born in 1985

Nationality: Republic of Turkey

Tel: +(90) 262 605 33 17 / 3327

E-mail: osercinoglu AT gtu DOT edu DOT tr

Address: Gebze Technical University, Faculty of Engineering, Bioengineering Department, E-152, Gebze, Kocaeli, Turkey

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Education


PhD in Bioengineering
2012 - 2018

Marmara University, İstanbul, Turkey

MSc in Biotechnology
2008 - 2011

Hamburg University of Technology (TUHH), Hamburg, Germany

Exchange Student
2007

Åbo Akademi, Turku, Finland

BSc in Bioengineering
2003 - 2008

Ege University, İzmir, Turkey

High School
1999 - 2003

Bornova Anatolian High School, İzmir, Turkey

Scientific Activity


Research Article Sercinoglu, O., Ozbek, P.,
Sequence-structure-function relationships in class I MHC: a local frustration perspective, PLoS ONE, 15(5), e0232849 doi: 10.1371/journal.pone.0232849
Research Article Bunsuz, A., Sercinoglu, O., Ozbek, P.,
Computational investigation of peptide binding stabilities of HLA-B*27 and HLA-B*44 alleles, Computational Biology and Chemistry, 84, 107195. doi: 10.1016/j.compbiolchem.2019.107195
Research Article Aydınkal, RM., Sercinoglu, O., Ozbek, P.,
ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism, Nucleic Acids Research, gky390, Web Server Issue 2019. doi: 10.1093/nar/gkz390
Research Article Bingöl, EN., Sercinoglu, O., Ozbek, P.,
How Do Mutations and Allosteric Inhibitors Modulate Caspase-7 Activity? A Molecular Dynamics Study, Journal of Biomolecular Structure and Dynamics, just accepted, doi: 10.1080/07391102.2018.1517611
Research Article Sercinoglu, O., Ozbek, P.,
gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations, Nucleic Acids Research, gky381, Web Server Issue 2018. doi: 10.1093/nar/gky381
Research Article Sercinoglu, O., Ozbek, P.,
HLA Proteinlerinin GNM Metodu ile Dinamik Karakterizasyonu, Dokuz Eylül Üniversitesi Fen Bilimleri ve Mühendislik Dergisi, 2018, 20(59), 376-399. doi: 10.21205/deufmd. 2018205931
Poster presentation Sercinoglu, O., Ozbek, P.,
A Software Tool for Parallel Computation and Characterization of Residue Interaction Energies from Molecular Dynamics Simulations, ChemViaComp Symposium, Boğaziçi University, İstanbul, Turkey, 30 October 2017.
Short talk and Poster presentation Sercinoglu, O., Ozbek, P.,
Steered Molecular Dynamics Simulation for Efficient Ranking of MHC Class I Peptide Ligands, 5th BAU Drug Design Congress, İstanbul, Turkey, 19-21 October 2017.
Poster presentation Sercinoglu, O., Ozbek, P.,
Allelic dependence of MHC I stability on peptide termini contacts in MD simulations
11th EBSA Congress, Edinburgh, Scotland, UK, 16-20 July 2017.
Poster presentation Bunsuz, A.Sercinoglu, O., Ozbek, P.,
Investigation of Peptide Binding Affinity and Thermal Stability of Human Leukocyte Antigens (HLAs).
11th EBSA Congress, Edinburgh, Scotland, UK, 16-20 July 2017.
Research article Sercinoglu, O., Ozbek, P.,
Computational characterization of residue couplings and micropolymorphism-induced changes in the dynamics of two differentially disease-associated human MHC class-I alleles.Journal of Biomolecular Structure and Dynamics, 2017, 36:3, 724-740. doi:10.1080/07391102.2017.1295884
Poster presentation Bunsuz, A.Sercinoglu, O., Ozbek, P.,
Investigation of Peptide Binding Affinity and Complex Stability of Human Leukocyte Antigens (HLAs).
4th International BAU-Drug Design Congress, İstanbul, Turkey, 12-15 October 2016.
Poster presentation Bingöl, EN.Sercinoglu, O., Ozbek, P.,
Searching a communication pathway between allosteric site and binding region in effector caspase molecules
4th International BAU-Drug Design Congress, İstanbul, Turkey, 12-15 October 2016.
Poster presentation Sercinoglu, O., Ozbek, P.,
Allelic modulation of global dynamics of HLA-B*27:05 and HLA-B*27:09 molecules
13th Greta Pifat Mrzljak International Biophysics School, September 1-10 2016, Croatia
Poster presentation Bunsuz, A.Sercinoglu, O., Ozbek, P.,
HLA-B*44 Alellerinin Peptid Bağlanma Davranış Mekanizmalarının Hesaplamalı Olarak araştırılması
Biruni Üniversitesi Bilgisayar Destekli İlaç Tasarımı, İstanbul, Türkiye, 16-17 Mayıs 2016.
Research article Sercinoglu, O., Ozcan, G., Kutlu-Kabaş, Z., Ozbek, P.,
A computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis. Journal of Computer-Aided Molecular Design, 30(7), 569-581.doi:10.1007/s10822-016-9934-z
Poster presentation Bingöl, EN.Sercinoglu, O., Ozbek, P.,
Investigating Dynamics of HLA Molecules By Energy Dissipation
60th Biophysical Society Meeting, Los Angeles, USA, February 27-March 2, 2016.
Poster presentation Sercinoglu, O., Ozbek, P.,
Peptide-dependent Binding Stabilization Effect of β-2-microglobulin on HLA-B27 Alleles: A Computational Study
EBSA 2015 10th European Biophysics Congress, Dresden, Germany, July 18-22, 2015.
Poster presentation Ozcan, G., Kutlu Kabas, Z., Sercinoglu, O., Ozbek, P.,
Computational Study on the Effect of pH on the Binding Behaviour of HLA-B Alleles
EBSA 2015 10th European Biophysics Congress, Dresden, Germany, July 18-22, 2015.
Poster presentation Ozcan, G., Kutlu Kabas, Z., Sercinoglu, O., Ozbek, P.,
Binding Behaviour of HLA-B Alleles Related to Ankylosing Spondylitis (AS) Disease: A Comparative Study by Computational Methods
ECCB '14 13th European Conference on Computational Biology, Strasbourg, France, September 7-10, 2014.
Poster presentation Kutlu Kabas, Z., Ozcan, G., Sercinoglu, O., Ozbek, P.,
Computational Study on the Effect of pH on the Binding Behaviour of HLA-B Alleles
ECCB '14 13th European Conference on Computational Biology, Strasbourg, France, September 7-10, 2014.
Poster presentation Sercinoglu, O., Ozcan, G., Ozbek, P.,
Computational Investigation of the Energy Exchange Pathways in Peptide-loaded Major Histocompatibility Complex Proteins
Biophysical Society Thematic Meeting: Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations, Istanbul, Turkey, September 10-14, 2014.
Poster presentation Ozcan, G., Sercinoglu, O., Kutlu Kabas, Z., Ozbek P.
Comparison of the Binding Behavior of HLA-B Alleles Related to Ankylosing Spondylitis Disease by Computational Methods
Biophysical Society Thematic Meeting: Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations, Istanbul, Turkey, September 10-14, 2014.
Poster presentation Sercinoglu, O. Ozbek, P.
An Investigation of the Effects of Model Simplification and Water Box Shell Size on the Molecular Dynamics Simulations of Peptide-loaded Major Histocompatibility Complex Proteins
Biophysical Society Thematic Meeting: Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations, Istanbul, Turkey, September 10-14, 2014
Oral presentation Studying intramolecular energy exchange in human Major Histocompatibility Complex Proteins
Workshop and Summer School on Protein Structure, Function and Dynamics, Manavgat, Turkey, September 14-19, 2014
Meeting participation 2nd International BAU-Drug Design Symposium, Bahcesehir University, Istanbul, Turkey, April 17-19, 2014.
Meeting abstract Sercinoglu, O., Platas Barradas, O., Sandig, V., Zeng, A.-P., & Pörtner, R. (2011).
DoE of fed-batch processes – model-based design and experimental evaluation. BMC Proceedings, 5(Suppl 8), P46. doi:10.1186/1753-6561-5-S8-P46

Academic & Research Experience


Assistant Professor
2020 - present

Gebze Technical University, Faculty of Engineering, Department of Bioengineering, Gebze, Kocaeli, Turkey

Assistant Professor
2019 - 2020

Recep Tayyip Erdogan University, Faculty of Engineering, Department of Bioengineering, Rize, Turkey

Researcher
2016 - 2018

Marmara University Research Fund Project FEN-A-100616-0273, Moleküler Dinamik Simülasyon Bazlı Sarsım Yöntemi ile Protein İçi Sinyal İletim Mekanizmasının Karakterizasyonu

Researcher
2015 - 2018

Marmara University Research Fund Project FEN-C-DRP-110915-0436, Computational Dynamical Characterization of Human Major Histocompatibility Complex Proteins

Researcher
2013 - 2015

TÜBİTAK Project 113M93, Dynamic Characterization of HLA Molecules

Research Assistant
since 2013

Marmara University, İstanbul, Turkey
Department of Bioengineering

Teaching Assistant
since 2013

Marmara University, İstanbul, Turkey
Department of Bioengineering

Laboratory courses assisted:

  • BIOE 1011.1: General Biology for Bioengineers Laboratory
  • CHEM 213: Biochemistry for Bioengineers I
  • CHEM 214: Biochemistry for Bioengineers II
  • BIOE 311: Bioengineering Laboratory I
  • BIOE 312: Bioengineering Laboratory II

Problem-solving sessions:

  • BIOE 262: Mathematical Applications in Bioengineering Systems
  • BIOE 324: Biotransport Phenomena

Trainee
July - October 2006

Umweltforschungzentrum, Leipzig, Germany
Department of Environmental Microbiology

Skills


Programming

MATLAB (advanced), Python (advanced), R (intermediate), C (beginner), Javascript (beginner)

Software

VMD, NAMD, Gromacs, ProDy, Autodock and Autodock Vina, Rosetta Suite

Dry Laboratory Skills

Scientific Programming, Molecular Dynamics Simulations, Molecular Docking Simulations

Wet Laboratory Skills

Microbiological methods, light microscopy, mammalian cell culture, bioprocess engineering (bioreactors), analytical & separation methods (standart spectroscopy analyses, HPLC, GC/MS, Column Chromatography, TLC, Solid-phase microextraction), molecular biology methods (gel electrophoresis, PCR, FISH & DGGE)

Languages

Turkish (native), English (proficient), German (proficient)

Awards


Scholarship
2008 - 2011

TEV/DAAD Joint Scholarship for Masters Studies in Germany

Intership
2006

IAESTE Internship Award

MOOC Accomplishments


Coursera

Introduction to Genomic Technologies
Genomic Data Science with Galaxy
Python for Genomic Data Science
Command Line Tools for Genomic Data Science
Experimentation for Improvement
Bioinformatics: Life Sciences on Your Computer
The Data Scientist's Toolbox
Introduction to Genomic Technologies
The Arduino Platform and C Programming