Ph.D. Qualifying Written Exam

Ph.D. Qualifying Written Exam

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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 - Cavit Ağca
  2. Immunology - Tunç Akkoç
  3. Molecular biology and biochemistry - Nur Mustafaoğlu and Hüveyda Başağa
  4. Gene regulation and disease - Cavit Ağca
  5. Neurobiology - Nur Mustafaoğlu

 
Bioinformatics

  1. Computational biology - Ogün Adebali and Öznur Taştan
  2. Structural biology - Zehra Sayers and Canan Atılgan
  3. Systems Biology - Christopher Mayack

 
Bioengineering:

  1. Biosensors - Nur Mustafaoğlu
  2. Tissue engineering - Nur Mustafaoğlu
  3. Genetic Engineering - Christopher Mayack

 
 
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 22 Responses to Abiotic Stress
    • Chapter 23 Mineral Nutrient Acquisition, Transport, and Utilization

     

  • Cell biology exam: Textbook: Molecular Biology of The Cell
    • Chapters 10 - 19

     

  • 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 examBiochemistry;
    • 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)

    Textbook: Principles of Biocemistry (David Nelson and Michael Cox) recent edition or any Biochemistry text book. Molecular Biology;

    • Biosignaling
    • Transcription
    • Apoptosis and autophagy
    • Regulation of gene expression
    • Principles of methods used in molecular biology

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

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  • Molecular medicine examTextbook: The Biology of Cancer (Weinberg)
    • Chapter 2: Nature of Cancer
    • Chapter 11: Multi-step Tumorigenesis
    • Chapter 14: Moving out: Invasion and Metastasis

     

  • Computational biology exam: Textbook:
    • 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, https://compgenomr.github.io/book/stats.html (Not the coding part but the concepts)

     

  • Structural biology exam: Textbooks:
    • Introduction to Protein Structure Branden & Tooze
    • Crystallography Made Crystal Clear: A Guide for Users of Macromolecular Models, Gale Rhodes
    • Protein Structure and Function, Gregory Petsko

     

  • Integrative Biology exam
    • Computational Systems Biology Authors: Andres Kriete and Roland Eils Publisher ‏ : ‎ Academic Press; 1st edition (October 31, 2005) Language ‏ : ‎ English Paperback ‏ : ‎ 424 pages ISBN-10 ‏ : ‎ 1493300075 ISBN-13 ‏ : ‎ 978-1493300075

     

  • Animal Physiology exam:Textbook:
    • Animal Physiology 4th Edition by Richard W. Hill (Author), Gordon A. Wyse (Author), Margaret Anderson (Author) Publisher: Sinauer Associates is an imprint of Oxford University Press; 4th edition (September 13, 2016) Language: English Loose Leaf: 828 pages ISBN-10: 1605355941 ISBN-13: 978-1605355948

     

  • Animal Behavior exam:Textbook:
    • Animal Behavior 2nd Edition Authors: Michael Breed Janice Moore eBook ISBN: 9780128016831 Paperback ISBN: 9780128015322 Imprint: Academic Press Published Date: 1st February 2015 Page Count: 552

     

  • Integrative Organismal Biology exam:Textbook:
    • Editor(s): Lynn B. Martin Cameron K. Ghalambor H. Arthur Woods First published:14 November 2014 Print ISBN:9781118398784 |Online ISBN:9781118398814 |DOI:10.1002/9781118398814 Copyright © 2015 John Wiley & Sons, Inc

     

  • Neurobiology exam:Textbook:
    • 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

     

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

     

  • Genetic Engineering exam:Textbook:
    • An Introduction to Genetic Engineering 3rd Edition by Desmond S. T. Nicholl (Author), Publisher : Cambridge University Press; 3rd edition (June 1, 2008) Language : English Paperback : 347 pages ISBN-10 : 0521615216 ISBN-13 : 978-0521615211

     

  • Gene regulation and disease exam: TBA