Below is a list of the relevant book chapters and articles for each course week.
Page numbers are indicated for the third edition [and for the second edition in square brackets].
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Course Week 1 -?Intro, basic molecular biology & sequence comparison
Chapter 1 "Where in the Genome Does DNA Replication Begin?", page 60 (Detours: "Directionality of DNA strands")
Chapter 6 "Are There Fragile Regions in the Human Genome?", pages 330-333 [325-328] ("Epilogue: Synteny Block Construction: Genomic dot-plots", "Epilogue: Synteny Block Construction: Finding shared k-mers")
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Course Week 2 -?Introduction to high-throughput sequencing and its applications
Chapter 3 "How Do We Assemble Genomes", pages 171-173 ("Detours: A short history of DNA sequencing technologies", "Detours: Repeats in the human genome")
Chapter 9 "How Do We Locate Disease-Causing Mutations", page 520 ("Detours: The reference human genome")
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Course Week 3 -?Sequence comparison and alignment
Chapter 5 "How Do We Compare Biological Sequences", pages 224-231 ("Cracking the Non-Ribosomal Code" and "Introduction to sequence alignment")
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Course Week 4 -?Sequence alignment by dynamic programming
Chapter 5 "How Do We Compare Biological Sequences", pages 231-271 ("The Manhattan Tourist Problem", "Sequencing is the Manhattan Tourist Problem in disguise", "An Introduction to Dynamic Programming: The Change Problem", "The Manhattan Tourist Problem Revisited", "From Manhattan to an Arbitrary DAG", "Backtracking in the Alignment Graph", "Scoring Alignment", "From Global to Local Alignment", "The Changing Faces of Sequence Alignment", "Penalizing Insertions and Deletions in Sequence Alignment")
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Course Week 5 -?Optimal alignments in linear space + Scoring matrices
Chapter 5 "How Do We Compare Biological Sequences", pages 271-279 and 288-290 ("Space Efficient Sequence Alignment", "Detours: PAM Scoring matrices")
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Course Week 6 -?Heuristic database searches with protein sequences
Chapter 9 "How Do We Locate Disease-Causing Mutations", pages 510-511 ("BLAST: Comparing a sequence against a database")
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Course Week 7 -?Heuristic database searches with nucleotide sequences
BLAT article by Kent
Course Week 8 -?Mapping using suffix tries, trees, and arrays, Burrows-Wheeler-transform and FM-index
Chapter 9 "How Do We Locate Disease-Causing Mutations", pages 468-528 ("What causes Ohdo Syndrome", "Introductio to multiple Pattern Matching", "Herding Patterns into a Trie", "Preprocessing the Genome Instead", "Suffix Trees", "Suffix arrays", "The Burrows-Wheeler Transform", "Inverting the Burrow-Wheeler Transform", "Pattern Matching with the Burrows-Wheeler Transform", "Speeding Up Burrows-Wheeler Pattern Matching", "Where are the Matched Patterns?", "Burrows and Wheeler Set Up Checkpoints", "Epilogue: Mismatch-Tolerant Read Mapping")
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Course Week 9 -?Genome sequence assembly
Chapter 3 "How Do We Assemble Genomes", pages 116-170 ("Exploding Newspapers", "The String Reconstruction Problem", "String Reconstruction as a Walk in the Overlap Graph", "Another Graph for String Reconstruction", "Walking in the de Bruijn Graph", "The Seven Bridges of K?nigsberg", "Euler's Theorem", "From Euler's Theorem to an Algorithm for Finding Eulerian Cycles", "Assembling Genomes from Read-Pairs", "Epilogue: Genome Assembly Faces Real Sequencing Data", "Charging Stations")
Articles by Simpson & Pop and by Mathé et al.
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Course Week 10 -?Clustering
Chapter 8 "How Did Yeast Become A Wine Maker?", pages 416-462 ("An Evolutionary History of Wine Making", "Identifying Genes Responsible for the Diauxic Shift", "Introduction to Clustering", "The Good Clustering Principle", "Clustering as an Optimization Problem", "Farthest First Traversal", "k-Means Clustering", "The Lloyd Algorithm", "Clustering Genes Implicated in the Diauxic Shift", "Limitations of k-Means Clustering", "From Coin Flipping to k-Means Clustering", "Making Soft Decisions in Coin Flipping", "Soft k-Means Clustering", "Hierarchical Clustering", "Epilogue: Clustering Tumor Samples", "Detours: Whole genome duplication or a series of duplications", "Detours: Measuring gene expression", "Detours: Microarrays")
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Course Week 11 -?Multiple sequence alignment
Chapter 5 "How Do We Compare Biological Sequences", pages 280-285 and 293-294 ("Epilogue: Multiple Sequence Clustering", "Detours: Scoring multiple alignments")
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Course Week 12 -?Phylogenetic reconstruction
Chapter 7 "Which Animal Gave Us SARS?", pages 352-400 ("The Fastest Outbreak", "Transforming Distance Matrices into Evolutionary Trees", "Toward An Algorithm for Distance-Based Phylogeny Construction", "Additive Phylogeny", "Using Least Squares to Construct Approximate Distance-Based Phylogenies", "Ultrametric Evolutionary Trees", "The Neighbor-Joining Algorithm", "Character-Based Tree Reconstruction", "The Small Parsimony Problem", "The Large Parsimony Problem", "Epilogue: Evolutionary Trees Fight Crime")
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Course Week 13 -?Motif discovery
Chapter 2 "Which DNA Patterns Play the Role of Molecular Clocks?", pages 66-105, 113-115 ("Do we have a 'clock' Gene?", "Motif Finding Is More Difficult Than You Think", "Scoring Motifs", "From Motif Finding to Finding a Median String", "Greedy Motif Search", "Motif Finding Meets Oliver Cromwell", "Randomized Motif Search", "How Can a Randomized Algorithm Perform So Well?", "Gibbs Sampling", "Gibbs Sampling in Action", "Detours: Complications in motif finding", "Detours: Relative entropy")
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Course Week 14 -?Searching with sequence profiles and hidden Markov models
Chapter 10 "Why Have Biologists Still Not Developed an HIV Vaccine?",?pages 530-569 ("Classifying the HIV Phenotype", "Gambling with Yakuza", "Two Coins up the Dealer's Sleeve", "Finding CG-Islands", "Hidden Markov Models", "The Decoding Problem", "Finding the Most Likely Outcome of an HMM", "Profile HMMs for Sequence Alignment", "Classifying proteins with profile HMMs")
HMM article by Eddy
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Course Week 15 -?Gene prediction
Chapter 11 "Was T. rex Just a Big Chicken?", pages 626-627 ("Detours: Gene Prediction")
Gene prediction article by Mathé et al.
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