2012-2013 Computational Biology and Bioinformatics Ph.D. Qualifying Examination

Department of Computer Science, Virginia Tech

Exam committee

• Alexey Onufriev, Chair
• T. M. Murali
• Yang Cao

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. In some areas, the emphasis is on the ability to solve fairly simple problems.

Process and Format

• Students must register for this exam. Send your request to register to Alexey Onufriev. Students currently registered are here:

  Student	Area
  Shou Wang	Computational Biology
  T.C. Jones	Computational Biology
  ...	Systems Biology
  ...	Structural Bioinformatics

• Students must do the following:
  1. Write a synthesis of the assigned research papers as a 5-6 page paper, written in 11 point or larger font. By a synthesis, we mean that you should not merely summarize each paper individually but must group, compare, and contrast the papers.
  2. On a specific day, take an oral exam administered by the committee and based on the research papers and your synthesis paper.

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

Schedule

• 12/7/2011: Exam details made available.
• 12/12/2011: Last day to register for the exam. Send your request to Alexey Onufriev. Specify which research area you have chosen.
• 1/22/2012: Synthesis paper due. Send your paper as a PDF to Alexey Onufriev.
• TBA: Oral exam.
• 2/15/2012: 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.

1. Computational Biology

   Retrieve the following papers for the Computational Biology research area:

   1. Computational systems biology H. Kitano,  Nature,  420, 206-210, Nov. 14, 2002. 

   2. Design principles of biochemical oscillators. Novak, B., and Tyson, J.J. (2008).   Nature Rev. Mol. Cell Biol 9:981-991

   3. Functional motifs in biochemical reaction networks.  Tyson, J.J., and Novak, B. (2010).  Annu. Rev. Phys. Chem..  61:219-240.

   4.  doi:10.1021/j100540a008  Exact Stochastic Simulation of Coupled Chemical Reactions, .  Gillespie, Daniel T. (1977) The Journal of Physical Chemistry 81 (25): 2340–2361. 

   5.  doi:10.1063/1.2919546 A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks Slepoy, Alexander; Thompson, Aidan P.; Plimpton, Steven J. (2008). Journal of Chemical Physics,  128 (20): 205101. 

2. Structural Bioinformatics

   Retrieve the following papers for the Structural Bioinformatics research area:

   1. Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons Richard J. Morris, Rafael J. Najmanovich, Abdullah Kahraman, and Janet M. Thornton. Bioinformatics 10, 2005, 2347-2355.

   2. Contact order, transition state placement and the refolding rates of single domain proteins, Plaxco, K.W., Simons, K.T., and Baker, D., J. Molecular Biology 277, 1998, 985-994.

   3. Solvent-accessible surfaces of proteins and nucleic acids, Michael L. Connolly. Science 221, 1983, 709-713.

   For this area, special instructions apply.

   For the first and second papers, do not submit a synthesis. Instead, you must answer specific questions about each paper, given below. Format: Quote the question and provide your answer, no more than one page per answer, unless otherwise stated in the specific question. For paper three (Connolly) only, write a one-page summary. Tell us what problem you think the paper solves, what advantages and disadvantages the solutions have, what the significance of the paper is, and how would you improve the techniques used. This is a "general interest" paper; it may help with understanding some of the more technical ideas in the Morris et al. work.

   Retrieve questions on the first paper.

   Retrieve questions on the second paper.

3. Systems Biology

   Retrieve the following papers for the Systems Biology research area:

   1. Subnetwork state functions define dysregulated subnetworks in cancer, Salim A. Chowdhury, Rod K. Nibbe, Mark R. Chance, and Mehmet Koyuturk. Journal of Computational Biology 18, 2011, 263-281.

   2. DEGAS: De novo discovery of dysregulated pathways in human diseases, Igor Ulitsky, Akshay Krishnamurthy, Richard M. Karp, and Ron Shamir. PLoS ONE 5, 2010, e13367.

   3. Protein networks as logic functions in development and cancer, Janusz Dutkowski and Trey Ideker. PLoS Computational Biology 7, 2011, e1002180.

   4. A scalable approach for discovering conserved active subnetworks across species, Raamesh Deshpande, Shikha Sharma, Catherine M. Verfaillie, Wei-Shou S. Hu, and Chad L. Myers. PLoS Computational Biology 6, 2010, e1001028.

   5. Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity, Esti Yeger-Lotem, Laura Riva, Linhui J. Su, et al. Nature Genetics 41, 2009, 316-323.