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 Alana Mendelsohn
4. Sequence Alignment
1. Pairwise Sequence Alignment and Substitution Matrices Ethan Karp Pairwise Sequence Alignment
2. Fast Sequence Similarity Search Algorithms Sam Bakkila Substitution Matrices and Fast Sequence Similarity Search Algorithms
3. Multiple Sequence Alignment And Protein Motifs Jack Allen
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 Gene Expression Index Pan-Pan Jiang
3. Differential Gene Expression and Hypothesis Testing Maude Baldwin + Brandon Bartch
4. Microarray Clustering Methods and Gene Ontology
5. Microarray Dimension Reduction Techniques Amy Chen + Serene Chen
6. Microarray Classification Methods Rohan Kekre
6. Transcriptional Regulation
1. Transcription Regulation and Transcription Factor Motif Finding
2. System biology of transcription regulation
3. Expectation Maximization and Gibbs Sampling Nealia kuan
4. Phylogenetic Trees and Comparative Genomics Daniel Boada Comparative Genomics and Phylogenetic trees
5. ChIP-on-chip and Genome Tiling Microarrays Xiaohua Shen + Bryan Chang
6. Epigenetic regulation Jacob Carlson + Josh Paulk
7. Transcription Regluatory Network Nigel Delaney
7. Post Transcriptional Regulation
1. RNA Folding Aneesh Vaman Kulkarni
2. siRNA and miRNA Meng Xiao He + Helen Yang
8. Proteomics
1. Protein Structure Prediction Samir Rao
2. Molecular Dynamics
3. Mass Spectrophotometry and Protein Interaction Networks Alexei Finski
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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