Exam Committee
Exam Format
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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.
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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.
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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.
Key Dates
Note: This schedule is tentative and subject to change. Be sure you check this page periodically for updates.
- 12/02/2024: Finalize area-specific committee chairs and committees.
- 12/20/2024: Exam details made available.
- 01/06/2025: Ph.D. Qualifier Exam webpages go online. Students register for the exam.
- 01/13/2025 -- 01/20/2025: Committees release decisions on qualifier waiver to students who requested it.
- 02/15/2025: Written component due. Send your PDF file to Debswapna Bhattacharya.
- TBD: Oral exam.
- 3/15/2025: Committees finalize the results for Qualifier Exam and Excellence in Depth, and share it with GPC.
- 3/20/2025: Results released to students.
Evaluation Criteria
The grading policy is as below:
- Pass 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.
- Fail if the oral presentation is confusing and/or the written component is a mere summary or paraphrasing of published papers or needs an end-to-end rewrite.
- Waive based on studnt's research track-record including publications, presentations, and progress towards degree.
After the exam, the committee will discuss the result and give students comments, feedback, and suggestions. Finally, the chair will email students and GPC about the score.
Problem Statement
In the context of SARS-CoV-2 and COVID-19, there is a rich literature on the various topics provided below to help students 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 are the computational challenges of viral surveillance?
- What is the effect of RNA viral mutagenesis and the impact on pathogenesis of SARS-CoV-2 variants?
- 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 have scientists learnt about the host immune response to SARS-CoV-2?
- How can computational modeling of protein/RNA structures and protein-protein and/or protein/RNA complex structures inform the host-pathogen interactions involving SARS-CoV-2 proteins?
- What computational strategies have been used to discover and test drugs against COVID-19?
- How have epidemiologists studied host-host transmission dynamics of SARS-CoV-2?
Academic Integrity
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.