A. NEVRA ÖZER, Ph.D.

 

Assistant Professor

 

Marmara University, Faculty of Engineering, Department of Bioengineering

Goztepe Campus 34722, Kadikoy, Istanbul TURKEY

Office : MC-370

Phone : 90 216 418 23 57 ext.698

E-mail : nevra.ozer AT marmara.edu.tr

 

 

RESEARCH INTERESTS

 

Computational Biology and Bioinformatics

- Theoretical and computational investigation of biomolecular complexes

- Modeling and simulations of macromolecules with emphasis on structure and dynamics

- Sequence and structure-based methods to understand specificity and function

- Vibrational collective dynamics of proteins with elastic network models

- Characterization of intermolecular (protein-protein, protein-peptide) interactions

- Network of interactions within proteins via communication pathways

 

 

EDUCATION

 

Ph.D., Chemical Engineering, Bogazici University, 2002-2008 

Dissertation: “Recognition and Binding Processes in HIV-1 Protease”

Supervisor: Prof. Turkan Haliloglu

 

M.Sc., Chemical Engineering, Bogazici University, 1997-1999

Thesis: “A Study on Protein and DNA Analysis by Capillary Electrophoresis”

Supervisors: Prof. Kutlu Ulgen, Prof. Betul Kirdar

 

B.Sc., Chemical Engineering, Bogazici University, 1993-1997

 

Beyoglu Anadolu Lisesi, 1986-1993

 

 

ACADEMIC EXPERIENCE

 

Assistant Professor, Department of Bioengineering, Marmara University, 2008-present

   Courses taught: Proteins: Structure and Function, Computational Structural Biology, Advanced Bioinformatics, Special Topics in Bioengineering-II, Computational Bioengineering, Molecular Modeling, Introduction to Biomedical Engineering and Instrumentation, Differential Equations, Numerical Methods, General Chemistry

 

Visiting Researcher, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA, Summers of 2004-2005

   “NIH AIDS-FIRCA” grant, Celia A. Schiffer Lab

 

Research Assistant, Polymer Research Center, Bogaziçi University, 2002-2008

   Systems Administrator

 

Research and Teaching Assistant, Chemical Engineering Dept., Bogaziçi University, 1998-1999

   Courses assisted: Physicochemical Systems I-II, Chemical Engineering Laboratory I-II, Mass Transfer Operations, Graduation Projects

 

 

PUBLICATIONS

 

Papers in SCI Journals:  

 

G. Ozdemir Isik, N. Ozer, "Prediction of Substrate Specificity in NS3/4A Serine Protease by Biased Sequence Search Threading", Journal of Biomolecular Structure and Dynamics, DOI: 10.1080/07391102.2016.1171801, 2016.

 

N. Ozer, A. Ozen, C. A. Schiffer, T. Haliloglu, “Drug resistant HIV-1 protease regains functional dynamics through cleavage site coevolution”, Evolutionary Applications, 8(2):185-198, 2015.

 

N. Ozer, C. A. Schiffer, T. Haliloglu, “Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease”, Biophysical Journal, 99(5):1650-1659, 2010.

 

N. Ozer, T. Haliloglu, C. A. Schiffer, “Substrate Specificity of HIV-1 Protease by a Biased Sequence Search Method”, Proteins: Structure, Function and Bioinformatics, 64(2):444-456, 2006.

 

K. Y. Arga, T. Cakir, P. Pir, N. Ozer, M. M. Altintas, K. Ulgen, “Transfer function approach in structured modeling of recombinant yeast utilizing starch”, Process Biochemistry, 39(10):1237-1248, 2004.

 

M. M. Altintas, N. Ozer, K. Ulgen, “Purification of TaqI Endonuclease from Thermus aquaticus”, Journal of Chromatography A, 828(1-2):373-381, 1998.

 

Oral Presentations in International Scientific Conferences:

 

A.C. Serdaroglu, B. Ayan, B. Sariyar Akbulut, N. Ozer, “Distribution of Amino Acids in Extremophiles", Istanbul Conference on Mathematical Methods and Modeling in Life Sciences and Biomedicine, Istanbul, Turkey, 2011.

 

N. Ozer, A. Ozen, C.A. Schiffer, T. Haliloglu, “Dynamic Analysis of HIV-1 Protease Complex Structures by the Anisotropic Network Model”, 14. Istanbul Statistical Physics Days, Bogazici University, 2007.

 

N. Ozer, N. Kurt, C.A. Schiffer, T. Haliloglu, “Structure-based Prediction of Peptide Binding to HIV-1 Protease”, EMCC-3, Thessaloniki, Greece, 2003.

 

Poster Presentations in International Scientific Conferences:

 

G. Ozdemir Isik, N. Ozer, "Prediction of Cleavage Specificity in HCV NS3/4A Serine Protease and AdV2 Cysteine Protease Systems by Biased Sequence Search Threading", The 29th Annual Symposium of the Protein Society, Barcelona, Spain, 2015.

 

G. Ozdemir Isik, N. Ozer, "Prediction of Substrate Specificity in NS3/4A Serine Protease by a Threading Methodology", Biophysical Society Thematic Meeting, "Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations", Istanbul, Turkey, 2014.

 

T.F. Guclu, P. Ozbek, N. Ozer, "Comparative Study of Functional Dynamics in Mutant von Hippel-Lindau Tumor Suppressor Protein Structures", Biophysical Society Thematic Meeting "Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations", Istanbul, Turkey, 2014.

 

G. Ozdemir Isik, N. Ozer, "Prediction of Substrate Specificity in NS3/4A Serine Protease by Biased Sequence Search Threading", 2nd International BAU Drug Design Congress, Istanbul, Turkey, 2014.

 

T.F. Guclu, P. Ozbek, N. Ozer, "Dynamic Analysis of Mutant von Hippel-Lindau Tumor Suppressor Protein Structures", 2nd International BAU Drug Design Congress, Istanbul, Turkey, 2014.

 

A.C. Serdaroglu, N. Ozer, “Co-operative Fluctuations of PTP1B by an Elastic Network Model Analysis”, BITS 2012 Ninth Annual Meeting of the Bioinformatics Italian Society, Catania, Italy, 2012.

 

N. Ozer, A. Ozen, C.A. Schiffer, T. Haliloglu, “Co-operative Fluctuations of HIV-1 Protease Complex Structures”, VIIth European Symposium of the Protein Society, Stockholm, Sweden, 2007.

 

N. Ozer, C.A. Schiffer, T. Haliloglu, “Patterns of Energetic and Dynamic Correlates in HIV-1 Protease”, 20th Symposium of the Protein Society, San Diego, CA, USA, 2006.

 

N. Ozer, C.A. Schiffer, T. Haliloglu, “Patterns of Energetic and Dynamic Correlates in HIV-1 Protease”, VIth European Symposium of the Protein Society, Barcelona, Spain, 2005.

 

N. Ozer, C.A. Schiffer, T. Haliloglu, “Prediction of Substrate Specificity in HIV-1 Protease”, 15th European Symposium on QSAR and Molecular Modelling, Istanbul, Turkey, 2004.

 

N. Ozer, T. Haliloglu, C.A. Schiffer, “Prediction of Substrate Specificity in HIV-1 Protease”, 18th Symposium of the Protein Society, San Diego, CA, USA, 2004.

 

N. Ozer, N. Kurt, C.A. Schiffer, T. Haliloglu, “Structure-based Prediction of Peptide Binding to HIV-1 Protease”, 17th Symposium of the Protein Society, Boston, MA, USA, 2003.

 

K.Y. Arga, T. Cakir, P. Pir, N. Ozer, M.M. Altintas, K. Ulgen, “Structured Modelling of Recombinant Yeast Utilizing Starch”, EMCC-3, Thessaloniki, Greece, 2003.

 

M.M. Altintas, N. Ozer, K. Ulgen, “Optimization of Operating Conditions For Restriction Enzyme Purification”, HPLC’98, St.Louis, MO, USA, 1998.

 

 

PROJECTS

 

Researcher, “Dynamic Characterization of Protein-protein Interfaces using Gaussian Network Model”, Marmara University Research Fund Project, PI: Assist. Prof. Pemra Ozbek, 2014-2015.

 

Researcher, “Establishment of a Bioprocess Automatic Control Research Development and Education Center”, Marmara University Research Fund Project, PI: Prof. A. Alp Sayar, 2013-2015.

 

Researcher, “Dynamic Characterization of Protein Binding Mechanism”, Marmara University Research Fund Project, PI: Assist. Prof. Pemra Ozbek, 2012-2014.

 

PI, “Structural Analysis of Von Hippel-Lindau Tumor Suppressor Protein with the Anisotropic Network Model”, Marmara University Research Fund Project, 2010-2013.

 

Researcher, “Establishment of a Bioremediation Laboratory in the Bioengineering Department”, Marmara University Research Fund Project, PI: Prof. Dilek Kazan, 2009-2011.

 

Researcher, “Prediction of Protein-Protein Interactions by Machine Learning”, Bogazici University Research Fund Project, PI: Prof. Turkan Haliloglu, 2008-2009.

 

Researcher, “Study of the Interactions between P53 Tumor Suppressor Protein and DNA by Elastic Network Models”, Bogazici University Research Fund Project, PI: Prof. Turkan Haliloglu, 2006-2008.

 

Researcher, “COSBIOM – Towards Excellence in Computational Structural Biology and Biomaterials”, Avrupa Birliði FP6-2004-ACC-SSA-2 projesi, PI: Prof. Turkan Haliloglu, 2005-2009.

 

Researcher, “Predicting Substrate Specificity in HIV-1 Protease”, Bogazici University Research Fund Project, PI: Prof. Turkan Haliloglu, 2004-2006.

 

Researcher, “Predicting Substrate Specificity in HIV-1 Protease”, NIH-FIRCA (Fogarty International Research Collaboration Award) project, PI’s: Prof. Turkan Haliloglu, Prof. Celia A. Schiffer, 2003-2006.

 

Researcher, “Analysis of Polymer α-Synuclein (a-s) Conformations and Aggregation”, Bogazici University Research Fund Project, PI: Prof. Turkan Haliloglu, 2003-2005.

 

Researcher, “Peptide Membrane Interactions”, Bogazici University Research Fund Project, PI: Prof. Turkan Haliloglu, 2002-2004.

 

 

TRAININGS

 

Schrödinger Workshop, "Computational Drug Discovery", Yeditepe University, Istanbul, Turkey, April 2012.

 

Computational Structural Biology Workshop on HADDOCK, "Information-driven modelling of biomolecular complexes: Challenges and Perspectives", Utrecht University & Bogazici University Polymer Research Center, Istanbul, Turkey, June 2011.

 

Workshop on Computer Aided Drug Design and Development, “QSAR, Quantitative Structure-Activity Relationship”, Koc University, Istanbul, Turkey, February 2007.

 

Integrated Approaches for Functional Genomics Workshop, “Protein Structure Determination”, European Science Foundation & Sabanci University, Antalya, Turkey, November 2002.

 

Short Course on Practical Capillary Electrophoresis, Weinberger R., HPLC’98 Symposium, St.Louis, MO, USA, 1998.