Course Overview and General Information for Computational Molecular Biology Journal Club

Anyone is welcome to attend and participate in our Journal Club. Students seeking to receive credit for Journal Club have specific responsibilities described below.

Scope of the Journal Club

The Computational Molecular Biology Journal Club is a forum for discussing important and recent research results in computational and systems biology. Biological areas of interest to this seminar are wide-ranging, including (but not limited to) genomics and other -omics, metabolic and regulatory models, discovery of genotype-phenotype associations, phylogenetics and evolution, metagenomics, and synthetic biology. The unifying theme is that the works being studied should make a substantial computational or formal contribution. This contribution may be analytic -- e.g. data mining, data analysis, and hypothesis generation -- or synthetic -- e.g. modeling, prediction, and design of new experiments. Papers that rely heavily on existing, nontrivial computational methods to produce important biological results are also welcome but should be presented together with an explanation of these underlying methods.

Here is an extremely non-exhaustive list of conferences and journals that feature research relevant to the Journal Club:

Student Responsibilities

The following information applies only to students who are taking Journal Club for seminar credit, whether graded (for DBBS students) or ungraded (for CSE students).

To receive credit for Journal Club, you must do three things:

These three factors are weighted roughly equally in assigning credit and grades.

Paper Selection and Scheduling of Presentations

The range of topics for each semester of Journal Club is negotiated at an initial organizational meeting. Individual papers and presentation dates are selected by each student, with suggestions and final approval from the course masters.

Each student must select a paper at least five days before the meeting in which it is presented, to give others time to read the paper and submit responses.

Written Responses

To ensure that everyone is prepared to participate in each meeting at the highest level, we ask that students submit a written response to each scheduled paper in the week before it is presented. (If you are presenting that week, you don't need to submit a written response.) Written responses should be posted to the Journal Club's Blackboard discussion forum. To reach the forum, go to and select the course "Computational Molecular Biology Journal Club". Go to the discussions page, which will show the "Paper Responses" forum where you will post your responses. Your fellow students will be able to read and reply to your posts. Please do not look at others' responses until you have posted your own; after that, feel free to browse at will.

Written responses should be around a page in length. They should include three components: a brief summary of the paper, an assessment of its key strengths and weaknesses, and a reflection on what steps to take next. Your assessment should focus on the following areas:

  1. Significance: what questions do the authors pose, what claims do they make, and what do they want you to believe? Why is the world a better place for this work having been done? What is the work's potential impact on the field?
  2. Innovation: how does this work increase the totality of the discipline's knowledge and/or skills? How does it relate to previous work in the same area?
  3. Approach: what are the strengths and limitations of the methods invented and/or employed? Are they correct, efficient, and appropriate to the questions being asked? How might they bias the results? Are there issues of statistical significance and power, and if so, are they addressed appropriately?
  4. Validation: does the paper advance evidence that leads you to believe its claims? For methods papers, is there validation on real (vs. simulated) data, and are there appropriate comparisons to other methods? Identify the key figures in the paper and what each one communicates.

To the extent possible, please try to identify both strengths and weaknesses in every paper. Papers that pass peer review in respected forums generally have some value, whatever their limitations. The goal is not to "shoot down" a paper but rather to assess what can usefully be taken away from it.

Finally, after assessing the paper, you should consider and respond to the following question. If you were a student joining the authors' research group and had to take over the project described in the paper, what would your next step be to continue the research? This could be additional validation, extension of a method, followup experiments, statistical tests, or whatever seems most useful.

The key in answering this question is to propose a specific, well-justified course of action. For example, don't just say, "I would perform further testing on my HMM to check its specificity;" instead, say "I would test my HMM on the SCOP database and draw ROC curves to assess its performance on beta-barrel proteins in particular because beta barrel proteins have unusual sequence composition. Alternative training sets may be required for optimal performance on beta barrel proteins."