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BCB Written Qualifying Exam (Year 1*)

In May of their first year (although see Exceptions below), students are required to take a written qualifying exam to demonstrate proficiency in the fundamentals of bioinformatics and computational biology, as well as competence in synthesizing these fundamentals into original scientific hypotheses or approaches.

The written qualifying exam is scheduled two weeks after the spring (3rd) rotation, in the first part of May. An exam committee consisting of the DGS and BCB faculty with knowledge of the material covered in the module is assembled to create and evaluate the exams. Each committee member is expected to serve at least two consecutive years so that membership can be staggered to maintain consistency and experience among the committee as a whole. The written exam planned for 2025 comprises 8 questions spread across 5 broad subject areas (exam writers after the dash; questions per exam writer indicated in parentheses):

  1. Dynamic Modeling – Jeremy Purvis (Q1), Adam Palmer (Q2)
  2. Evolutionary Genomics – Dan Schrider (Q1)
  3. Statistical Modeling Applications in Genetics & Genomics – Natalie Stanley (Q1) Will Valdar (Q2)
  4. Structural Bioinformatics – Konstantin Popov (Q1 & Q2)
  5. Data Science Writing – Michael Love (Q1)

Each question is based on 1-3 research articles provided in a reading list.

Exam format: The exam comprises a two-week reading period followed by a five-day exam period. At the start of the reading period, students are assigned the reading lists for all 8 questions. During this time, students are allowed to collaborate in studying the material, including using generative AI tools if desired. They may not, however, communicate about the exam with the exam writers.

The exam period consists of an open-book take-home exam spread over five days. Students are required to complete and submit written answers to exactly 5 of the 8 questions. Each question is independent of the others, so any combination may be submitted. If a question is multipart, then it will indicate how points or percentages of the grade are allotted. The questions do not expect the examinee to be a subject area expert but do expect the examinee to look up unfamiliar concepts or material. During this period, however, students are prohibited from collaborating with others or using generative AI tools (except for non-content related matters, e.g., checking grammar is okay). Students may ask the exam writers to clarify aspects of exam questions but only through the Student Services Manager (SSM) to maintain student anonymity.

Grading is performed by the exam writers and the exam committee. Answers to each question are graded anonymously on the H/P/L/F scale, and the exam overall is graded as either pass or fail. Passing the exam requires a minimum score of four Ps and one L; students who obtain Ls in two or more questions or an F in one or more questions will be considered to have failed part or all of the exam. Students who fail all or part of the exam have the option to retake the exam the following year; the conditions of the retake, namely whether this involves retaking the whole exam or a subset, are determined by the exam committee during the final exam meeting, and this determination is blind to the identity of the student. In the case of students retaking only a subset (eg, when the exam committee allows them to carry over exam questions they performed well on the previous year, such that they need only take, eg, 3 questions from prescribed categories), the length of the exam period is shortened accordingly (eg, 3 days for 3 questions). Students who fail the exam on the second attempt are dismissed from the PhD program; in such cases, depending upon the sum of their performance over both exams, those students may be eligible to apply for the Exit Masters program.

Exceptions: In certain cases, it may be more appropriate for a student to defer the written exam to May of their 2nd year. For example, if that student did not complete sufficient BCB coursework in their first year to cover the subject areas for at least five exam questions, as is sometimes the case, eg, for students who considered joining BCB only relatively late in their first year.

Dates for 2025 Exam

  • Monday, April 21, 2025: 2-week exam reading period begins. — Students receive journal articles and may study on their own or participate in study groups in preparation for the exam.
  • Monday, May 5-Friday, May 9, 2025: Exam period. — Students receive exam questions at 9am Monday morning. All final answer documents must be received by 4:30pm on Friday afternoon. Faculty exam authors will be available as needed for clarifications throughout the exam period (via Student Services Manager John Cornett). No collaboration between students is allowed once the exam has opened.

Example material from previous exams

Previous exams sometimes had different structures and often different examiners. Information is provided here for historical interest only. The exam research articles for subsequent exams will be different, potentially substantially so.

The research articles used in the 2022 written exam were:

  1. Dynamic Modeling (Q1: 27136688, 22218529; Q2: 26479923, 18838440)
  2. Evolutionary and Functional Genomics (Q1: 1560824, 8375663, 26494843; Q2: 34446078)
  3. Quantitative Genetics (Q1: 33712590, Q2: 33200985)
  4. Structural Bioinformatics (Q1: 27151862 , 35332283; Q2: 30568301)

Frequently Asked Questions

Question: Can faculty advisors assist students with their written exam, either in understanding the reading material or answering the questions?

Answer: As a general rule, no.

During the exam period in which students are working on answering exam questions, this would be a clear honor code violation. Students must work alone during that period and, save for communication with the examiners via the student services manager, they must not collaborate with any other person.

During the reading period, students are allowed to discuss the material with their peers, form study groups, etc. However, students’ advisors should not actively participate in such activities, and we recommend against faculty advisors providing any direct help regarding exam reading material, although it is okay to discuss concepts in the abstract, out of the specific context of those papers.

The main reason for limiting or avoiding faculty advisor participation in the reading period is that the written exam is testing the student in skills acquired primarily outside the specific context of their thesis or laboratory; unlike the oral exam, the written exam is not a product of work generated in collaboration with an advisor. Additional reasons for limiting or avoiding faculty participation relate to equity, namely that:

  1. some faculty advisors happen to be more knowledgeable about the areas covered by the exam than others, and this creates or exacerbates potential inequities among students taking the exam;
  2. some faculty advisors are themselves writing one of the exam papers, which puts those advisors in an immediate conflict of interest regarding discussing some of the reading material;
  3. if faculty were able to help students in this way, students of faculty writing parts of the exam would arguably be disadvantaged relative to their peers because there are some research articles their advisors could not discuss.

Question: To what extent are students allowed to collaborate during the reading period?

Answer: Students are allowed to discuss the material with their peers, form study groups, etc. Collaboration during this period should be limited to discussion, whether this is verbal, as written conversations, or the use of explanatory tools such as illustrations/diagrams. It should not extend to collaborating on the formulation of, eg, pre-prepared written answers to likely questions or computer code that may be deployed during the exam. The work by each individual during the exam period must be their own, and this is violated by any direct use of pre-prepared, group materials.