2019-2020 Computational Biology and Bioinformatics Ph.D. Qualifying Examination

Department of Computer Science, Virginia Tech

Exam committee

• Lenwood S. Heath, Chair
• Young Cao
• T. M. Murali

Philosophy of Examination

• This exam is based on a set of CBB research papers. Each student chooses his/her set of papers from one of three research areas (see below).

• Each student is responsible for reading beyond the set of assigned papers so as to thoroughly understand the assigned area.

• Each student will be evaluated on his/her written paper synthesizing the area and via an oral exam.

Process and Format

• Students must register for this exam, including the selection of an area (below). Send your request to register to Lenwood S. Heath. Students currently registered are here:

  Student	Area
  Reem Aldaihani	Alignment-Free Biological Sequence Analysis

• Students must do the following:
  1. Write a paper written in 11 point or larger font as directed by the area below.
  2. On a specific day in February, take an oral exam administered by the committee and based on the research papers and your paper.

• Grading: Written synthesis: 50%. Oral exam: 50%.

Schedule

• 11/15/2019: This page made available.
• 12/1/2019: Exam details made available.
• 12/6/2019: Last day to register for the exam. Send your request to Lenwood S. Heath. Specify which research area you have chosen.
• 1/30/2020: Synthesis paper due. Send your paper as a PDF to Lenwood S. Heath.
• TBD: Oral exam.
• 2/15/2020: Exam results due to GPC.

Before each of the dates above make sure you check this page for updates.

Research Areas

Choose one of these three research areas. To be announced by 12/1/2019.

1. Alignment-Free Biological Sequence Analysis

   Retrieve the genome comparison exam description and follow the instructions given there. You will want this paper.

2. Computational Systems Biology

   Retrieve the computational systems biology instructions and follow the steps given there.

   You will need these three papers:

   1. Gillespie01.pdf
   2. Systems_Biology_2012.pdf
   3. ToggleSwitch_Nature.pdf

3. Network Biology

   See the instructions here for network biology.