Online Computational Biology Textbook

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1. Introduction and Basic Molecular Biology
2. Basic Tools
1. Basic HTML
2. Basic Python
3. Basic R
4. Basic Bioconductor
3. Literature Retrieval and Mining
4. Sequence Alignment
1. Pairwise Sequence Alignment and Substitution Matrices Ethan Karp Pairwise Sequence Alignment
2. Fast Sequence Similarity Search Algorithms Alana Mendelsohn Substitution Matrices and Fast Sequence Similarity Search Algorithms
3. Multiple Sequence Alignment And Protein Motifs Jack Allen Multiple Sequence Alignment
4. Hidden Markov Model
5. Genome Sequencing and Annotation David Robinson Genome Sequencing and Assembly
5. Gene Expression
1. Gene Expression Microarrays and Experiments
2. Microarray Normalization and Expression Index Pan-Pan Jiang Microarray Normalization and Gene Expression Index
3. Differential Gene Expression and Hypothesis Testing
4. Microarray Clustering Methods and Gene Ontology
5. Microarray Dimension Reduction Meng Xiao He + Helen Yang Microarray Dimension Reduction Techniques
6. Microarray Classification Amy Chen Microarray Classification Methods
6. Transcriptional Regulation
1. Transcription Regulation and Transcription Factor Motif Finding
2. System biology of transcription regulation
3. EM and Gibbs Sampling Nealia Kuan Expectation Maximization and Gibbs Sampling
4. Phylogenetic Trees and Comparative Genomics Daniel Boada Comparative Genomics and Phylogenetic trees
5. ChIP-on-chip on Tiling Microarrays Xiaohua Shen + Bryan Chang ChIP-on-chip and Genome Tiling Microarrays
6. Epigenetic Regulation Jacob Carlson + Josh Paulk + Linjiao Luo Epigenetic regulation
7. Transcription Regluatory Network
7. Post Transcriptional Regulation
1. ncRNA Aneesh Vaman Kulkarni RNA Folding siRNA and miRNA
2. siRNA and miRNA
8. Proteomics
1. Protein Structure Prediction
2. Molecular Dynamics
3. Mass Spectrophotometry Brandon Bartch Mass Spectrophotometry and Protein Interaction Networks
9. Genome Variations
1. SNPs, CNVs, and SNP chip James Cronican + David Tse SNPs and Association Studies
2. Association Studies and Haplotype Inference Stephen Yee + Kristi Fenstermacher Haplotype Inference and SNP Chip

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