• Debswapna Bhattacharya, Chair
• T.M. Murali
• Liqing Zhang

• We will provide students a set of questions as a basis for brainstorming of their own research projects in Computational Biology and Bioinformatics (CBB).
• Students will need to define some potential research directions, find relevant literature, and take it at least to the point of defining one viable computational research problem along with a set of justified computational approaches to try.
• The exam will comprise of the following components:
  (1) Written Component. the deliverable will be a proposal-like document (using the LaTeX template here). The written component will evaluate students' ability to articulate a well-defined research project in CBB.
  (2) Oral Component. will comprise of a 15 minute in-person oral presentation with 15-25 minutes of Q/A, which may be interspersed with the presentation, scheduled one week after the written submission. The oral component will evaluate students' ability to communicate the ideas presented in the proposal and answer questions.
• Preliminary results are not required, but if students can get to the point of having some preliminary results, it will count favorably towards the overall points on the qualifier.

• Students must register for this exam by 12/07/2022.
• Send an email to Debswapna Bhattacharya to sign up for the exam. Please include CBB Qualifier 2023 in the subject of the email. The content of the email must include: (1) your name, (2) your enrollment year, and (3) your advisor. Note that this qualifier exam is exclusively for students involved in Computational Biology and Bioinformatics research.
• You may withdraw from the exam without penalty up until 12/14/2022 by sending an email to Debswapna Bhattacharya. From that point, you are committed to being scored unless some extraordinary event intervenes.

• 11/23/2022: This page made available.
• 11/30/2022: Exam details made available.
• 12/07/2022: Last day to register for the exam.
• 12/14/2022: Last day to withdraw.
• 1/31/2023: Written component due. Send your PDF file to Debswapna Bhattacharya.
• 2/7/2023 (Tentative): Oral exam in 3160A Torgersen between 10:00 AM and 2:00 PM.
• 2/15/2023: Exam results due to GPC.

• 0 points if the oral presentation is confusing and the written component is a mere summary or paraphrasing of published papers. The written component needs an end-to-end rewrite.
• 1 point if the written component is sufficient, but the oral presentation is unsatisfactory (e.g., poor content organization, hard-to-understand explanation, failure to answer questions). The writing needs major overhauling.
• 2 points if both the written component and oral presentation are satisfactory but not in sync with the future plan (e.g., contains unconvincing, inconsistent arguments). The writing quality barely meets the bar.
• 3 points if both written component and oral presentation are cohesive, the analysis is substantial and contains depth, and the vision is well-thought-out, justified, and backed by solid reasoning. The writing quality meets or exceeds the bar.

In the context of SARS-CoV-2 and COVID-19, there is rich literature both computationally and experimentally on various topics below to synthesize a research proposal. Students need to choose one of the questions in the following. We are interested in (new) computational methods that have been developed or applied to answer these questions but also want to learn about the insights that these methods have yielded on the virus or the disease. Note, personal brainstorming and creativity are encouraged. The questions are meant to be starting points for an investigation.

• What computational strategies have been used to discover and test drugs against COVID-19?
• What have scientists learnt about the host immune response to SARS-CoV-2?
• How have epidemiologists studied host-host transmission dynamics of SARS-CoV-2?
• What is the key significance of the spike protein as opposed to other SARS-CoV-2 proteins?
• How can computational modeling of protein structures and protein-protein interactions inform the host-pathogen interactions involving SARS-CoV-2 proteins?
• What SARS-CoV-2 variants have occurred and what can be said about the rate and number of mutations discovered so far?
• How can computational approaches help in predicting the effect of mutations, in particular the immune-escape mutations?
• What computational problems can you identify considering COVID and antibiotic resistance together?
• What are the computational challenges of viral surveillance?

The submission by every student should reflect their individual effort. This examination is conducted under the University's Graduate Honor System Code. Students are encouraged to draw from published literature to the extent that this strengthens their arguments. However, the submissions must represent the sole and complete work of the student. Material substantially derived from other sources, whether published in print or found on the web, must be explicitly and fully cited. Your score will be more strongly influenced by arguments you make rather than arguments you quote or cite.