Weekly Questions

Before each class, students will formulate 2–3 questions to facilitate discussions. These questions are due by 10 pm on the day before class and should be related to the assigned papers for that week. Questions may be about the papers' background material, techniques, data generation and analysis, interpretation of results or follow-up experiments.

Midterm Written Assignment (Due Week 7; Reviewed in Class on Week 9)

Write a short summary and critique of the distributed paper:

Stoeckius, M., D. Grun, and N. Rajewsky. "Paternal RNA contributions in the Caenorhabditis elegans zygote." EMBO Journal 33(2014): 1740–50.

Include the following components:

  1. A brief description (about one paragraph) of the paper’s goals, methods, major results, and conclusions.


  2. Three points of criticism, written as if you were reviewing the paper for publication. Explain in a few sentences why you think each point makes the paper weaker. Consider but do not limit yourself to the following questions:
    - Does the data support the authors’ claim?
    - Have the authors done the appropriate controls for each experiment?
    - Have the authors done the appropriate statistics for their study?
    - Do the authors overstate or exaggerate their conclusions?
    - Are figures and approaches explained well?


  3. Three possible follow-up experiments to further explore the authors’ conclusions. For each, briefly describe your rationale, hypothesis, strategy, and controls. Concentrate on concept rather than experimental detail.


You are encouraged to consult Pubmed, the Internet, textbooks, friends, and each other for ideas and examples of possible follow-up experiments.

In Week 9, we will use our class to do a mock peer review of the student proposals. Each student will be assigned a classmate's proposal and will lead a brief discussion of its strengths and weaknesses for the class. The goal of this exercise is to introduce students to the process of peer review first-hand. The focus will be on improving rather than simply criticizing the proposal.

Final Oral Presentation (Week 14)

On the last day of class, students will give a 15 minute presentation about a paper related to one of the topics discussed in this course. The students should choose a paper themselves and then discuss it with the instructors to be sure an appropriate paper has been selected. The deadline for choosing a paper is Week 11. The presentation should be about 10 slides long and prepared using PowerPoint or other slide presentation software. At the end of each presentation, we will have 5 minutes for questions and discussion. The presentation should have the following format: 

  1. Introduction (1–3 slides): Provide any background material or previous work necessary to understand the paper. Outline the major questions posed by the authors.
  2. Results (4–6 slides): This section should be the main focus of your presentation. Describe the methods used in the paper and present the results from the key experiments and controls. Interpret the results and point out any flaws in the paper. Consider the following questions in your analysis: Do the data support the author’s claim? Have the appropriate controls been done? Have the appropriate statistics been used? Are the conclusions exaggerated or overstated?
  3. Conclusions (1–2 slides): Summarize the paper and provide suggestions for 3 follow-up experiments/analyses.