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
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PhD in Bioengineering |
Marmara University, İstanbul, Turkey |
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MSc in Biotechnology |
Hamburg University of Technology (TUHH), Hamburg, Germany |
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Exchange Student |
Åbo Akademi, Turku, Finland |
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BSc in Bioengineering |
Ege University, İzmir, Turkey |
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High School |
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
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Assistant Professor |
Gebze Technical University, Faculty of Engineering, Department of Bioengineering, Gebze, Kocaeli, Turkey |
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Assistant Professor |
Recep Tayyip Erdogan University, Faculty of Engineering, Department of Bioengineering, Rize, Turkey |
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Researcher |
Marmara University Research Fund Project FEN-A-100616-0273, Moleküler Dinamik Simülasyon Bazlı Sarsım Yöntemi ile Protein İçi Sinyal İletim Mekanizmasının Karakterizasyonu |
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Researcher |
Marmara University Research Fund Project FEN-C-DRP-110915-0436, Computational Dynamical Characterization of Human Major Histocompatibility Complex Proteins |
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Researcher |
TÜBİTAK Project 113M93, Dynamic Characterization of HLA Molecules |
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Research Assistant |
Marmara University, İstanbul, Turkey |
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Teaching Assistant |
Marmara University, İstanbul, Turkey Laboratory courses assisted:
Problem-solving sessions:
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Trainee |
Umweltforschungzentrum, Leipzig, Germany |
Skills
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Programming |
MATLAB (advanced), Python (advanced), R (intermediate), C (beginner), Javascript (beginner) |
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Software |
VMD, NAMD, Gromacs, ProDy, Autodock and Autodock Vina, Rosetta Suite |
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Dry Laboratory Skills |
Scientific Programming, Molecular Dynamics Simulations, Molecular Docking Simulations |
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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) |
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Languages |
Turkish (native), English (proficient), German (proficient) |
Awards
Scholarship |
TEV/DAAD Joint Scholarship for Masters Studies in Germany |
Intership |
IAESTE Internship Award |
MOOC Accomplishments