This textbook is recommended for the course:
Buy at Amazon Zvelebil, Marketa J., and Jeremy O. Baum. Understanding Bioinformatics. Garland Science, 2007. ISBN: 9780815340249. [Preview with Google books]

The instructors have also selected various texts as particularly useful in specific areas, if you are looking for more information. See the textbook section on the syllabus.

1 Course Introduction; Overview No readings for this lecture.
2 Local Alignment; Statistics

National Center for Biotechnology Information. "The Statistics of Sequence Similarity Scores." BLAST Tutorial.

Metzker, Michael L. "Sequencing Technologies—The Next Generation." Nature Reviews Genetics 11, no. 1 (2010): 31–46.

3 Global Alignment of Protein Statistics No readings for this lecture.
4 Comparative Genomics

Sabeti, P. C., S. F. Schaffner, et al. "Positive Natural Selection in the Human Lineage." Science 312, no. 5780 (2006): 1614–20.
Read the first three pages.

Bejerano, Gill, Michael Pheasant, et al. "Ultraconserved Elements in the Human Genome." Science 304, no. 5675 (2004): 1321–5.

Pennacchio, Len A., Nadav Ahituv, et al. "In Vivo Enhancer Analysis of Human Conserved Non–coding Sequences." Nature 444, no. 7118 (2006): 499–502.

Visel, Axel, Shyam Prabhakar, et al. "Ultraconservation Identifies a Small Subset of Extremely Constrained Developmental Enhancers." Nature Genetics 40, no. 2 (2008): 158–60.

Bejerano, Gill, Craig B. Lowe, et al. "A Distal Enhancer and an Ultraconserved Exon are Derived from a Novel Retroposon." Nature 441, no. 7089 (2006): 87–90.

Lareau, Liana F., Maki Inada, et al. "Unproductive Splicing of SR Genes Associated with Highly Conserved and Ultraconserved DNA Elements." Nature 446, no. 7138 (2007): 926–9.

Lewis, Benjamin P., I–hung Shih, et al. "Prediction of Mammalian MicroRNA Targets." Cell 115, no. 7 (2003): 787–98.

Lewis, Benjamin P., Christopher B. Burge, et al. "Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets." Cell 120, no. 1 (2005): 15–20.

Kheradpour, Pouya, Alexander Stark, et al. "Reliable Prediction of Regulator Targets Using 12 Drosophila Genomes." Genome Research 17, no. 12 (2007): 1919–31.

Friedman, Robin C., Kyle Kai–How Farh, et al. "Most Mammalian mRNAs are Conserved Targets of MicroRNAs." Genome Research 19, no. 1 (2009): 92–105.

Graveley, Brenton R. "Mutually Exclusive Splicing of the Insect Dscam Pre–mRNA Directed by Competing Intronic RNA Secondary Structures." Cell 123, no. 1 (2005): 65–73.

Jansen, Ruud, Jan Embden, et al. "Identification of Genes that are Associated with DNA Repeats in Prokaryotes." Molecular Microbiology 43, no. 6 (2002): 1565–75.

Bolotin, Alexander, Benoit Quinquis, et al. "Clustered Regularly Interspaced Short Palindrome Repeats (CRISPRs) have Spacers of Extrachromosomal Origin." Microbiology 151, no. 8 (2005): 2551–61.

5 Read Alignment

Langmead, Ben, Cole Trapnell, et al. "Ultrafast and Memory–efficient Alignment of Short DNA Sequences to the Human Genome." Genome Biology 10, no. 3 (2009): R25.

Li, Heng, and Richard Durbin. "Fast and Accurate Short Read Alignment with Burrows–wheeler Transform." Bioinformatics 25, no. 14 (2009): 1754–60.

Trapnell, Cole, and Steven L. Salzberg. "How to Map Billions of Short Reads onto Genomes." Nature Biotechnology 27, no. 5 (2009): 455.

Burrows–Wheeler Aligner

Bowtie: An ultrafast memory–efficient short read aligner

6 Genome Assembly

Simpson, Jared T., and Richard Durbin. "Efficient De Novo Assembly of Large Genomes Using Compressed Data Structures." Genome Research 22, no. 3 (2012): 549–56.

Zerbino, Daniel R., and Ewan Birney. "Velvet: Algorithms for De Novo Short Read Assembly Using De Bruijn Graphs." Genome Research 18, no. 5 (2008): 821–9.

7 ChIP-seq / IDR

Guo, Yuchun, Georgios Papachristoudis, et al. "Discovering Homotypic Binding Events at High Spatial Resolution." Bioinformatics 26, no. 24 (2010): 3028–34.

Li, Qunhua, James B. Brown, et al. "Measuring Reproducibility of High–throughput Experiments." The Annals of Applied Statistics 5, no. 3 (2011): 1752–79.

8 RNA–seq Analysis

Trapnell, Cole, Brian A. Williams, et al. "Transcript Assembly and Quantification by RNA–seq Reveals Unannotated Transcripts and Isoform Switching during Cell Differentiation." Nature Biotechnology 28, no. 5 (2010): 511–5.

Anders, Simon, and Wolfgang Huber. "Differential Expression Analysis for Sequence Count Data." Genome Biology 11, no. 10 (2010): R106.
Licensed under CC–BY.

Wang, Zhong, Mark Gerstein, et al. "RNA–Seq: a Revolutionary Tool for Transcriptomics." Nature Reviews Genetics 10, no. 1 (2009): 57–63.

Shalek, Alex K., Rahul Satija, et al. "Single–cell Transcriptomics Reveals Bimodality in Expression and Splicing in Immune Cells." Nature 498 (2013): 236–40.

Smith, Lindsay I. This resource may not render correctly in a screen reader."A Tutorial on Principal Components Analysis." (PDF) February 26, 2002.

9 Modeling and Discovery of Sequence Motifs (Gibbs Sampler, Alternatives)

D'haeseleer, Patrik. "What are DNA Sequence Motifs?" Nature Biotechnology 24, no. 4 (2006): 423–25.

———. "How does DNA Sequence Motif Discovery Work?" Nature Biotechnology 24, no. 8 (2006): 959–61.

Eddy, Sean R. "What is Bayesian Statistics?" Nature Biotechnology 22, no. 9 (2004): 1177–8.

Bailey, Timothy L., and Charles Elkan. "Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization." Machine Learning 21, no. 1–2 (1995): 51–80.

Lawrence, Charles E., Stephen F. Altschul, et al. "Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment." Science 262, no. 5131 (1993): 208–14.

10 Markov and Hidden Markov Models

Eddy, Sean R. "What is a Hidden Markov Model?" Nature Biotechnology 22, no. 10 (2004): 1315–6.

Rabiner, Lawrence. "A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition." Proceedings of the IEEE 77, no. 2 (1989): 257–86.

11 RNA Secondary Structure Prediction Eddy, Sean R. "How do RNA Folding Algorithms Work?" Nature Biotechnology 22, no. 11 (2004): 1457–8.
12 Introduction to Protein Structure

Buy at Amazon Scheeff, Eric D., and J. Lynn Fink. "Fundamentals of Protein Structure." In Structural Bioinformatics. Edited by Philip E. Bourne and Helge Weissig. Wiley–Liss, 2003, pp. 15–39. [Preview with Google Books]

13 Predicting Protein Structure Moretti, Rocco, Sarel J. Fleishman, et al. "Community‐wide Evaluation of Methods for Predicting the Effect of Mutations on Protein–protein Interactions." Proteins: Structure, Function, and Bioinformatics 81, no. 11 (2013): 1980–7.
14 Predicting Interactions

Tuncbag, Nurcan, Attila Gursoy, et al. "Predicting Protein–protein Interactions on a Proteome Scale by Matching Evolutionary and Structural Similarities at Interfaces Using PRISM." Nature Protocols 6, no. 9 (2011): 1341–54.

Zhang, Qiangfeng Cliff, Donald Petrey, et al. "Structure–based Prediction of Protein–protein Interactions on a Genome–wide Scale." Nature 490, no. 7421 (2012): 556–60.

Jansen, Ronald, Haiyuan Yu, et al. "A Bayesian Networks Approach for Predicting Protein–protein Interactions from Genomic Data." Science 302, no. 5644 (2003): 449–53.

15 Gene Regulatory Networks Marbach, Daniel, James C. Costello, et al. "Wisdom of Crowds for Robust Gene Network Inference." Nature Methods 9, no. 8 (2012): 796–804.
16 Protein Interaction Networks No readings for this lecture.
17 Logic Modeling of Cell Signaling Networks. Guest Lecture: Doug Lauffenburger

Morris, Melody K., Julio Saez–Rodriguez, et al. "Logic–based Models for the Analysis of Cell Signaling Networks." Biochemistry 49, no. 15 (2010): 3216–24.

Saez‐Rodriguez, Julio, Leonidas G. Alexopoulos, et al . "Discrete Logic Modelling as a Means to Link Protein Signalling Networks with Functional Analysis of Mammalian Signal Transduction." Molecular Systems Biology 5, no. 1 (2009): 331.

18 Analysis of Chromatin Structure

Hoffman, Michael M., Orion J. Buske, et al. "Unsupervised Pattern Discovery in Human Chromatin Structure through Genomic Segmentation." Nature Methods 9, no. 5 (2012): 473–6.

Zhou, Vicky W., Alon Goren, et al. "Charting Histone Modifications and the Functional Organization of Mammalian Genomes." Nature Reviews Genetics 12, no. 1 (2010): 7–18.

Sherwood, Richard I., Tatsunori Hashimoto, et al. "Discovery of Directional and Nondirectional Pioneer Transcription Factors by Modeling DNase Profile Magnitude and Shape." Nature Biotechnology 32, no. 2 (2014): 171–8.

Dostie, Josée, and Job Dekker. "Mapping Networks of Physical Interactions between Genomic Elements Using 5C Technology." Nature Protocols 2, no. 4 (2007): 988–1002.

19 Discovering Quantitative Trait Loci (QTLs)

Bloom, Joshua S., Ian M. Ehrenreich, et al. "Finding the Sources of Missing Heritability in a Yeast Cross." Nature 494, no. 7436 (2013): 234–7.

Buy at Amazon Broman, Karl W., and Saunak Sen. "Single–QTL Analysis." Chapter 4 in A Guide to QTL Mapping with R/qtl. Springer, 2009. ISBN: 9780387921242. [Preview with Google Books]

20 Genome Wide Associate Studies

Li, Heng. "A Statistical Framework for SNP Calling, Mutation Discovery, Association Mapping and Population Genetical Parameter Estimation from Sequencing Data." Bioinformatics 27, no. 21 (2011): 2987–93.

Roberts, Nicholas J., Joshua T. Vogelstein, et al. "The Predictive Capacity of Personal Genome Sequencing." Science Translational Medicine 4, no. 133 (2012): 133ra58.

1000 Genomes. "Variant Call Format."

Goldstein, David B., Andrew Allen, et al. "Sequencing Studies in Human Genetics: Design and Interpretation." Nature Reviews Genetics 14, no. 7 (2013): 460–70.

21 Synthetic Biology: From Parts to Modules to Therapeutic Systems. Guest Lecture: Ron Weiss No readings for this lecture.
22 Causality, Natural Computing, and Engineering Genomes. Guest Lecture: George Church No readings for this lecture.