| SES # | TOPICS | ASSIGNMENTS |
|---|---|---|
| 1 | Course organization/introduction Genomics and protein function | |
| 2 | Genomics and RNA function | Assignment 1 Write 1 page on the topic "What is computational and systems biology?" This assignment will not be graded. |
| 3 | Signal transduction | Assignment 2 The two methods detailed in this week's papers both describe novel technologies to assay signal transduction pathways. Describe specific advantages and limitations of each assay. Although both assays use fluorescent reporters, each assay uses a different detection scheme. Describe the consequences (pros and cons) of the measurement techniques. |
| 4 | Genetics of gene regulation | Assignment 3 The two papers describe different approaches — a genetic approach and a combined experimental/comparative genomics approach — for understanding transcriptional regulation in an organism. Describe specific advantages and limitations of each approach generally, and discuss the applicability of each approach to different systems (e.g., yeast, Ciona, mouse, human). |
| 5 | Statistical approaches | Assignment 4 Paper 1 introduces a concept called the q-value, and argues that this is often a more appropriate statistic than the p-value for genome-wide studies. Find another study (in the area of computational and systems biology) — similar to the examples presented in the paper — where p-values were used to assess significance of, e.g., a set of predictions. Briefly summarize this study (max 1 paragraph), and include the reference. Describe how the results and conclusions of the paper might have been different (or not) if a criterion based on q-values rather than p-values had been used. Consider what criteria are important for determining an appropriate q-value cutoff, and what q-value cutoff would have been appropriate in the study in question. |
| 6 | Gene expression and medicine | Assignment 5 Design an original experiment involving microarrays. Be sure to describe what biological question you are asking, what system (e.g., organism) you will use, why this system is appropriate to the question, and the nature of the experiment. Briefly summarize how the results will be analyzed and interpreted, and the nature of any proposed follow-up experiments. |
| 7 | Kinetics in biology | Assignment 6 The papers describe the role of kinetic proofreading (KP) in translation. Identify a primary research paper that proposes a role for KP in a process other than translation. Summarize the role that KP is proposed to play. Critically evaluate the evidence for the authors' conclusions about KP and compare the proposed role in the process under study to that described in the Hopfield and Rodnina papers. Be sure to include the reference for the paper you are discussing. |
| 8 | Protein structure and function | Assignment 7 The two papers, by Wiedemann et al. and Stiffler et al., address essentially the same problem using related methods. Both involve carrying out extensive binding experiments, and then using these to develop a predictive model for PDZ-peptide binding specificity. Think carefully about how the two approaches are similar and how they are different, both in terms of the experiments and the computational models. Outline these differences, highlighting those that you think are most important. |
| 9 | Devices and detection | Assignment 8 Write a critical review of paper 2. Do you recommend publication? Why/why not? |
| 10 | Synthetic biology | Assignment 9 The two primary papers address challenges in the emerging field of synthetic biology, while the supplemental papers focus on aspects of 'classical' biology. How do the goals and approaches of synthetic biology and 'classical' biology differ from each other? What types of issues do the two fields share and which are unique to one or the other? Use examples from each of the 4 papers listed above to illustrate your points. You'll probably want to include one-sentence definitions of the fields (your own or from public sources). |
| 11 | Randomness in biology | Assignment 10 These papers discuss the measurement of and potential consequences of noise in the expression of bacterial and yeast genes. Identify a primary research paper that proposes a role for gene expression noise in the regulation of some biological process. Summarize the role that noise is proposed to play. Critically evaluate the evidence for the authors' conclusions about noise. Be sure to include the reference for the paper you are discussing. |
| 12 | Gene networks | Assignment 11 Paper 1 makes an analogy between the concept of homology between genes based on sequence motifs and the notion of similarity between connectivity patterns in gene networks based on network motifs, suggesting that this may be helpful in gaining insight into the dynamic behavior of newly discovered gene circuits. Critically evaluate this analogy, considering aspects of these notions that are different as well as similar in terms of: (i) methodology — how genes/networks are or might be compared; (ii) goals of the analysis and assumptions needed for its applicability; and (iii) potential applications. |
| 13 | Computational and systems biology | Assignment 12 Write an essay explaining your personal definition of the field(s) of computational and systems biology. Your essay should begin with a crisp, but comprehensive definition one or a few sentences in length, set off in italics. You may choose to define computational biology and systems biology separately or together as seems appropriate. Illustrate your definition using as examples a few carefully chosen papers from weeks 1-12 of this course (you may include supplementary/optional papers and/or primary papers), discussing how the papers relate to your definition. Generally speaking, those papers which are at or near the boundary of the field are likely to be most helpful in illustrating the scope of your definition, rather than papers which are clearly included or excluded, though you may mention these if you wish. The 6 assigned papers this week — and any past assignments from your fellow students posted on the course Web site — are background for this assignment, and may be used in any way (up to and including direct quotation, as long as the source is cited), or may be ignored completely. This assignment will not be graded. |