INTRODUCTION TO BIOINFORMATICS

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INTRODUCTION TO BIOINFORMATICS

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=课程主页:http://ocw.metu.edu.tr/course/view.php?id=37,

Instructor: Tolga CAN

Added: 18 November 2009

Topic outline

General

INTRODUCTION TO BIOINFORMATICS
- Course OverviewPage
- National Center for Biotechnology Information, USA.URL
- Protein Data BankURL
Topic 1

Introduction to Bioinformatics
- Lecture SlidesFile
- Week 1 - Lecture 1 [Video]File
Topic 2

Introduction to biology, biological databases, and high-throughput data sources. Overview of bioinformatics problems.

Pairwise sequence alignment algorithms: Dynamic programming
- Lecture SlidesFile
- Assignment 1File
- Reading: Bioinformatics - An Introduction for Computer ScientistsFile
- Reading: Cells and GenomesFile
- Reading: How Cells Read the Genome: From DNA to ProteinFile
- Reading: The Nucleic Acid WorldFile
- Reading: Producing And Analzying Sequence AlignmentsFile
- Week 2 - Lecture 1 [Video]File
- Week 2 - Lecture 2 [Video]File
- Week 3 - Lecture 1 [Video]File
- Week 3 - Lecture 2 [Video]File
- Week 4 - Lecture 1 [Video]File
- Week 4 - Lecture 2 [Video]File
Topic 3

Statistical significance of alignments - Part I

Statistical significance of alignments - Part II
- Lecture SlidesFile
- Reading: Pairwise Sequence AlignmentFile
- Week 5 - Lecture 1 [Video]File
- Week 5 - Lecture 2 [Video]File
- Week 5 - Lecture 3 [Video]File
Topic 4

Suffix Trees, Suffix Arrays
- Lecture SlidesFile
- Week 6 - Lecture 1 [Video]File
- Week 6 - Lecture 2 [Video]File
Topic 5

Patterns, Profiles, and Multiple Alignments
- Lecture SlidesFile
- Assignment 2File
- Week 6 - Lecture 3 [Video]File
Topic 6

Hidden Markov Models

Week 5 Lecture Slides Continued
- Week 7 - Lecture 1 [Video]File
- Week 7 - Lecture 2 [Video]File
- Week 7 - Lecture 3 [Video]File
Topic 7

Multiple Sequence Alignment Algorithms

Week 5 Lecture Slides Continued
- Week 8 - Lecture 1 [Video]File
- Week 8 - Lecture 2 [Video]File
- Week 8 - Lecture 3 [Video]File
Topic 8

Midterm Review and Midterm Exam
- Midterm ExamFile
- Midterm KeyFile
- Phylogenetic trees
- Lecture SlidesFile
Topic 9

Introduction to protein structures

Structure Prediction
- Lecture SlidesFile
- Assignment 3 for Computer Engineering MajorsFile
- Assignment 3 for Biology or Genetics MajorsFile
- Week 9 - Lecture 1 [Video]File
- Week 9 - Lecture 2 [Video]File
- Week 9 - Lecture 3 [Video]File
- Week 9 - Lecture 4 [Video]File
Topic 10

Protein Structure Prediction (continued)
- Week 10 - Lecture 1 [Video]File
- Week 10 - Lecture 2 [Video]File
- Week 10 - Lecture 3 [Video]File
Topic 11

Protein Structure Prediction (continued)
- Week 11 - Lecture 1 [Video]File
- Week 11 - Lecture 2 [Video]File
- Week 11 - Lecture 3 [Video]File
Topic 12

Structural Alignment of Proteins
(lecture notes continued)
- Week 12 - Lecture 1 [Video]File
- Week 12 - Lecture 2 [Video]File
- Week 12 - Lecture 3 [Video]File
Topic 13

Microarray data normalization, analysis

Clustering techniques
- Lecture SlidesFile
- K-means DemoFile
- Self Organizing Maps DemoFile
- Reading: Microarrays Intro Paper - 1File
- Reading: Microarrays Intro Paper - 2File
- Reading: Microarrays Intro Paper - 3File
- Week 13 - Lecture 1 [Video]File
- Week 13 - Lecture 2 [Video]File
Topic 14

Introduction to Systems Biology

Gene regulatory networks
- Lecture SlidesFile
- Assignment 4File
- Dataset for Assignment 4File
- Week 14 - Lecture 1 [Video]File
Topic 15

Construction and Analysis of protein networks:
Monte Carlo Sampling, Random Walks on Graphs
- Lecture SlidesFile
- Likelihood Computation ExampleFile
- Week 15 - Lecture 1 [Video]File
- Week 15 - Lecture 2 [Video]File
- Final review