Publications, Patents and Invention Disclosures
27
Karagöl A, Karagöl T. (2025) Molecular Behaviour of Beta-Sheet Self Assemblies from Helical Splice Isoforms of the Glutamate Transporter EAA1 (in prep)
26
Karagöl A, Karagöl T. (2025) pH-Dependent Membrane Binding Specificity of Synaptogyrins 1-3 with Distinct Isoelectric Points (pI) Identified by Structural Bioinformatics and Molecular Dynamics Journal of Biochemistry (Submitted) https://doi.org/10.1101/2025.03.03.641025
25
Karagöl A, Karagöl T. (2025) Cross-Reactivity of Glutamate Transporter EAAT1 and Truncated EAAT2 Isoforms Revealed via Structural Neuroinformatics (EAN- Accepted) https://www.ean.org/congress2025
24
Karagöl A, Karagöl T. (2024) Regulation of Immune Activation and Inflammatory Response with STING Truncated Isoform for The Treatment of Autoimmune Diseases and Inflammation. Patent application No: 2024/018993. The early publication request has been approved.
23
Karagöl A, Karagöl T. (2024) Method for Designing Ph-Specific Proteins Using Evolutionary Informed Sequential Single Base Substitutions. Patent application No: 2024/018998.
22
Karagöl A, Karagöl T. (2024) Inhibition of Snare Complex Formation and VAMP2 Dimerization by The VAMP2 Truncated Isoform, Targeting Pain Management, Neuromuscular Blockade, and Synaptic Modulation. Patent application No: 2024/018735. The early publication request has been approved.
21
Karagöl A, Karagöl T. (2025) Water-Soluble QTY Variant of the Gamma-Secretase Complex Provides Insights into Amyloid Precursor Protein Recognition (EAN- Accepted) https://www.ean.org/congress2025
20
Karagöl A, Karagöl T. (2025) Lipid Rafts Modulate Pocket Stability and Spermidine Binding in Trace Amine-Associated Receptor 9: Insights from Comparative Molecular Dynamics Simulations (in prep)
19
Karagöl A, Karagöl T. (2025) Water-Soluble QTY Variant of the Gamma-Secretase Complex Provides Insights into Amyloid Precursor Protein Recognition (Submitted to EAN)
18
Karagol, A., & Karagol, T. (2024). Benchmarking GROMACS on Optimized Google Colab Processors and the Flexibility of Cloud Computing for Molecular Dynamics. bioRxiv, 2024-11. https://doi.org/10.1101/2024.11.14.623563
17
Karagöl A, Karagöl T. (2025) Evolutionary Divergence of Helix-to-Sheet Transformation in EAA1 splice homologs (in prep)
16
Karagöl A, Karagöl T, Zhang S. (2024). Co-evolution of Alpha-helical Transmembrane Protein Residues: Large-Scale Variant Profiling and Complete Mutational Landscape of 2277 known RCSB Entries Representing 504 UniProt Sequences. Journal of Molecular Evolution (Revision Under Review)
15
Karagöl A, Karagöl T. Kernel Regression and Stochastic Dominance Analysis Unveil Asymetric Residue-wise Evolutionary Dynamics of Coagulation Factors F9 and F8 (Submitted to EHGC)
14
Johnsson F., Karagöl A, Karagöl T. Zhang S. (2024). Structural bioinformatics studies of olfactory receptors, TAAR9and their AlphaFold3 predicted water-soluble QTY variants and odorant binding. QRB Discovery https://doi.org/10.1017/qrd.2024.18
13
Akash S., Karagöl A, Karagöl T., Zhang S. (2024) Structural bioinformatics of bacterial integral alpha-helical membrane enzymes and their AlphaFold2 predicted water-soluble QTY variants. Molecular Simulation (Revision Under review)
12
Karagöl A., Karagöl T., Zhang S. (2024). Structural bioinformatics and evolutionary studies of synaptic vesicle glycoprotein 2 family members, synaptophysin, synaptogyrins, and their AlphaFold3 predicted water-soluble QTY variants. Journal of Molecular Evolution (Under Review)
11
Karagöl A., Karagöl T., Zhang S. (2024) Adaptation to Solvent Environment in Toll-like Receptor 5: A Comparative Evolutionary Analysis of Membrane-bound and Soluble Forms in Epinephelus coioides. Biological Journal of the Linnean Society (Submitted) https://doi.org/10.1101/2025.02.28.640895
10
Karagöl A., Karagöl T. Zhang S.(2024) Multi-level Comparative Genomic Analysis Reveals Evolutionary Influence of Truncated Isoforms in Glutamate Transporter Genes Journal of Molecular Evolution (Under review)
9
Karagol, A., & Karagol, T. (2024). An Evolutionary Statistics Toolkit for Simplified Sequence Analysis on Web with Client-Side Processing. bioRxiv, 2024-08. doi: https://doi.org/10.1101/2024.08.01.606148
8
Karagöl A., Karagöl T., Zhang S. (2024) Molecular Dynamic simulations reveal that water-soluble QTY-variants of glutamate transporters EAA1-3 retain the conformational characteristics of native transporters. Pharmaceutical Research. PMCID: PMC39322794
7
Karagöl A., Karagöl T., Li M., Zhang S. (2024) Inhibitory effects of the truncated isoforms on glutamate transporter oligomerization revealed by the analysis of gene-centric isoform maps. Pharmaceutical Research
PMID: PMC39487385
6
Karagöl T, Karagöl A. Zhang S. (2024) Structural bioinformatics studies of serotonin, dopamine and norepinephrine transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, I->T, F->Y and Q->L, T->I and Y->F. PLOS ONE
PMCID: PMC10959339
https://doi.org/10.1371/journal.pone.0300340
5
Karagöl et. al. (2023) A genomic and structural analysis provides enhanced insights into molecular mechanisms of hemophilia B. Journal of Thrombosis and Haemostasis. (Under review, Aug 2023)
4
Perkisn S.J, Karagöl T., Karagöl A., Spencer H. (2023) Factor IX Variant Database: Genetic variants in the human coagulation factor 9 as a service for clinicians and biochemists. © Copyright 2003-2023, Structural Immunology Group, University College London (2003- 2023)
3
Alper Karagöl, Taner Karagöl, Eva Smorodina, & Shuguang Zhang. (2022) Structural bioinformatics studies of glutamate transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, V->T, F->Y and vice versa. PLOS ONE.
PMCID: PMC11006163
2
Çetin A., Acar A.C., Karagöl H.A., Gülseren I., Koç M., Ergin O.S., Gürsoy Y.K. (2020). Çıkar Çatışması Kılavuzu [Conflict of Interest Guideline], European Medical Student Association Turkey.
Available at: https://emsa-turkey.org/cikar-catismasi-kilavuzu/ [Accessed 3 Feb. 2023].
1
Karagöl, H.A. and Karagöl, M.T. (2018). Multipl sklerozun olası tedavisi için in silico makromolekül dizaynı ve hesaplamalı analizi. [In silico macromolecule design and computational analysis for possible treatment of multiple sclerosis.], [online] Google Science Fair. Available at: https://www.googlesciencefair.com/projects/2018/db7a23df00c2891d75b5a625e5d9
Publications on Congresses,
Symposium Proceedings Books, and Scientific Events
13
Karagöl Alper, Karagöl Taner, Perkins S.J. (2025) A Kernel Regression and Analysis of Evolutionary Amino Acid Varieties Reveals Extensive Nodes of Coagulation Factor 9 variants in the development of Hemophilia B (Submitted for Presentation-Oral) 2025 European Human Genetics Conference organized by the European Society of Human Genetics (ESHG). Milan, Italy.
12
Karagöl Alper, Karagöl Taner, Spencer H., Perkins S.J. (2025) A genomic and structural analysis provides enhanced insights into molecular mechanisms of hemophilia B. (Submitted for Presentation-Oral) 2025 European Human Genetics Conference organized by the European Society of Human Genetics (ESHG). Milan, Italy.
11
Karagöl Alper, Karagöl Taner (2025). Water-Soluble QTY Variant of the Gamma-Secretase Complex Provides Insights into Amyloid Precursor Protein Recognition. (Presentation-Oral) 11th European Academy of Neurology Annual Congress. Helsinki, Finland. GRANT WINNER
10
Karagöl Alper, Karagöl Taner (2025). Cross-Reactivity of Glutamate Transporter EAAT1 and Truncated EAAT2 Isoforms Revealed via Structural Neuroinformatics (Presentation-Oral) 11th European Academy of Neurology Annual Congress. Helsinki, Finland. GRANT WINNER
9
Karagöl Alper, Karagöl Taner, Shuguang Zhang (2024). Comparative genomic analysis of glutamate transporters reveals the evolutionary landscape and splicing plasticity of truncated isoforms. Poster at the 2024 KSBNS Annual Meeting co-organized by Korean Society for Brain and Neural Sciences and the Asian-Pacific Society for Neurochemistry. Gyeongju, South Korea. FELLOWSHIP WINNER
8
Karagöl Taner, Karagöl Alper, Mengke Li, Shuguang Zhang (2024). Inhibitory effects of the truncated isoforms on glutamate transporter oligomerization revealed by the analysis of gene-centric isoform maps. Poster at the 2024 KSBNS Annual Meeting co-organized by Korean Society for Brain and Neural Sciences and the Asian-Pacific Society for Neurochemistry. Gyeongju, South Korea. FELLOWSHIP WINNER
7
Karagöl Alper, Karagöl Taner, Smorodina Eva, Shuguang Zhang (2024, 1-3 March). Structural studies of glutamate transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural QTY-code mutations. Poster presented at the XXI. International IUGEN Winter School on Molecular biology and Genetics- Istanbul University, Istanbul, Turkey
6
Taner Karagöl, Alper Karagöl, Shuguang Zhang (2024, April). Evolutionary and structural comparison of serotonin, dopamine and norepinephrine transporters and their water-soluble QTY variants. Oral Presentation at the 28th International Medical Sciences Student Congress (IMSSC) -Istanbul University, Istanbul Turkey
5
Karagöl Alper, Karagöl Taner, Smorodina Eva, Shuguang Zhang (2023). Structural bioinformatics studies of glutamate transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, I->T, F->Y and Q->L, T->I and Y->F. Poster presented at the fifth International Conference on Proteins and Peptides, Structure, Function, and Biotechnology, co-organized by Menicon, MIT, and the University of Geneva, Geneva, Switzerland
4
Karagöl, H.A. and Karagöl, M.T. (2018).In silico macromolecule design and computational analysis for possible treatment of multiple sclerosis [Multipl sklerozun olası tedavisi için in silico makromolekül dizaynı ve hesaplamalı analizi]. Attended to Google Science Fair 2018-2019.
3
Karagöl, H.A. and Karagöl, M.T. (2017). In silico macromolecule design and competition analysis for treatment of multiple sclerosis [Multiple Skleroz Hastalığının Olası Tedavisi için in silico Makromolekül Dizaynı ve Hesaplamalı Analizi]. Presentation to BAYER - Turkey Science Projects competition
2
Karagöl, H.A. and Karagöl, M.T. (2017). Multiple Skleroz Hastalığının Araştırılmasında Moleküler Modellemenin Kullanımı [Utilization of molecular modeling in Multiple Sclerosis research], 49th TUBITAK (Scientific and Technological Research Council of Turkey) Research Projects competition. https://www.tubitak.gov.tr/en/competitions/content-2204-a-high-school-students-research-projects-competition
1
Educational Presentations on Endocrinology and Open Science (2020-2024), Istanbul University Student Scientific Research Club.
https://www.alperkaragol.com/resources
Softwares and Projects
5
KernelNodes (2024, in prep)
A web-based program to identify evolutionary node networks of proteins, for causal mutational pathways and functional domain screening.
4
Molecular Dynamics on Cloud Computing (2024)
3
Evolutionary Statistics Toolkit (2024) - live
An Evolutionary Statistics Toolkit for Simplified Sequence Analysis on Web with Client-Side Processing. bioRxiv, 2024-08. doi: https://doi.org/10.1101/2024.08.01.606148
2
Phyton - BASIC scripts for analyzing QTY-variants to increase solubility. (2023-2024)
https://github.com/karagol-alper
Honours and Awards
▪ The European Academy of Neurology (2025) - Congress Bursary
▪TUBITAK Scientist Support Programs - 2224 International Scientific Meetings Fellowship Program (2024) for “presenting proceedings in scientific meetings abroad to share their original studies with the world of science”. - Fellowship
▪ TUBITAK Scientist Support Programs - 2205 Undergraduate Scholarship (2018 -2025) for "Turkish Citizens who received medals in the National Science Olympiads, the International Science Olympiads and the International Project Contest" - Granted Scholarship for 7 years
▪ Istanbul University Istanbul Medical Faculty English Program, settled with honours for "having the highest exam score among accepted"- 1st place🥇
▪ National Higher Education Institutions Exam (YKS) 2018 - top 350 out of 2,381,090 (in 0.015%)
▪ Several Undergraduate Educational Scholarships 2018 – 2023
▪ TUBITAK 25th Biology Olympiad Jan 2018: National Medalist - Bronze Medal🏅
▪ TUBITAK 25th Biology Olympiad 13 May 2017: 2nd place🥈 in the Marmara Region (Including Istanbul and Bursa), sixth in Turkey.
▪ Republic of Turkey Ministry of National Education - 2011 Scholarship exam for primary and secondary education institutions - Educational Scholarship (2012 – 2018) - Educational Scholarship
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