Rm. D223, L.S.R.C.
Office Phone: 660-6568
e-mail: denita@cs.duke.edu
SYNOPSIS OF COURSE CONTENT:
Section A Introduction: to Biopolymer Structures
& Recombinant DNA Techniques
Section B Nanosystems: Atomic Force Microscope,
Molecular Probes, DNA NanoAssembly & Molecular Electronics
Section C: Introduction to DNA Computing
Section D: Surface Based Chemistry:
DNA Chips & Surface Based DNA Computation
Section E: Bioinformatics, Sequencing, and Tagging
Required Textbooks (at Duke Bookstore)
Introduction to Computational Molecular Biology
Setubal and Meidanis ISBN: 0-534-95262-3
Introduction to Computational Biology,
Waterman ISBN: 0-412-99391-0
Assignments will be made available on-line from this site as the semester progresses.
Exams:
There will be no Midterm or Final Exam
Projects:
There will be due a project paper on a topic of your choice. Potential projects should be discussed with me before a final topic is chosen.
Some of the Class lecture notes are in PostScript and are on-line and those will be made available on-line from this site as the semester progresses. Hard copies of the other lecture note will also be made available.
Detailed Course Outline
Section A Introduction:
to Biopolymer Structure & Recombinant DNA Techniques
Lecture 1:Overview of Course Material
-DNA & Protein Structure
-Overview of Bioinformatics Topics
-Recombinant DNA Operations
-DNA Computation: Adeleman's Experiment
Lecture 2:Introduction to DNA structure
Lecture 3: Intro to Recombinant DNA Techniques, Part I: Cutting and Joining DNA Operations
Lecture 4: Intro to Recombinant DNA Techniques, Part II: Separation and Amplification Techniques
Lecture 5: Duke Laboratory on
Recombinant DNA Techniques
Lecture 6: Mathematical Models & Simulation Software for Recombinant DNA
-kinetics
-reaction models
-hybridization models
-error resiliency in word design
Lecture 7: Introduction to Protein Structure
Lecture 8: Molecular Simulation Algorithms & Software for Protein Structure Prediction
Lecture 9: Introduction to RNA Structure & Directed Evolutionary Techniques
Section B Nanosystems:
Lecture 10:Intro to DNA NanoAssembly
Lecture 11:DNA Comp. by Self-Assembly
-Tiling Theory
-Computations by Self-Assembly
Lecture 12: Mathematical Models and Software Simulations of DNA Self-Assembly
Lecture 13: DNA Self-Assembly Experiments
Lecture 14: Atomic Force Microscope Lab
-Duke Lab: Atomic Force Microscope
-Imaging of DNA NanoAssemblies
Lecture 15: DNA and Protein Motors
Section B Nanosystems, continued
Lecture 16:Carbon Nano-Tubes
structure & assembly
Lecture 17:Molecular Electronic Components Using Organic Compounds
Lecture 18: UNC Laboratory:
Molecular Force Feedback Systems & Molecular Probe Systems for Molecular Electronics
Section C: Introduction to DNA Computing
Lecture 18: Theoretical Models & Algorithms
in DNA Computing:
-Test Tube Models
-Splicing Models
-Associative Matching Models
Lecture 19: Experiments in DNA Computing
-details of Adelman's experiment
-Experiments based on
Primer Extension
-Whip-Lash DNA Computations
Section D: Surface Based Chemistry:
DNA Chips & Surface Based DNA Computation
Lecture 20:Intro to Surface Based Chemistry
Lecture 21:Intro to DNA Chips
& Applications
Lecture 22: DNA Computation Using
Surface Based Chemistry
Section E: Sequencing, Tagging, and Bioinformatics
Lecture 23:DNA Sequencing Techniques
-Traditional DNA Sequencing Techniques
-Sequence reconstruction by fragment
assembly
-Shotgun Sequencing Techniques
Lecture 24: DNA Tagging Techniques
Lecture 25: Databases for storage of
DNA Sequence Information
Lecture 26: Algorithms & Software for
DNA Sequence Alignment
Lecture 27: Statistical Processing of Sequence Information
Lecture 28:
Phylogenetic tree construction
-Phylogenetic tree construction
-Comparative analysis
-RNA evolution