2022 Computational Biology and Bioinformatics Ph.D. Qualifying Examination
Department of Computer Science, Virginia Tech
Exam committee
Philosophy of Examination
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This year, we are adopting a new format for the exam.
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We will
provide students a set of questions as a basis for brainstorming
of their
own research projects in CBB.
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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 written component or deliverable will be a proposal-like document (using the LaTeX
template here).
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The oral component will be exclusively to answer questions
about the document.
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Each student will be evaluated on his/her written document regarding the question chosen
and
via an oral exam.
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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.
Process and Format
- Students must register
for this exam, including the selection of a question (below).
Send your request to register to Liqing Zhang.
Students currently registered are here:
| Student |
Question |
|
Question |
|
Question |
Schedule
- 11/24/2021: This page made available.
- 12/5/2021: Exam details made available.
- 12/20/2021: Last day to register for the exam.
Send your request to Liqing Zhang.
Specify which research question you have chosen.
- 1/28/2022: Research proposal due.
Send your PDF file to Liqing Zhang.
- 2/5/2022 (Saturday): Oral exam in 3160A Torgersen, 10:00 AM to noon.
- 2/14/2022: Exam results due to GPC.
Before each of the dates above make sure you check this page for updates.
Research Questions
In the context of SARS-CoV-2 and COVID-19, there is rich literature both computationally and experimentally on various topics
below to
synthesise 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?
What SARS-CoV-2 variants have occurred and what can be said about the rate
and number of mutations discovered so far?
What computational problems can you identify considering COVID and antibiotic resistance together?
What are the computational challenges of viral surveillance?