PhD BCB Comprehensive Exam


Schedule for 2025 BCB Comp Exam: Friday, January 17, 2025 From 10:00 am to 5:00 pm via Zoom meeting

The comprehensive exam focuses on the synthesis of knowledge learned in the Program's core areas, as demonstrated by the student's ability to apply knowledge of course material to a variety of situations.


BINF 731 Protein Structure Analysis - Updated for 2025 Comp Exam

Exam questions for Protein Structure Analysis will be related to the content of the assigned papers listed below. This section of the exam permits open books and notes. If you have any questions, please contact Iosif Vaisman at ivaisman@gmu.edu.

Edelsbrunner H, Koehl P. Computational Topology for Structural Molecular Biology. doi: 10.1201/9781315119601-65
http://binf.gmu.edu/vaisman/binf731/hdcc2017_edelsbrunner.pdf

Villegas JA, Levy ED. A unified statistical potential reveals that amino acid stickiness governs nonspecific recruitment of client proteins into condensates. doi: 10.1002/pro.4361
http://binf.gmu.edu/vaisman/binf731/protsci2022_villegas.pdf

Swanson S et al. Tertiary motifs as building blocks for the design of protein-binding peptides. doi: 10.1002/pro.4322
http://binf.gmu.edu/vaisman/binf731/protsci2022_swanson.pdf

Soskine M, Tawfik DS. Mutational effects and the evolution of new protein functions. doi: 10.1038/nrg2808
http://binf.gmu.edu/vaisman/binf731/natrevgen2010_soskine.pdf

Caldararu O et al. Systematic Investigation of the Data Set Dependency of Protein Stability Predictors. doi: 10.1021/acs.jcim.0c00591?ref=pdf
http://binf.gmu.edu/vaisman/binf731/jcim2020_caldararu.pdf


BINF 701 Systems Biology - Updated for 2025 Comp Exam

The exam will cover material from the following lectures based on the textbook Eberhard Voit’s “A First Course in Systems Biology” (Second Edition): Chapters 1, 2, 3, 4, 5, 8, 9, and 12.

Students must complete the exercises in these chapters and be familiar with systems biology approaches.

Important Notes:
No resources, including books or notes, are allowed during the exam.
For any questions, please email Aman Ullah at aullah3@gmu.edu.


BINF 690 Numerical Methods in Bioinformatics - Updated for 2025 Comp Exam

The comprehensive exam will be based upon the material covered in BINF690 Lectures and on the textbook: Chapra & Canale, "Numerical Methods for Engineers", McGraw Hill. Topics will include: 1. Taylor series. Error propagation (Chapter 4). 2. Roots of equations (Chapters 5 and 6). 3. Linear algebraic equations (Chapter 9) 4. Optimization and minimization (Chapters 13 and 14) 5. Curve fitting (Chapters 17 and 18) 6. Numerical differentiation and integration (Chapters 21 and 22) 7. Solution of ordinary differential equations (Chapter 25). Boundary value and eigenvalue problems (Chapter 27).

During the exam any materials, including books or notes, and access to internet are permitted. You will need access to computer to run codes. If you have any questions, please contact Dmitri Klimov at dklimov@gmu.edu.


BINF 702 Research Methods/Biological Data Analysis - Updated for 2025 Comp Exam

This is an open book
Applied Statistics for Bioinformatics Using R 2nd Edition as revised by Riley (Chpts. 1-9)

An Introduction to Statistical Learning With Applications in R (ISLR) (Chpts. 1-5, 8-10)

The Art of R Programming (Mainly for context on functions and scope of the workspace and functions.) exam.

Field, A., Miles, J., & Field, Z. (2012). Discovering statistics using R. Sage publications. (Required)

In addition, you are allowed to use R/RStudio. You are not allowed to seek additional outside assistance from individuals or other web sources unless approved. Make sure that you are using the latest version. Alternatively, you can use Google Colab but you must insure that the Generative AI help is turned off.

Choose 2 problems from problems 1,2,3,4 and 2 problems from problems 5,6,7,8. Do not do additional problems. My grading rubric is as follows: Below 70 (Fail), 70-80 (Low Pass), 80-90 (Pass), 90-100 (High Pass). The scores from this rubric will be used by the Comprehensive Scoring Committee to map into the Categories that Dr. Klimov discussed earlier. Look for an update on my section of the exam by November 1, 2023.

The best way to study for the exam is to read through my slides including working through the examples, review the problems at the end of chapters in the Krijnen text and the labs that were assigned at the end of the ISLR text. Also see the review sheet based on the Spring 2023 class schedule that is posted on the comprehensive exam review webpage.

It will be extremely difficult to complete the exam if you are attempting to calculate the solutions “by hand.” It should be relatively easy to complete the exam if you have prepared and use R/RStudio.

The various parts of each problem are constructed based on the values returned by the appropriate R function.

A notional construction of the comprehensive exam is provided below.

Problem 1 Each part is worth 5 points
(a)
(b)
(c)
(d)
(e)
Problem 2 Each part is worth 5 points
(a)
(b)
(c)
(d)
(e)
Problem 3 Each part is worth 5 points
(a)
(b)
(c)
(d)
(e)
Problem 4 Each part is worth 5 points
(a)
(b)
(c)
(d)
(e)
Problem 5 each part is work 5 points
(a)
(b)
(c)
(d)
(e)
Problem 6 parts (a) and (b) are worth 8 points while part c is worth 9 points
(a)
(b)
(c)
Problem 7 parts (a) and (b)are worth 8 points while part (c) is worth 9 points
(a)
(b)
(c)
Problem 8 parts (a) and (b) are worth 8 points each and part(c) is work 9 points
(a)
(b)
(c)

For more information on what to study click here

BINF 730 Biological Sequence Analysis - Updated for 2025 Comp Exam

1. Pairwise and Multiple Sequence Analysis
2. Next-Generation Sequence Analysis
3. Phylogeny
4. Markov Models
5. Database Searching
6. Gene Finding

Exam Details:
Format: Similar to the final exam administered in class reduced to be done in one hour.
Focus: Implementing algorithms manually (as done in class or via coding exercises).
Resources: The exam is closed books and closed notes. You will only need a pen and paper.

BINF 740 Biophysics - Updated for 2025 Comp Exam

Exam questions will be based on the material covered in Biophysics class and required textbooks. Specific topics will include:
1. Lectures 1, 2, 3, and 4.
2. Lectures 6 and 7.
3. Lectures 10, 12, and 13.
Exam questions will emphasize good understanding of the biophysical concepts discussed in the lectures above.  The exam permits open books and notes. Students may use internet, computers or other materials or sources. If you have any questions, please contact Dmitri Klimov at dklimov@gmu.edu.

 


Notes

Schedule for 2025 BCB Comp Exam:
Friday, January 17, 2025
The exam will be conducted online through Zoom. Students must turn on web cameras. Further technical details will be provided closer to the exam date.

10-11 Ullah: Biol Seq analysis 730

11-12 Klimov: Biophysics 740

12-1 Klimov: Numerical Methods 690

1-2 lunch

2-3 Ullah: Systems Biology 701

3-4 Vaisman: Protein Structure Analysis 731

4-5 Solka: Research Methods/Biological Data Analysis 702


For any questions, please contact Dr. Dmitri Klimov (dklimov@gmu.edu).