2007-8 Bioinformatics Qualifying Examination

Examining Faculty

This page is pretty much finalized. The exam date is set, but check for possible updates.

The exam will take place on Sat., Feb. 9 at 2 pm. Please report to 2160 Torgersen Hall, the "conference room" in the back. The whole thing should take approximately 2 hours. Bring the papers, notes, blank sheets, etc. Above all, bring your clear, well-rested heads.

Format of the Examination

The exam is divided into 3 major themes. These will include the following: Structural Bioinformatics, Algorithms in Bioinformatics, and Modeling and Simulation. We will explore each theme via a set of related papers in the reading list below. We expect you to read all the papers in the reading list and obtain a detailed understanding of each paper. We also expect you to acquire any pre-requisite or background knowledge required to understand these papers. The exam has two parts:
  1. Written examination Write a 1 page synopsis on each paper. Use 11pt or 12pt times font (\usepackage{times} in Latex) with 0.5 inch margins on each side and single-spaced type. Submit the combined synopsis as one file in PDF format by email to Alexey Onufriev (alexey at cs vt dot edu) by 5PM on January 31, 2007. Tell us what problems you think each paper solves, what advantages and disadvantages the solutions have, what the significance of each paper is, and how would you improve the techniques used. Also, you MUST answer specific questions that we ask on each paper, the list is given below. Format: quote the question and provide your answer below. The space used for the answers to the specific questions does not count towards the page limit of the synopsis; the answers page should directly follow the synopsis page for the corresponding paper. No more than 1 page per each answer, UNLESS otherwise stated in the specific question.
  2. Oral Examination The oral examination will involve in-depth questions on the issues you have covered in the synopsis. We encourage you to read other related papers on these themes to understand how research in each theme is evolving. We will elicit your opinion on potential avenues of research in each theme. Questions will drill down into the statistical, algorithmic, and computational details of the papers in the reading list. We will also examine your understanding of the biological relevance and significance of the papers. The exam will be 45-60 minutes long.

Reading List (complete )

All the papers are available in the library, most of the papers should also available on-line. You should be able to access them from a VT computer.