The assigned readings are from primary literature. You are responsible for understanding the essential ideas, results and methods used in papers 1 and 2 for each session, which may require reading the optional supplementary information or background reference material.
Tips on reading papers and leading a discussion about a paper (PDF)
Background reading on probability and statistics (
PDF - 5.2MB)
(Courtesy of Woolf, P., C. Burge, A. Keating, and M. Yaffe. Used with permission.)
Readings
| WEEK # | TOPICS | READINGS |
|---|---|---|
| 1 |
Course organization/introduction Genomics and protein function |
Paper 1Marcotte, E. M., M. Pellegrini, H. Ng, D. W. Rice, T. O. Yeates, and D. Eisenberg. "Detecting Protein Function and Protein-Protein Interactions from Genome Sequences." Science 285 (1999): 751-53. Paper 2Pellegrini, M., E. M. Marcotte, M. J. Thompson, D. Eisenberg, and T. O. Yeates. "Assigning Protein Functions by Comparative Genome Analysis: Protein Phylogenetic Profiles." Proc Natl Acad Sci 96 (1999): 4285-88. |
| 2 | Function of nucleic acid binding factors |
Paper 1Lim, L. P., N. C. Lau, P. Garett-Engele, A. Grimson, J. M. Schelter, J. Castle, D. P. Bartel, P. S. Linsley, and J. M. Johnson. "Microarray Analysis Shows that Some microRNAs Downregulate Large Numbers of Target mRNAs." Nature 433 (2005): 769-73. Paper 2Johnson, D. S., et al. "Genome-Wide Mapping of in Vivo Protein-DNA Interactions." Science 316 (2007): 1497-1502. OptionalDu, T., and P. D. Zamore. "microPrimer: The Biogenesis and Function of microRNA." Development 132 (2005): 4645-52. Metzker, M. "Sequencing Technologies—the Next Generation." Nature Reviews Genetics 11 (2010): 31-46. |
| 3 | Gene expression & medicine |
Paper 1Hughes, T. R., et al. "Functional Discovery via a Compendium of Expression Profiles." Cell 102 (2000): 109-126. Paper 2Alizadeh, A., et al. "Distinct Types of Diffuse Large B-cell Lymphoma Identified by Gene Expression Profiling." Nature 403 (2000): 503-11. Optional
(The first chapter gives a basic overview of immunology; chapter 7, p. 91 talks about B lymphocytes; and chapter 17, pp. 249-255, talks about lymphomas.) |
| 4 | Evolutionary dynamics |
Paper 1Hegreness, M., N. Shoresh, D. Hartl, and R. Kishony. "An Equivalence Principle for the Incorporation of Favorable Mutations in Asexual Populations." Science 311 (2006): 1615-17. Paper 2Weinrich, D. M., N. F. Delaney, M. A. DePristo, and D. L. Hartl. "Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins." Science 312 (2006): 111-114. OptionalPoelwijk, F. J., D. J. Kiviet, D. M. Weinreich, and S. J. Tans. "Empirical Fitness Landscapes Reveal Accessible Evolutionary Paths." Nature 445 (2007): 383-6. |
| 5 | Proofreading in biology |
Paper 1Hopfield, J. J. "Kinetic Proofreading: A New Mechanism for Reducing Errors in Biosynthetic Processes Requiring High Specificity." PNAS 71 (1974): 4135-4139. Paper 2Drummond, A., J. D. Bloom, C. Adami, C. O. Wilke, and F. H. Arnold. "Why Highly Expressed Proteins Evolve Slowly." PNAS 102 (2005): 14338-43. OptionalZaher, H. S., and R. Green. "Fidelity at the Molecular Level: Lessons from Protein Synthesis." Cell 136 (2009): 746-62. |
| 6 | Sequencing & translation |
Paper 1Ingolia, N. T., S. Ghaemmaghami, J. R. S. Newman, and J. S. Weissman. "Genome-wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling." Science 324 (2009): 218-223. OptionalHinnebusch, A. G. "Translational Regulation of Yeast GCN4." The Journal of Biological Chemistry 272 (1997): 21661-4. Metzker, M. L. "Sequencing Technologies - the Next Generation." Nature Reviews Genetics 11 (2010): 31-46. |
| 7 | Network motifs in biology |
Paper 1Shen-Orr, S. S., R. Milo, S. Mangan, and U. Alon. "Network Motifs in the Transcriptional Regulation Network of Escherichia Coli." Nature Genetics 31 (2002): 64-68. Paper 2Ma, W., A. Trusina, H. El-Samad, W. A. Lim, and C. Tang. "Defining Network Topologies that Can Achieve Biochemical Adaptation." Cell 138 (2009): 760-73. OptionalAlon, U. "Network Motifs: Theory and Experimental Approaches." Nature Publishing Group 8 (2007): 450-461. |
| 8 | Pathway modeling |
Paper 1McAdams, H. H., and L. Shapiro. "Circuit Simulation of Genetic Networks." Science 269 (1995): 650-6. Paper 2Gutenkunst, R. N., J. J. Waterfall, F. P. Casey, K. S. Brown, C. R. Myers, and J. P. Sethna. "Universally Sloppy Parameter Sensitivities in Systems Biology Models." PLoS Computational Biology 3, e189 (2007): 1871-8. |
| 9 | Variability between cells |
Paper 1Suel, G. M., R. P. Kulkarni, J. Dworkin, J. Garcia-Ojalvo, and M. B. Elowitz. "Tunability and Noise Dependence in Differentiation." Science 315 (2007): 1716-19. Paper 2Spencer, S. L., S. Gaudet, J. G. Albeck, J. M. Burke, and P. K. Sorger. "Non-Genetic Origins of Cell-to-Cell Variability in TRAIL-Induced Apoptosis." Nature 459 (2009): 428-33. |
| 10 | Synthetic biology |
Paper 1Elowitz, M. B., and S. Leibler. "A Synthetic Oscillatory Network of Transcriptional Regulators." Nature 403 (2000): 335-8. Paper 2Tabor, J., H. M. Salis, Z. Booth Simpson, A. A. Chevalier, A. Levskaya, E. M. Marcotte, C. A. Voigt, and A. D. Ellington. "A Synthetic Edge Detection Program." Cell 137 (2009): 1272-81. OptionalPurnick, E. M., and R. Weiss. "The Second Wave of Synthetic Biology: From Modules to Systems." Nature Reviews Molecular Cell Biology 10 (2009): 410-22. |
| 11 | Metagenomics |
Paper 1Tringe, S. G., C. von Mering, A. Kobayashi, A. A. Salamov, K. Chen, H. W. Chang, M. Podar, J. M. Short, E. J. Mathur, J. C. Detter, P. Bork, P. Hugenholtz, and E. M. Rubin. "Comparative Metagenomics of Microbial Communities." Science 308 (2005): 554-7. Paper 2Andersson, A. F., and J. F. Banfield. "Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities." Science 320 (2008): 1047-50. OptionalBarrangou, R., C. Fremaux, H. Deveau, M. Richards, P. Boyaval, S. Moineau, D. A. Romero, and P. Horvath. "CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes." Science 315 (2007): 1709-12. |
| 12 | Signal transduction |
Paper 1Bhattacharrya, R. P., A. Remenyi, M. C. Good, C. J. Bashor, A. M. Falick, and W. A. Lim. "The Ste5 Scaffold Allosterically Modulates Signaling Output of the Yeast Mating Pathway." Science 311 (2005): 822-6. Paper 2Malleshaiah, M. K., V. Shahrezaei, P. S. Swain, and S. W. Michnick. "The Scaffold Protein Ste5 Directly Controls a Switch-Like Mating Decision in Yeast." Nature 465 (2010): 101-105. |
