Online Computational Biology Textbook

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1. Introduction and Basic Molecular Biology(Camille Bonneaud)
2. Basic Tools
1. Basic HTML (Y Liu)
2. Basic Python (Simi Chen HWB3)
3. Basic R (K Williams)
4. Basic Bioconductor (K Williams)
5. Statistical Inference
3. Literature Retrieval and Mining(J Zhang)
4. Sequence Alignment
1. Pairwise Sequence Alignment (Iqbal)
2. Substitution Matrices and Fast Sequence Similarity Search Algorithms (Bartz)
3. Multiple Sequence Alignment (Gutman)
4. Hidden Markov Model (D Lin & A Cheng)
5. Genome Sequencing and Assembly (Iqbal HW3B)
6. Phylogenetic trees (J Yang HW3B)
5. Gene Expression
1. Gene Expression Microarrays and Experiments (N Lin)
2. Microarray Normalization and Gene Expression Index (N Lin HW3B)
3. Differential Gene Expression and Hypothesis Testing (L Mulvey HW3B)
4. Microarray Clustering Methods and Gene Ontology (Mulvey & Gingold)
5. Microarray Dimension Reduction Techniques (J Lee HW3B)
6. Microarray Classification Methods (Geiler HW3B)
6. Transcriptional Regulation
1. Transcription Regulation and Transcription Factor Motif Finding (T Schmidt)
2. System biology of transcription regulation (D Lin & A Cheng)
3. Expectation Maximization and Gibbs Sampling (Ying Lei)
4. Comparative Genomics (D He)
5. Transcription Regluatory Network (R Ng HW3B)
6. ChIP-on-chip and Genome Tiling Microarrays (Geiler & Rogers)
7. Post Transcriptional Regulation
1. RNA Folding (Rogers HW3B)
2. siRNA and miRNA (Elisa Zhang & Cenik)
8. Proteomics
1. Protein Structure Prediction (J Yang & I Sun)
2. Mass Spectrophotometry and Protein Interaction Networks (P Chen)
9. Single Nucleotide Polymorphism
1. SNPs and Association Studies (R Ng)
2. Haplotype Inference and SNP Chip (Lee & L Li)

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Transcription Regulation and Transcription Factor Motif Finding