A key assessment (totaling 20% of your grade) will be both a written and oral review of a recent bioinformatics research paper. This will expose you to cutting-edge research in bioinformatics algorithms and provide you with experience in summarising and critiquing literature.

Paper Selection

You will select your own bioinformatics-related primary research paper (i.e., not a review paper) published in or after 2020. This paper will be submitted via Brightspace by 23:59 on March 21st. Your selection will then be approved within 24 hours (with an alternative suggested if it your selection has issues due to quality, topic, or complexity) and form the basis of a written review and 13-15 minute oral presentation as described below. Please speak to me or Jee if you have any questions or concerns about this before the deadline.

Journals and proceedings check for papers that seem interesting include:

Also try to avoid more “predatory” publishers such as MDPI and Frontiers.

You are definitely more than welcome to use papers from major general audience journals like Nature, Science, Cell, Proceedings of the National Academy of Sciences etc but you will often find these papers involve a LOT of data and a LOT of different analyses. This can make them challenging to summarise well especially with more limited biological background knowledge.

Written Summary

You will prepare a written summary of the paper, the ideas it contains, the methods it uses, and the reported findings. This is marked out of 20 and will be worth 10% of your final grade. The written summary must be submitted via brightspace by 23:59 on April 4th. This should be a .docx or .pdf formatted file named following this scheme: “BannerID_LastName_PaperReview.{pdf,docx}”

The key to this exercise is to demonstrate the insights you have gained from throughout the course. We’re also interested to hear your opinion of the work that was reported in the paper!

A note on plagiarism: Obviously the report must be done in your own words and cited appropriately. However, some elements of the paper may be necessary to reproduce. This is totally fine as long as they are cited correctly. For example, you don’t need to make an equation your own by changing the notation – you can include it and cite as (Equation x from [citation]). If your paper is Open Access then you’re not violating any license agreement if you include a figure from the original paper in your report. But don’t lift text directly from the paper: in general it’s not necessary to quote original wording the way one might expect to see in a report in the humanities (for example) unless it’s really provocative.

Mark scheme for written summary:

  • Length: Maximum 4 pages double spaced plus a figure or two.
  • Background and Motivation (3 points): Explain the importance of the work that was done. You might want to look at other information such as references that are cited by your paper to get a broader perspective.
  • Rationale for approach (3 points): Why did the authors take the approach? Does the approach taken seem like a good idea to you? How is it meant to improve on other methods?
  • Explain the method (4 points): Again, in your own words, using insights you have gained from the course.
  • Interpret the results (4 points): What were the key findings? Do you think the results are clearly presented? Are there analyses you think should have been done that were not done?
  • Future work (2 points): What do the authors suggest? Where would you go next, given the opportunity?
  • Clarity (4 points): Appropriate grammar, citations, clarity of your arguments. Any citation style is permitted as long it consistently used and clearly attributes where material/ideas are derived from. If in doubt

Oral Summary

You will prepare a 10 minute presentation summarising the paper, the ideas it contains, the methods it uses, and the report findings. This is also marked out of 20 and will be worth 10% of your final grade. Presentations will be scheduled in random order after your paper selection is finalised and will take place during the last week of class: April 4th-6th.

Mark scheme for the oral summary is the same as the written summary with the exception of Clarity:

  • Length: 10 minutes max
  • Background and Motivation (3 points): Explain the importance of the work that was done. You might want to look at other information such as references that are cited by your paper to get a broader perspective.
  • Rationale for approach (3 points): Why did the authors take the approach? Does the approach taken seem like a good idea to you? How is it meant to improve on other methods?
  • Explain the method (4 points): Again, in your own words, using insights you have gained from the course.
  • Interpret the results (4 points): What were the key findings? Do you think the results are clearly presented? Are there analyses you think should have been done that were not done?
  • Future work (2 points): What do the authors suggest? Where would you go next, given the opportunity?
  • Clarity (4 points): Effective use of visual/presentation medium i.e., effective use of slides and good presentation skills.