11062b_07c9f021ca654ce5ada434b21a67e1e9~

Publications

Karagöl A, Karagöl T. (2025) Reverse-QTY Re-design of Truncated Isoforms for Glutamate Transporter Bioassembly Inhibition (in prep)

Karagöl A, Karagöl T. (2025) Alternative Splicing Generates Isoforms that Inhibit Vesicular Polyamine Transporter Homodimerization (to be submitted)

Karagöl A, Karagöl T. (2025) Graphiet and Seqiet: A cross-platform mobile pipeline for visualizing and analysing biological data (to be submitted)

Karagöl A, Karagöl T. (2025) Acrylonitrile Pre-membrane Self-Assembly in Liquid Methane Under Titan-like Cryogenic Dynamics (to be submitted)

Karagöl A, Karagöl T. (2025)Integration of Fokker-Planck Dynamics and Bayesian Deep Learning for Enhanced Brain Tumor Classification Journal of Neuro-Oncology. (submitted)

Karagöl A, Karagöl T. (2025) pI as a Potential Factor Influencing Evolutionary Residue Selection and Structural Stability Among Junctional Adhesion Molecules Heredity. (submitted) https://doi.org/10.1101/2025.10.12.681872

Karagöl A, Karagöl T. (2025) Computational Design of Lipid-soluble ApoE N-terminal Segment Using Reverse-QTY Code (full manuscript to be submitted after conference embargo). Society of Neuroscience 2025

Karagöl A, Karagöl T. (2025). Cross-Reactivity Between Truncated EAA2 Isoforms and Canonical EAA1 Revealed Through Atomistic Molecular Dynamics in Lipid Bilayer System. Molecular Neurobiology. (submitted)

Karagöl A, Karagöl T. (2025). Splice Isoform Induced Selective Inhibition of Vesicular Monoamine Transporter Canonical Assembly Revealed by Multi-level Combinatorial Analysis Journal of Neural Transmission.(submitted) https://doi.org/10.1101/2025.11.29.691296

Karagöl A, Karagöl T. Zhang S. (2025). Hetero-oligomiration of Odorant Receptor GPCRs with truncated splice isoforms. (in prep)

Karagöl A, Karagöl T. (2025). Truncated-Isoform Interference in Serotonin and Dopamine Transporter Oligomerization Exposed by Million-Atom Tetrameric Simulations Pharmaceutical Research. (to be submitted)

Karagöl A, Karagöl T. Perkins SJ. (2025) Alternative Splicing Induced Mutational Bypass of FactorIX Modulates Peptide Binding Stability: A Combinatorial Multi-Omics Study (to be submitted this month)

Karagöl A, Karagöl T. (2025) A Conserved Motif as an Evolutionary Kernel for β-Sheet Oligomerization Revealed by Divergence Analysis of Helix-to-Sheet Transitions in EAA1 Isoforms Journal of Molecular Evolution (Under review) https://doi.org/10.1101/2025.10.02.679742

Karagöl A, Karagöl T. (2025). What Do Membrane Proteins Really Want?. Springer Nature Behind the Paper https://go.nature.com/3KnbhdB

Karagöl A, Karagöl T. (2025) Helix-to-Beta-Sheet Transition Drives Self-Assembly of Glutamate Transporter EAA1 Splice Peptides Molecular Neurobiology (Under review) https://doi.org/10.1101/2025.08.13.670123

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 European Biophysics Journal (Under review) https://doi.org/10.1101/2025.03.03.641025

Karagöl A, Karagöl T. (2025) Cross-Reactivity of Glutamate Transporter EAAT1 and Truncated EAAT2 Isoforms Revealed via Structural Neuroinformatics European Journal of Neurology Special Issue https://doi.org/10.1111/ene.70191

Karagöl A, Karagöl T. (2024) Regulation of Immune Activation and Inflammatory Response with STING Truncated Isoform for The Treatment of Autoimmune Diseases and Inflammation. The early publication request has been approved. Patent application No: 2024/018993.

Karagöl A, Karagöl T. (2024) Method for Designing Ph-Specific Proteins Using Evolutionary Informed Sequential Single Base Substitutions. The early publication request has been approved. Patent application No: 2024/018998.

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. The early publication request has been approved. Patent application No: 2024/018735.

Karagöl A, Karagöl T. (2025) Water-Soluble QTY Variant of the Gamma-Secretase Complex Provides Insights into Amyloid Precursor Protein Recognition European Journal of Neurology Special Issue https://doi.org/10.1111/ene.70191

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)

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

https://doi.org/10.1007/s11095-024-03769-0

Karagol, A., & Karagol, T. (2024). Benchmarking GROMACS on Optimized Google Colab Processors and the Flexibility of Cloud Computing for Molecular Dynamics. Journal of Molecular Modelling. (Submitted) https://doi.org/10.1101/2024.11.14.623563

Karagöl A, Karagöl T. (2025) Directional Variant Tension (Tᵥ): A Causal Framework for Quantifying Substitution Asymmetry (to be submitted)

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 PMID: 40993375 https://doi.org/10.1007/s00239-025-10262-8

Karagöl A, Karagöl T. Perkins SJ. (2025) Kernel Regression and Stochastic Dominance Analysis Unveil Asymetric Residue-wise Evolutionary Dynamics of Coagulation Factors F9 European Journal of Human Genetics Special Issue https://www.nature.com/articles/s41431-025-01935-5

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

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 https://doi.org/10.1080/08927022.2025.2562932

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 (accepted with revision)

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. Integrative Biology (Under Review) https://doi.org/10.1101/2025.02.28.640895

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 (Revision Under review)

Karagol, A., & Karagol, T. (2024). An Evolutionary Statistics Toolkit for Simplified Sequence Analysis on Web with Client-Side Processing. Biochemical Genetics (submitted) https://doi.org/10.1101/2024.08.01.606148

https://doi.org/10.1007/s11095-024-03769-0

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

https://doi.org/10.1007/s11095-024-03786-z

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

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)

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)

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

https://doi.org/10.1371/journal.pone.0289644

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].

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

Karagöl Alper, Karagöl Taner (2025). Integration of Fokker-Planck Dynamics and Bayesian Deep Learning for Enhanced Brain Tumor Classification and Uncertainty Quantification. (Presenter) AI for Discovery and Research Automation Conference, organized by Nature Machine Intelligence

Karagöl Alper, Karagöl Taner, Li Mengke, Zhang Shuguang (2025). Computational Data Driven Methods In Discovery Of Native Neurological Transporter Modulators. (Speaker) AI for Discovery and Research Automation Conference, organized by Nature Machine Intelligence

Karagöl Alper, Karagöl Taner (2025). Variant Dynamics of the Molecular Environment. (Speaker) Sixth International Conference on Proteins and Peptides, Structure, Function, and Biotechnology, co-organized by Menicon, MIT, and the University of Geneva, Geneva, Switzerland

Karagöl Alper Lecture Title: Biological Machines in Molecular Nanotechnology BORASTEM’25 Festival at Marmara University, Istanbul. Public Engagement of Science - (Distinguished Speaker)

Karagöl Alper Speaker Neuroscience Conference Experiences 10 July 2025 R&D and Innovation Supreme Coordination Office, Istanbul University, Turkey

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

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

Karagöl Alper, Karagöl Taner (2025). Karagöl Alper, Karagöl Taner. Computational design of lipid-soluble ApoE N-terminal segment using reverse-QTY code. Neuroscience 2025 (SfN Annual Meeting). San Diago, USA. Late-breaking

Karagöl Alper, Karagöl Taner (2025). Karagöl Alper, Karagöl Taner. Helix-to-β-Sheet Transitions in Glutamate Transporter EAA1 Splice Isoforms Drive Oligomeric Self-Assemblies and Reveal Conserved Evolutionary Motifs. Neuroscience 2025 (SfN Annual Meeting). San Diago, USA. Late-breaking

Karagöl Alper Karagöl Taner (2025). Multi-Level Comparative Genomic Analysis Reveals Functional Influence of Truncated Isoforms in Glutamate Transporter Genes. Sixth International Conference on Proteins and Peptides, Structure, Function, and Biotechnology, co-organized by Menicon, MIT, and the University of Geneva, Geneva, Switzerland (Poster)

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 (Poster) 2025 European Human Genetics Conference organized by the European Society of Human Genetics (ESHG). Milan, Italy.

Karagöl Alper, Karagöl Taner, Spencer H., Perkins S.J. (2025) A genomic and structural analysis provides enhanced insights into molecular mechanisms of hemophilia B. (Poster) 2025 European Human Genetics Conference organized by the European Society of Human Genetics (ESHG). Milan, Italy.

Karagöl Alper, Karagöl Taner, Shuguang Zhang (2025). Structural Bioinformatic Studies of Synaptic Vesicle Proteins with Their Alphafold3 Predicted Water-Soluble QTY Variants and Uncovering the T<=>V Co-Evolution - The 2nd Lund Spring Symposium: Enabling Novel Therapeutic Principles. Lund University, Sweden (Poster presentation)

Karagöl Alper, Karagöl Taner, Shuguang Zhang (2025). Multi-Level Comparative Genomic Analysis Reveals Functional Influence of Truncated Isoforms in Glutamate Transporter Genes The 2nd Lund Spring Symposium: Enabling Novel Therapeutic Principles. Lund University, Sweden (Poster presentation)

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

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

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

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

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

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.

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

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

Educational Presentations on Endocrinology and Open Science (2020-2024), Istanbul University Student Scientific Research Club.

https://www.alperkaragol.com/resources

Softwares and Projects

Factor IX Variant Database: Genetic variants in the human coagulation factor 9 as a service for clinicians and biochemists. Perkins S.J, Karagöl T., Karagöl A., Spencer H. (2025, soon be available) © Copyright 2003-2024, Structural Immunology Group, University College London (2003- 2024)

KernelNodes (2024, in prep)

A web-based program to identify evolutionary node networks of proteins, for causal mutational pathways and functional domain screening.

https://www.alperkaragol.com/

Molecular Dynamics on Cloud Computing (2024)

https://www.tanerkaragol.com/post/molecular-dynamics-on-google-compute-engine-aws-amazon-web-services-and-other-cloud-computing-se

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

https://www.alperkaragol.com/toolkitdocu

Stroke Detection from CT Images for Hackhaton. Karagöl A, Yılmaz ME, Karagöl T. Aerospace and Technology Festival, Artificial Intelligence in Healthcare Compatiton

https://www.alperkaragol.com/ctstrokedetection

Phyton - BASIC scripts for analyzing QTY-variants to increase solubility. (2023-2024)

https://github.com/karagol-alper

Pymol scripts for variation analysis (2023-2024)

https://github.com/karagol-alper

Pleese see my Github account for more information:

https://github.com/karagol-alper

Honours and Awards

▪ Dean’s Award for Scientific Excellence 2025, Istanbul University. This recognition is reserved for top-performing students who have demonstrated outstanding research achievements during medical training. Issued for my work on "Developing New Therapeutic Strategies Targeting the Molecular Architecture of Neuronal Transporters”.

▪ Ministry of Industry and Technology, Turkish Patent Office PatentleTürkiye Grants awarded for my patents: "Method for Designing Ph-Specific Proteins Using Evolutionary Informed Sequential Single Base Substitutions.", "Regulation of Immune Activation and Inflammatory Response with STING Truncated Isoform for The Treatment of Autoimmune Diseases and Inflammation.", "Inhibition of Snare Complex Formation and VAMP2 Dimerization by The VAMP2 Truncated Isoform, Targeting Pain Management, Neuromuscular Blockade, and Synaptic Modulation. "

▪The European Academy of Neurology (2025) - Congress Bursary Awarded to my work titled "Water-Soluble QTY Variant of the Gamma-Secretase Complex Provides Insights into Amyloid Precursor Protein Recognition".

▪ Scientific and Technological Research Council of Turkey Scientist Support Programs Scholar- 2205 Award (2018 -2025) for "Turkish Citizens who received medals in the National Science Olympiads, and the International Science Olympiads

To reveal their creative and investigative aspects,

To ensure their development of scientific thinking and research skills and to train them as scientists of the future."

Granted Scholarship for 7 years

▪Erich Frank Scholarship – Erich-Frank-Gesellschaft, Universität München, Germany (2022).
Awarded in recognition of academic merit, to conduct an internship in Germany. The award named after Prof. Dr. med. Ephraim (Erich) Frank (1884–1957), a physician who modernised internal medicine in Istanbul. (not attended the internship, pursued another opportunity).

▪Scientific and Technological Research Council of Turkey 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

▪ Istanbul Medical Faculty Doctor of Medicine Acceptance Honor (2018) English Program, settled with honors for "having the highest national score among accepted"- 1st place🥇

▪ BAYER - Turkey High School Science Projects Competition Jan 2017: Certificate of Achievement "In silico macromolecule design and competition analysis for treatment of multiple sclerosis. "

▪ National Higher Education Institutions Exam (YKS) 2018 - top 350 out of 2,381,090 (in 0.015%)

▪ Several Undergraduate Educational Scholarships 2018 – 2023

▪ Scientific and Technological Research Council of Turkey 25th Biology Olympiad Jan 2018: National Medalist - Bronze Medal🏅

▪ Scientific and Technological Research Council of Turkey 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