Ph.D. Qualifying Written Exam

Ph.D. Qualifying Written Exam


Students must pass exams in 4 topics. Topics must be selected such that two of them are from one subject area and two of them could be from the remaining two subject areas or one of each*. Main subjects and the topics are listed below.
*One of the topics may be selected from the topics of other PhD programs with the approval of the student's adviser.

Subject areas and topics:

Plant Biotechnology:

  1. Plant biotechnology - Selim Çetiner
  2. Plant physiology - Levent Öztürk


Molecular Biology

  1. Cell biology - Zehra Sayers
  2. Immunology - Özgür Kütük
  3. Molecular biology and biochemistry - Nur Mustafaoğlu and Hüveyda Başağa
  4. Cancer biology - Alex Lyakhovich
  5. Neurobiology - Nur Mustafaoğlu
  6. Genetics - Ogün Adebali



  1. Computational biology - Ogün Adebali and Öznur Taştan
  2. Structural biology - Zehra Sayers and Canan Atılgan



  1. Biosensors - Nur Mustafaoğlu
  2. Tissue engineering - Nur Mustafaoğlu


The faculty members of the MBGB program suggest that the following are appropriate study subjects/references for these exams. If a resource is not indicated please consult with a faculty member whos research is similar to the subject in question or the graduate area advisor.

  • Plant biotechnology exam:
    Textbook: Plant Biotechnology The genetic manipulation of plants Second Edition Adrian Slater, Nigel Scott, and Mark Fowler ISBN: 9780199282616 


  • Plant physiology exam:
    Textbook: Biochemistry and Molecular Biology of Plants, 2nd Edition Bob B. Buchanan, Wilhelm Gruissem, Russell L. Jones ISBN: 978-0-470-71421-8
    • Chapter 1 Membrane Structure and Membranous Organelles
    • Chapter 3 Membrane Transport
    • Chapter 21 Responses to Plant Pathogens
    • Chapter 22 Responses to Abiotic Stress
    • Chapter 23 Mineral Nutrient Acquisition, Transport, and Utilization


  • Cell biology exam:
    Textbook: Molecular Biology of The Cell 7th edition, Alberts, B., Heald, R., Johnson, A., Morgan, D., Raff, M., Roberts, K. and Walter,
    Published by W. W. Norton & Company, 2022. ISBN: 9780393884821 (hardcopy), ISBN: 9780393884630 (epub)
    • Chapters 10 - 20


  • Immunology and signal transduction exam:
    Textbook: Janeway's Immunobiology (9th Ed), (or similar) with particular emphasis on the following chapters and subjects:
    • Chapters 1-10.


  • Molecular biology and biochemistry exam:


    • Amino acids, peptides, and proteins, their structure and function
    • Enzymes
    • Carbohydrates and lipids and nucleic acids (their structures and functions)
    • Nucleic acids and their functions
    • Membranes and transport
    • Bioenergetics and metabolism (electron transport chain and ox phosphorylation)

    Molecular Biology;

    • Genetic materials and structures
    • Central Dogma: DNA Replication Transcription, Translation
    • Mutability and Repair of DNA
    • Regulation of gene expression
    • Principles of methods used in molecular biology

    Textbook: Any recent biochemistry or molecular biology textbook and recent articles from literature. Students will be asked to comment on an article from literature in terms of hypothesis, methodology used and suggestions for furthering the research.


  • Cancer biology exam:
    Students should be familiar with the following chapters of the books:

    • Principles of Biochemistry Eighth  Edition|©2021 David L. Nelson; Michael M. Cox (or earlier editions but not older than 5th)
    • Chapter 12 Biosignaling
    • 12.8 Regulation of Transcription by Nuclear Hormone Receptors
    • 12.10 Regulation of the Cell Cycle by Protein Kinases
    • 12.11 Oncogenes, Tumor Suppressor Genes, and Programmed Cell Death
    • 25 DNA Metabolism
    • 25.1 Medicine: DNA Repair and Cancer
    • Biology Of The Cell - Bruce Alberts  (at least 4th Ed.)
    • Chapter 23 Cancer

In addition, the following textbooks are highly recommended to read:

      • Introduction to Cancer Biology Robin Hesketh, University of Cambridge Published 2023 2 Ed. or earlier ISBN: 9781316512616
      • The Biology of Cancer Third Edition by Robert A Weinberg ISBN: 978-0-393-88764-8


  • Neurobiology exam:
    • From Neuron to Brain by Author A. Robert Martin, David A. Brown, Mathew E. Diamond, Antonino Cattaneo, Francisco F. De-Miguel, and Foreword by John Nicholls ISBN: 9781605354392


  • Computational biology exam:
    • Biological sequence analysis. Probabilistic models of proteins and nucleic acids, edited by R. Durbin, S. Eddy, A. Krogh, and G. Mitchinson. 1998. Cambridge: Cambridge University Press
    • Altuna Akalın, Computational Genomics with R, (Not the coding part but the concepts)


  • Structural biology exam:
    Reference Textbooks:
    • Branden and Tooze, Introduction to Protein Structure, 2nd edition, Garland Science, 1999.
    • Bahar, Jernigan and Dill, Protein Actions, Taylor & Francis, 2017.
    • Petsko and Ringe, Protein Structure and Function, New Science Press, 2007


  • Biosensors exam:
    Students are responsible for current literature on biosensors. Please identify 15 research articles (only 3 review articles may be included) published in the last 5 years and share them with the professor prior to the exam.

    Suggested Textbooks:
    • Biosensors: Essential, Gennady Evtugyn, Springer ISBN 978-3-642-40241-8
    • Handbook of Immunoassay Technologies by Sandeep K. Vashist and John H.T. Loung ISBN 978-0-12-811762-0


  • Tissue Engineering exam:
    • Principles of Tissue Engineering by Robert Lanza, Robert Langer, Joseph Vacanti eBook ISBN: 9780128214015, Hardcover ISBN: 9780128184226


  • Genetics exam:
    • Concepts of Genetics, Global Edition by William S. Klug (Author), Michael R. Cummings (Author), Charlotte A. Spencer (Author), Michael A. Palladino (Author), Darrell Killian (Author)
      Publisher: Pearson; 12th edition (June 10, 2019)
      Language: English
      Paperback: 864 pages
      ISBN-10: 1292265329
      ISBN-13: 978-1292265322