Introductory Biology-Fall 2004 Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel Your Name:

Alternative materials and fabrication techniques Applications in biology and chemistry Applications in medicine A real MTL example of rapid prototyping

Ab initio =from the beginning in strictest sense uses first principles, not information about other protein structures In practice, all methods rely on empirical observations

Chapter 1 Introduction to the cell Learning Objectives 1. About Cell Biology 2. Look briefly at the history of cell theory; 3. Consider the basic properties of cells; 4. Compare some characteristics of two different classes of cells: prokaryotes and eukaryotes; 5.comprehend a special life: viruses

Why the hype? Microarray platforms CDNA VS oligo technologies Sample applications Analysis of microarray data clustering of co-expressed genes some classic microarray papers

Algorithms for detecting structure similarity Dynamic Programming works on 1D strings- reduce problem to this cant accommodate topological changes example: Secondary Structure Alignment Program(SSAP) 3D Comparison/Clustering

1. Grow crystals-structure determination by X-ray crystallography relies on the repeating structure of a crystalline lattice 2. Collect a diffraction pattern-periodically spaced atoms in the crystal give specific\spots\where x-rays interfere constructively

Review -Homology Modeling Identify a protein with similar sequence for which a structure has been solved (the template) Align the target sequence with the template Use the alignment to build an approximate structure for the target

Outline Brief review of protein structure chou -Fasman- predictions Garnier, Osguthorpe and Robson Helical wheels and hydrophobic moments Neural networks Nearest neighbor methods Consensus prediction approaches

Review of markov models DNA Evolution CpG Island HMM The viterbi algorithm Real World HMMs Markov models for dna evolution Ch. 4 of Mount