Uluslararası hakemli dergilerde yayımlanan makaleler:

Serçinoğlu, O., Eke, T.E., Ozbek, P., "i-gRINN: a next-generation web server for protein energy network analysis of heterogeneous biomolecular systems with natural language-based data exploration". Nucleic Acids Research (2026), DOI: 10.1093/nar/gkag516

Aksu, T.O., Serçinoğlu, O., Aktaş, F., Binay, B., "A novel Amycolatopsis sulphurea L-alanine dehydrogenase with enhanced bidirectional catalysis: Rational design, expression, and biochemical characterization". International Journal of Biological Macromolecules (2026), DOI: 10.1016/j.ijbiomac.2026.150108

Wang, S., Kong, L., Hu, D., Zheng, L., Fei, C., Du, L., Tang, Z., Garstka, M.A., Serçinoğlu, O., Zhang, L., Wang, S., Xu, S., Yang, H., Zhang, N., "Pan-prediction of major histocompatibility complex class II–restricted epitopes across species via an AlphaFold-based quantification scheme". hLife (2026), DOI: 10.1016/j.hlife.2025.10.005

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., "Vibe coding in scientific computing: a bioinformatics case study on LLM reliability and prompt sensitivity", 2nd International Yıldırım Bayezid Scientific Research and Innovation Symposium, 8-9 May 2026, Bursa.

Eke, T.E., Serçinoğlu, O., "Peptitlerin Hla-A Moleküllerinin Dinamik Davranışı Üzerindeki Etkilerinin Hesaplamalı Yöntemler İle Araştırılması", 7th International Istanbul Current Scientific Research Congress, 13-15 February 2026, İstanbul.

Turhal, G., Serçinoğlu, O., Demiroglu-Zergeroglu, A., "Repurposing existing drugs to discover allosteric inhibitors of ERK5", FEBS OPEN BIO, 15:31, 2025.

Şahin Ş., Serçinoğlu, O. "Expanding the scope of target fishing: assessing the performance of AF2 models and consensus docking beyond structurally-validated reference sets", Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2025, July 20-24, Liverpool, United Kingdom.

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:

Atak E., Eke T. E., Serçinoğlu, O. "Computational Prediction of Immune Epitopes". in: Reference Module for Life Sciences (Elsevier, 2025), Encyclopedia of Bioinformatics and Computational Biology, 2nd Ed.). DOI: 10.1016/B978-0-12-809633-8.20074-5

Okur, T., Serçinoğlu, O. "Computational Protein Engineering". in: Reference Module for Life Sciences (Elsevier, 2025) (Encyclopedia of Bioinformatics and Computational Biology, 2nd Ed.). DOI: 10.1016/B978-0-323-95502-7.00261-X

Şahin, Ş., Önel Ö., Kızılay, E. B., Serçinoğlu, O. "Drug Repurposing and Multi-target Therapies". in: Reference Module for Life Sciences (Elsevier, 2025) (Encyclopedia of Bioinformatics and Computational Biology, 2nd Ed.). DOI: 10.1016/B978-0-323-95502-7.00238-4

Serçinoğlu, O., Wezen, X. C., Fatima, A. "Molecular Dynamics Simulations in Drug Discovery". in: Reference Module for Life Sciences (Elsevier, 2025) (Encyclopedia of Bioinformatics and Computational Biology, 2nd Ed.). DOI: 10.1016/B978-0-323-95502-7.00273-6

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:

Serçinoğlu, O., "</span>Understanding allosteric stabilization of pMHC by peptide ligands through molecular dynamics simulations". Turkish Journal of Immunology (2025), 13(3):132-45, DOI: 10.36519/TJI.2025.576</span>

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

Ders Kodu	Ders Adı

Devam Eden Yüksek Lisans Tezleri

Şuara Şahin, Gebze Teknik Üniversitesi, Lisansüstü Eğitimi Enstitüsü, Biyomühendislik ABD, Biyoinformatik ve Sistem Biyolojisi Yüksek Lisans Programı, Danışman

Dilara Önal, Gebze Teknik Üniversitesi, Lisansüstü Eğitim Enstitüsü, Biyomühendislik ABD, Biyoinformatik ve Sistem Biyolojisi Yüksek Lisans Programı, Danışman

Öyküm Önel, Gebze Teknik Üniversitesi, Lisansüstü Eğitim Enstitüsü, Biyomühendislik ABD, Biyoinformatik ve Sistem Biyolojisi Yüksek Lisans Programı, Danışman

Emre Taha Çevik, Gebze Teknik Üniversitesi, Lisansüstü Eğitim Enstitüsü, Biyomühendislik ABD, Biyoinformatik ve Sistem Biyolojisi Yüksek Lisans Programı, Danışman

Tuğba Emine Eke, Gebze Teknik Üniversitesi, Lisansüstü Eğitim Enstitüsü, Biyomühendislik ABD, Biyoinformatik ve Sistem Biyolojisi Yüksek Lisans Programı, Danışman

Alper Tanrıkulu, Gebze Teknik Üniversitesi, Lisansüstü Eğitim Enstitüsü, Biyomühendislik ABD, Biyoinformatik ve Sistem Biyolojisi Yüksek Lisans Programı, </span>Danışman

Tamamlanan Yüksek Lisans Tezleri

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

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

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)