There will not be a required book for this class, most topics will be covered by research papers. This is mainly due to the fact that the field changes rapidly and many books are dated by the time they hit the shelves.
Having said that, for a lot of the topics in this class a copy of Durbin, Eddy, Krogh & Mitchison's book Biological Sequence Analysis is good reading. It is especially good at covering HMM's and other probabilistic approaches. It is "suggested" but not "required".
Two optional "reference" books are Waterman's Introduction to Computational Biology and Gusfield's Algorithms on Strings Trees and Sequences.
Lec # | Topic | Date | Reading | Handouts & Slides |
Genomes, Assembly & Evolution | ||||
1. | Overview: what is the genome, and where does it come from? Genome Assembly | Jan 9th |
EBI's Intro to Biology: Sections 1-3 JGI's Intro to Genomics Weber & Myers: Human Whole-Genome Shotgun Sequencing Medvedev et al: Models for Genome Assembly |
Lecture slides |
2. | Basic Evolution & Variation Detection | Jan 16th |
Section 1 of Speed's notes on Evolution and Phylogeny Chapter 9 of the Haubold book (only available from on-campus). pyroBayes paper by Marth et al |
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Alignment & Phylogeny | ||||
3. | Pairwise Alignment: Longest common subsequence, Substitution matrices, Global v Local | Jan 23 |
Speed: Lecture Notes on Sequence Alignment Myers & Miller: Alignments in Linear Space More Lecture Notes on Alignment |
Project Description |
4. | Modern Alignment programs: Gap penalties, Anchored Alignment | Jan 30th |
Reduction from LIS to LCS (Gusfield 12.4-12.5) Brudno & Dubchak: Comparisons of Long Genomic Sequences (Chapter 14 from Aluru's Handbook) Knuth-Morris-Pratt String Matching Algorithm |
HW1 out due February 13 Project Description out; Proposal due February 27 |
5. | Suffix Arrays, Burrows-Wheeler Transform, FM-index | Feb 6th |
Suffix Arrays Burrows Wheeler Transfor BWA Aligner | |
6. | Multiple Alignment & Phylogenetic Tree Reconstruction | Feb 13th |
Thompson et al: CLUSTALW Loytinoja & Golding: Progressive Alignment Lecture notes on phylogenetic trees |
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Genes, Epigenetics & Regulation | ||||
7. | CpGs & Hidden Markov Models | February 27th |
Rabiner's tutorial on HMMs Huson's notes on HMMs & CpGs |
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8. | Epigenetic Modification & ChiP-Seq | March 6th | ||
9. | Gene finding | March 13th |
Zhang's Review of Gene-Finding |
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10. | Measuring Gene Expression & Isoforms | March 20th | ||
11. | Motif finding | March 27th |
Blanchette et al.: Footprinter Lawrence et al.: Gibbs Sampling Bailey et al.: EM for Motif Finding (MEME) |