program is MBS 100 (MATH 196S): Introduction to Modeling Biological Systems.  A list of course electives for the certificate program is available on the program web site:
  http://www.genome.duke.edu/education/undergraduate/MBS/

• COMPSCI 111: Introduction to Computer Modeling

  This course, offered by the Department of Computer Science, is paired with Introduction to Systems Biology (BIOLOGY 147) and provides an introduction to techniques for developing, evaluating, and analyzing computational models for problems in the sciences, with a special emphasis on systems biology. This course is offered to science majors who want to enhance their quantitative reasoning skills.  Collaborative teams of students from this course and from BIOLOGY 147, Introduction to Systems Biology, will work together on in-depth problem sets.   
  

Department of Electrical and Computer Engineering

• ECE XXX: Statistical Methods in Biological Engineering

  This course, offered first in 2009-09, provides a practical, hands-on approach to using signal processing precepts to study and evaluate biological systems and to make decisions based on biological data.  Course topics include a review of probability, random variables, random processes and information theory, a review of digital signal processing, detection and estimation theory, modeling of biological systems, pattern recognition techniques for decision making, and inferences based on biological systems data.  Final projects will be based on such topics as computational methods for discovering biomarkers for early detection of disease, predicting protein structures and protein-protein interactions, computational methods for locating transcriptional factor binding sites, multiple sequence alignment algorithms, classification of protein families, and gene expression data analysis.  Teams of students with backgrounds in computational biology, engineering, and signal processing will work together, with each group building on the other’s strengths to find novel solutions to current biological problems.