Term papers are required for graduate students in this course. The paper should be 5-10 pages in length and should focus on analysis of a problem rather than on summarizing background information from a paper. In other words, we are looking for the quality of analysis, ideas, and thinking rather than a presentation of material abstracted from published papers.
The paper will be due on the last day of class, December 5.
The choice of what you write about is up to you, but possible topics could include:
1. Propose a novel bioinformatics algorithm or analysis, stating clearly the biological problem that it solves, and detailing how it addresses key questions of computational complexity, and statistical significance of evidence for the result. Identify strengths and weaknesses of the proposed algorithm, and how it differs from existing algorithms.
2. Select a paper reporting a bioinformatics-based analysis of biological data, and present a critical analysis of the paper’s methodology and results. Most importantly, present your ideas for how the analysis should be extended to improve accuracy / reliability and the kinds of information that it can produce from the data.
3. Select a paper reporting some kind of genomics dataset (e.g. sequence, microarray data, or any other kind of genomics/proteomics data). Present a biological question and analytic approach based on bioinformatics which you think can answer the biological question using this data.
4. Select a molecular biology paper, and design a genomics-style experiment that can address the same question(s) raised in the molecular biology paper, but in a high-throughput form. Present the design of the experiment and data collection, and bioinformatics methods to analyze these data, addressing issues of complexity (can the problem be reduced to an algorithmically soluble form?), sensitivity (can the desired pattern(s) be detected robustly?), validation (accurately estimating confidence of the results).