This textbook is recommended for the course:
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.
| LEC # | TOPICS | READINGS |
|---|---|---|
| 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. 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. 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. 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. “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 |
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. 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. |
