Uluslararası hakemli dergilerde yayımlanan makaleler:

Amarajeewa, A. W. P., Özcan, A., Mukhtiar, A., Ren, X., Wang, Q., Ozbek, P., Garstka, M. A. G., Serçinoğlu, O., "Polymorphism in F pocket affects peptide selection and stability of type 1 diabetes‐associated HLA‐B39 allotypes". Eur. J. Immunol. (2024), DOI: 10.1002/eji.202350683

Işık, E. B., Serçinoğlu, O., "Unraveling the ligand specificity and promiscuity of the Staphylococcus aureus NorA efflux pump: a computational study. J. Biomol. Struct. Dyn. (2024), DOI: 10.1080/07391102.2024.2326670

Kim, Y., Bereketoglu, C.,Serçinoğlu, O., Pradhan, A., "In Vitro, In Vivo, and In Silico Analysis of Pyraclostrobin and Cyprodinil and Their Mixture Reveal New Targets and Signaling Mechanisms". Chem. Res. Toxicol. (2024), DOI: 10.1021/acs.chemrestox.3c00371

Üner, G., Bedir, E., Serçinoğlu, O., Ballar Kırmızıbayrak, P., "Non-apoptotic cell death induction via sapogenin based supramolecular particles". Scientific Reports (2022), DOI: 10.1038/s41598-022-17977-4

Bingöl, E. N., Serçinoğlu, O., Ozbek, P. “Unraveling the Allosteric Communication Mechanisms in T-Cell Receptor–Peptide-Loaded Major Histocompatibility Complex Dynamics Using Molecular Dynamics Simulations: An Approach Based on Dynamic Cross Correlation Maps and Residue Interaction Energy Calculations". J. Chem. Inf. Model. (2021), DOI: 10.1021/acs.jcim.1c00338

Serçinoğlu, O., Bereketoglu, C., Olsson P. E., Pradhan, A. “In silico and in vitro assessment of androgen receptor antagonists”. Comput. Biol. Chem. (2021), DOI: 10.1016/j.compbiolchem.2021.107490

Serçinoğlu, O., Senturk, D., Altinisik Kaya, F. E., Avci, F. G., Frlan, R., Tomašič, T., Ozbek, P., Orelle, C., Jault, JM., Sarıyar Akbulut, B.. “Identification of novel inhibitors of the ABC transporter BmrA”. Bioorganic Chemistry (2020), DOI: 10.1016/j.bioorg.2020.104452

Serçinoğlu, O., Ozbek, P. “Sequence-structure-function relationships in class I MHC: A local frustration perspective”. PLoS One 15, e0232849 (2020), DOI: 10.1371/journal.pone.0232849

Bunsuz, A., Serçinoğlu, O., Ozbek, P., “Computational investigation of peptide binding stabilities of HLA-B*27 and HLA-B*44 alleles”. Comput. Biol. Chem. 84, 107195 (2020). DOI: 10.1016/j.compbiolchem.2019.107195

Aydınkal, R. M., Serçinoğlu, O., Ozbek, P., “ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism”. Nucleic Acids Res. 47, W471–W476 (2019), DOI: 10.1093/nar/gkz390

Bingöl, E. N., Serçinoğlu, O., Ozbek, P., “How do mutations and allosteric inhibitors modulate caspase-7 activity? A molecular dynamics study”. J. Biomol. Struct. Dyn. 37, 3456–3466 (2019), DOI: 10.1080/07391102.2018.1517611

Serçinoǧlu, O., Ozbek, P. “gRINN: A tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations”. Nucleic Acids Res. 46, W554–W562 (2018), DOI: 10.1093/nar/gky381

Serçinoğlu, 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”. J. Biomol. Struct. Dyn. 36, 724–740 (2018), DOI: 10.1080/07391102.2017.1295884

Serçinoğlu, O., Özcan, G., Kabaş, Z. K., Ozbek, P. “A computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis”. J. Comput. Aided. Mol. Des. 30, 569–581 (2016), DOI: 10.1007/s10822-016-9934-z

Uluslararası bilimsel toplantılarda sunulan ve bildiri kitabında basılan bildiriler:

Serçinoğlu O., Bereketoğlu, C., Pradhan, A., “Molecular modeling of pesticide androgen receptor interactions”., 7th International BAU Drug Design Congress, 19-21 Aralık 2019, İstanbul

Özer ME., Özdemir, Hİ., Serçinoğlu, O., Bingöl, EN., Sarica O. P., “A tool for investigating protein signaling network by perturbation of external energy dissipation”. 7th International BAU Drug Design Congress, 19-21 Aralık 2019, İstanbul

Bingöl, EN., Serçinoğlu, O., Ozbek, P., “Comparative dynamical characterization of TCR and MHC molecules upon binding via molecular dynamics simulations, Eurasian Congress on Molecular Biotechnology (ECOMB 2019), 19-21 Eylül 2019, Trabzon

Serçinoğlu, O., Ozbek, P., “Biophysical links between polymorphism, stability and peptide-binding in Major Histocompatibility Complex”, 6th International BAU Drug Design Congress, 13-15 Aralık 2018, İstanbul

Serçinoğlu, O., Sarica O. P., “Biophysical basis of MHC Class I polymorphism”., International conference on applied mathematics, modeling and life sciences (ICAMLS ’18), 3-5 Ekim 2018, İstanbul

Serçinoğlu, O., Ozbek, P., “Quantifying peptide binding affinities from non-equilibrium work”. (2018), Biophysical Journal 114 (3), 234a, DOI: 10.1016/j.bpj.2017.11.1305

Serçinoğlu, O., Sarica O. P., “A software tool for parallel computation and characterization of residue interaction energies from molecular dynamics simulations”. International Symposium on Chemistry via Computational: Applications on Molecular Nanosciences, 30 Ekim 2017, Boğaziçi University, Istanbul

Serçinoğlu, O., Sarica O. P., “Allelic dependence of MHC I stability on peptide termini contacts in MD simulations”. 19th IUPAB Congress and 11th EBSA Congress, 16-20 Temmuz 2017, Edinburgh, Birleşik Krallık

Bunsuz, A., Serçinoğlu, O., Sarica O. P., “Investigation of peptide binding affinity and thermal stability of Human Leukocyte Antigens (HLAs)”. 19th IUPAB Congress and 11th EBSA Congress, 16-20 Temmuz 2017, Edinburgh, Birleşik Krallık

Serçinoğlu, O., Ozbek. P., “Allelic modulation of global Dynamics of HLA-B*27:05 and HLA-B*27:09 molecules”. 13th Greta Pifat Mrzljak International School fof Biophysics, 1-10 Eylül 2016, Hırvatistan

Bingol EN., Serçinoğlu, O., Ozbek, P., “Investigating Dynamics of HLA Molecules by Energy Dissipation”. (2016), Biophysical Journal 110 (3), 381a-382a

Serçinoğlu, O., Ozbek, P., “Peptide-dependent Binding Stabilization Effect of β-2-microglobulin on HLA-B27 Alleles: A Computational Study”. 10th European Biophysics Congress, 18-22 Temmuz 2015, Dresden, Almanya

Serçinoğlu, 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, 10-14 Eylül 2014, İstanbul

Serçinoğlu, 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, 10-14 Eylül 2014, İstanbul

Sercinoglu, O., Platas Barradas, O., Sandig, V., Zeng, A.-P., Pörtner, R. “DoE of fed-batch processes – model-based design and experimental evaluation”. BMC Proc. 5, P46 (2011). DOI: 10.1186/1753-6561-5-S8-P46

Uluslararası kitaplar ve kitaplarda bölümler:

Ulucan-Karnak, F., Yilmaz-Sercinoglu, Z.,Sercinoglu, O., Ali, A. “Computational Approaches Used in Anticancer Plants”. in: Plant-derived Anticancer Drugs in the OMICS Era: Biosynthesis, Function, and Applications (Apple Academic Press, 2024). Hard ISBN: 9781774912652

Serçinoğlu, O., Sarica, P. O. “In Silico Databases and Tools for Drug Repurposing”. in: In Silico Drug Design 703–742 (Academic Press, 2019). doi:10.1016/b978-0-12-816125-8.00024-9

Ulusal hakemli dergilerde yayımlanan makaleler:

Bunsuz, A., Serçinoğlu, O., Sarica O, P., “HLA Moleküllerinde Peptit Ligandlarının Kompleks Stabilitesine Olan Etkisinin Araştırılması”. Marmara Fen Bilimleri Dergisi, 30 (2018) DOI: 10.7240/marufb.368789

Serçinoğlu, O., Sarica O. P., “HLA Proteinlerinin GNM Metodu ile Dinamik Karakterizasyonu”. Dokuz Eylül Üniversitesi Mühendislik Fakültesi Fen ve Mühendislik Dergisi, 20(59), 376-399, DOI: 10.21205/deufmd.2018205931

Go to CourseWeb pages

• BSB 511 Fundamentals of Bioinformatics
• BSB 533 Computational Biomolecular Dynamics
• BSB 685 Current Topics in Structural Bioinformatics
• BENG 211 Mass and Energy Balances
• BENG 451 Introduction to Bioinformatics
• BENG 456 Applications of Cancer Biology in Bioengineering
• BENG 466 Structural Bioinformatics and Computational Drug Design
• BENG 519 Applied Bioinformatics

Devam Eden Yüksek Lisans Tezleri

İlayda Erdoğan, Gebze Teknik Üniversitesi, Fen Bilimleri Enstitüsü, Biyomühendislik ABD, Biyoinformatik ve Sistem Biyolojisi Yüksek Lisans Programı, Danışman

Evren Atak, Gebze Teknik Üniversitesi, Fen Bilimleri Enstitüsü, Biyomühendislik ABD, Biyoinformatik ve Sistem Biyolojisi Yüksek Lisans Programı, Danışman

Tuba Okur, Gebze Teknik Üniversitesi, Fen Bilimleri Enstitüsü, Biyomühendislik ABD, Biyomühendislik Yüksek Lisans Programı, Danışman

Tamamlanan Yüksek Lisans Tezleri

Esra Büşra Işık, Gebze Teknik Üniversitesi, Fen Bilimleri Enstitüsü, Biyomühendislik ABD, Biyoinformatik ve Sistem Biyolojisi Yüksek Lisans Programı, Danışman

Halil İbrahim Özdemir, Marmara Üniversitesi, Fen Bilimleri Enstitüsü, Biyomühendislik ABD, "Development of a software tool for investigation of allosteric communication within protein structures via energy dissipation in molecular dynamics simulations", 2. Danışman

• Third Cycle (Doctoral): Marmara Üniversitesi / Fen Bilimleri Enstitüsü / Biyomühendislik ABD (2018)
• Second Cycle (Master's): Hamburg Teknoloji Üniversitesi / Kimya Mühendisliği / Biyoteknoloji (2011)
• First Cycle (Undergraduate): Ege Üniversitesi / Mühendislik Fakültesi / Biyomühendislik (2008)