Carnegie-Mellon University

Computational Biology Lecture Notes

Description

This course presents an overview of typical applications of computers to solve problems in biology. It is intended for students without computer programming experience (students with a desire to apply programming methods to these problems should take the more advanced course. Major topics covered are computational molecular biology (analysis of protein and nucleic acid sequences), biological modeling and simulation (including computer models of single and multiple neuron behavior, biochemical kinetics, and simulation of mutation) and biological imaging (comparison of techniques, impact of digital technology on light microscopy, digital image processing). 

Sequence Analysis Unit

Lecture

contents

Lecture01

Introduction

Lecutre02

Representing and Finding Sequence Features using Consensus Sequences

Lecture03

Representing and Finding Sequence Features using Frequency Matrices

Lecture A

More on Sequence Operations 

Lecture04

Protein Coding Regions

Lecture05

PCR Primer Design and Basics Principles of Entrez

Lecture B

C, C++, Java Review 

Lecture06

Sequence File Formats and Sequence Assembly

Lecture07

Similarity Functions and Sequence Comparison with Dot Matrices

Lecture08

Sequence Comparison with Dynamic Programming

Lecture09

Efficient Database Searching Methods

Lecture10

Protein Structure Prediction and Display

Lecture C

Family Pairwise Search and Cobbling 

Lecture11

Hydrophilicity & Multiple Sequence Alignment

Lecture D

Constructing Phylogenetic Trees

 

Biological Modeling Unit

Lecture
contents
Lecture12

Spreadsheet Basics I

Lecture E

Basics Principles of Computer Graphics 

Lecture13

Spreadsheet Basics II

Lecture F

Population Genetics 

Lecture14

Recursion Relations

Lecture15

Biochemical Kinetics I

Lecture16

Biochemical Kinetics II

Lecture17

Biochemical Kinetics III

Lecture18

Biochemical Kinetics IV

Lecture19

Compartmental Analysis

Lecture20

Neuronal Modeling

Lecture G

Representing Distributions using Fourier Transforms

 Biological Imaging Unit

Lecture
Contents
Lecture21

Biological Imaging I

Lecture22

Biological Imaging II

Lecture23

Biological Imaging III

Lecture24

Biological Imaging IV