2011-2012 Computational Biology and Bioinformatics Ph.D. Qualifying Examination

Department of Computer Science, Virginia Tech

Exam committee

• Lenwood S. Heath, Chair
• T. M. Murali
• Alexey Onufriev

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. Send your request to register to Lenwood S. Heath. Students currently registered are here:

  Student	Area
  Haitham Almarakeby	Networks
  Soha A. Ehssan Aly	Networks
  Fei Li	Networks
  Mingming Liu	Networks
  Ayat Mohammed	Networks
  Ahsanur Rahman	Systems Biology
  Hanaa Torkey	Networks

• 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

• 11/21/2011: This page made available.
• 12/2/2011: Exam details made available.
• 12/9/2011: Last day to register for the exam. Send your request to Lenwood S. Heath. Specify which research area you have chosen.
• 1/22/2012: Synthesis paper due. Send your paper as a PDF to Lenwood S. Heath.
• 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. Networks

   Retrieve the following papers for the Networks research area:

   1. Biological network comparison using graphlet degree, Natasa Przulj, Bioinformatics 23, 2006, e177-e183.

   2. Global alignment of multiple protein interaction networks with application to functional orthology detection, Rohit Singh, Jinbo Xu, and Bonnie Berger. PNAS 105, 2008, 12763-12768.

   3. IsoRankN: spectral methods for global alignment of multiple protein networks, Chung-Shou Liao, Kanghao Lu, Michael Baym, Rohit Singh, and Bonnie Berger. Bioinformatics 25, 2009, i253-i258.

   4. Optimal network alignment with graphlet degree vectors, Tijana Milenkovic, Weng Leong Ng, Wayne Hayes, and Natasa Przulj. Cancer Informatics 9, 2010, 121-137.

   5. Integrative network alignment reveals large regions of global network similarity in yeast and human, Oleksii Kuchaiev and Natasa Przulj. Bioinformatics 27, 2011, 1390-1396.

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.