Tandac Furkan Guclu

Postdoctoral Researcher at Sabancı University

Resume

Tandac Furkan Guclu

Sabanci University
Orta Mahalle, 34956 Tuzla – Istanbul/Turkey
tguclu@sabanciuniv.edu
Personal Website, ORCID, Google Scholar

Education

  • PhD, Molecular Biology, Genetics and Bioengineering
    Sabanci University, Istanbul, Turkey (2015 – 2021)
    Thesis: Molecular Level Understanding of the Functionality of PDZ3 Variants via Advanced All-Atom Simulations and Dynamic Residue Network Analyses
    Advisors: Dr. Canan Atilgan, Dr. Ali Rana Atilgan

  • MSc, Bioengineering
    Marmara University, Istanbul, Turkey (2013 – 2015)
    Thesis: Structural Dynamics of von Hippel-Lindau Tumor Suppressor Protein
    Advisor: Dr. Asuman Nevra Ozer

  • BSc, Biology
    Hacettepe University, Istanbul, Turkey (2007 – 2013)

Work Experience

  • Postdoctoral researcher, Sabanci University, Istanbul, Turkey (2021 – present)
    • Researcher at EuroCC4SEE (2024 – present)
    • Researcher at EuroCC2 project (2023 – 2024)
    • Researcher at EuroCC project (2022 – 2023)
    • Online open lecture: Molecular Dynamics Simulations of Small Molecules (View on Website)
    • Co-lecturer of Computational Techniques for Materials at the Nano-scale (MAT 306), two semesters
    • Undergraduate projects (Program for Undergraduate Research (PURE)):
      • Visual Assessment of AlphaFold2-Predicted Possible Transcytosis Protein Structures (with Dr. Nur Mustafaoğlu)
      • DeepMind vs. Academia: How good are the best AI models in discriminating similar sequences of a given protein? (with Dr. Canan Atilgan)
    • Graduation project (ENS491 – ENS492):
      • Temporal hydrogen-bond networks in proteins (with Dr. Ali Rana Atilgan)
  • Lecturer for School of Molecular and Theoretical Biology (2024 July – August)
    • Organized at Sabanci University, Turkey
    • Taught high school and undergraduate students from various countries
    • Delivered a six-week-long course titled “Exploring GB1 Protein Dynamics: A Graph Theoretical Perspective”
  • Lecturer, Kadir Has University, Istanbul, Turkey (2024 Spring Semester)
    • Molecular Biology and Genetics, project-based education
    • Protein Modeling and Simulation, project-based education
  • Short-term Visiting Scholar at Pennsylvania State University, University Park, PA, USA (2024 January)
    • Collaboration with Dr. Melik C. Demirel
    • Predicting the materials properties of tandem repeat proteins
  • Short-term Visiting Scholar at University of Texas Southwestern, Dallas, TX, USA (2023 February)
    • Collaboration with Dr. Erdal Toprak
    • Drug design and bioinformatics analyses of bacteria drug resistance pathways
  • Teaching Assistant, Sabanci University, Istanbul, Turkey (2015 – 2021)
    • Science of Nature (NS 101), seven semesters
    • Introduction to Bioinformatics (BIO 310), two semesters
    • Computational Biology (ENS 210), one semester
    • Computational Approaches to Problem Solving (IF 100), one semester
    • Fundamentals of Nanoscience (NS 218), one semester
    • Computational Techniques for Materials at the Nano-scale (MAT 306), one semester

Skills

  • Languages: English (Proficient, YDS: 85)
  • Programming:
    • Python (Advanced) – scipy, numpy, scikit-learn, matplotlib, networkx
    • Tcl (Advanced)
    • Advanced knowledge of Linux distributions
    • Bash scripting (Intermediate)
    • MATLAB (Intermediate)
    • Julia (Basic)
    • R (Basic)

Papers

  • Guclu T.F., Tayhan B., Cetin E., Atilgan A.R., Atilgan C., High Throughput Mutational Scanning of a Protein via Alchemistry on a High-Performance Computing Resource. Concurrency and Computation: Practice and Experience, 2025, 37, e8371. https://doi.org/10.1002/cpe.8371 – Research Article (Published). (Corresponding Author)

  • Guclu T.F., Atilgan A.R., Atilgan C., Deciphering GB1’s Single Mutational Landscape: Insights from MuMi Analysis. The Journal of Physical Chemistry B, 2024, 128 (33), 7987-7996. https://doi.org/10.1021/acs.jpcb.4c04916 – Research Article (Published). (Corresponding Author)

  • Kantarcioglu I., Gaszek I.K., Guclu T.F., Yildiz M.S., Atilgan A.R., Toprak E., Atilgan C., Structural shifts in TolC facilitate Efflux-Mediated β-lactam resistance. Communications Biology, 2024, 7, 1051. https://doi.org/10.1038/s42003-024-06750-0 – Research Article (Published).

  • Cetin E., Guclu T.F., Kantarcioglu I., Gaszek I.K., Toprak E., Atilgan A.R., Dedeoglu B., Atilgan C., Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR. Journal of Chemical Information and Modeling, 2023, 63 (15), 4839-4849. https://doi.org/10.1021/acs.jcim.3c00818 – Research Article (Published).

  • Guclu T.F., Atilgan A.R., Atilgan C., Dynamic Community Composition Unravels Allosteric Communication in PDZ3. The Journal of Physical Chemistry B, 2021, 125 (9), 2266-2276. https://doi.org/10.1021/acs.jpcb.0c11604 – Research Article (Published).

  • Guclu T.F., Kocatug N., Atilgan A.R., Atilgan C., N-Terminus of the Third PDZ Domain of PSD-95 Orchestrates Allosteric Communication for Selective Ligand Binding. Journal of Chemical Information and Modeling, 2021, 61 (1), 347-357. https://doi.org/10.1021/acs.jcim.0c01079 – Research Article (Published).

Current Projects

  • Mutational analysis of dihydrofolate reductase using free energy perturbation simulations to explain antibiotic resistance en masse, pilot access applications for MareNostrum 5 Supercomputer (640,000 core hours approximately 80,000 EUR worth) – role: PI; researchers: Dr. Ali Rana Atilgan and Dr. Canan Atilgan (2024 – present)

  • Predicting the materials properties of tandem repeat proteins – in collaboration with Dr. Melik C. Demirel (2024 – present)

  • High throughput mutational scanning of dihydrofolate reductase via in-silico alchemistry – in collaboration with Dr. Erdal Toprak, Dr. Ali Rana Atilgan and Dr. Canan Atilgan (2023 – present)

TUBITAK Projects

  • “Fonksiyonel Proteinlerin Dinamik Konformasyon Uzaylarında Tam Navigasyon Sağlayan Bütünleştirici Hesaplama Modeli”, 122F149, 1001 - Araştırma – Postdoctoral scholarship (2024 – present)

  • “Beyne İlaç Taşımak İçin Beyin Kılcal Damarlarında Bulunan Transitoz Proteinlerinin Hesaplamalı ve Deneysel Yöntemlerle Belirlenmesi”, 122S347, 1001 - Araştırma – Researcher (2022 – present)

  • “Supramoleküler Simetri Gösteren Nanoskopik Yapıların Sınıflandırılması”, 117F389, 1001 - Araştırma – PhD student scholarship (2018 – 2021)

  • “Katlanmış Proteinlerin Serbest Enerji Yüzeylerinin ‘Hesaplamalı Kuvvet Mikroskopisi’ Ile Haritalanması”, 116F229, 1001 - Araştırma – PhD student scholarship (2017 – 2018)

  • “Hücre İçinde Demir Taşıyan Proteinlerde Demir Bağlama-Bırakma Dinamiğinin Hesaplamalı ve Deneysel Yöntemlerle İncelenmesi”, 113Z408, Uluslararası – PhD student scholarship (2015 – 2016)

Training

  • Bilkent University Machine Learning Summer School (2020)
  • Koç University Machine Learning Summer School (2019)
  • Boğaziçi University Machine Learning Summer School (2018)
  • Workshop on Quantitative Evolutionary Biology (2016)

References

  • Canan Atilgan – Professor, thesis advisor
    Faculty of Engineering and Natural Sciences
    Sabanci University, Tuzla 34956, Istanbul, Turkey
    canan@sabanciuniv.edu
    +90 (216) 483 9523

  • Ali Rana Atilgan – Professor, thesis co-advisor
    Faculty of Engineering and Natural Sciences
    Sabanci University, Tuzla 34956, Istanbul, Turkey
    atilgan@sabanciuniv.edu
    +90 (216) 483 9525

  • Melik C. Demirel – Professor, colleague in Tandem Repeat project
    Huck Chair in Biomimetic Materials, Pearce Professor of Engineering
    The Pennsylvania State University, PA, USA
    mcd18@psu.edu
    814-863-2270

  • Ogün Adebali – Associate professor, PhD thesis jury member, researcher in Tubitak project (122S347)
    Faculty of Engineering and Natural Sciences
    Sabanci University, Tuzla 34956, Istanbul, Turkey
    oadebali@sabanciuniv.edu
    +90 (216) 483 7043

  • Nur Mustafaoğlu – Assistant professor, supervisor in Tubitak project (122S347)
    Faculty of Engineering and Natural Sciences
    Sabanci University, Tuzla 34956, Istanbul, Turkey
    nur.mustafaoglu@sabanciuniv.edu
    +90 (216) 483 9962

  • Kamer Kaya – Associate Professor, colleague in EuroCC project
    Faculty of Engineering and Natural Sciences
    Sabanci University, Tuzla 34956, Istanbul, Turkey
    kamer.kaya@sabanciuniv.edu
    +90 (216) 483 9566

  • Fyodor Kondrashov – Professor, reference for lecturing at School of Molecular and Theoretical Biology
    Okinawa Institute of Science and Technology
    1919-1 Tancha, Onna-son, Kunigami-gun
    Okinawa, Japan 904-0495
    fyodor.kondrashov@oist.jp
    (+81) 98-966-2184

  • Demet Akten – Professor, reference for lecturing at Kadir Has University
    Molecular Biology and Genetics Department
    Kadir Has University, Istanbul, Turkey
    demet.akten@khas.edu.tr
    +90 (212) 533 6532

  • Özge Şensoy – Associate professor, progress/PhD thesis jury member, colleague
    Istanbul Medipol University
    Kavacik Mah., Ekinciler Cad., No:19
    Beykoz, 34810, Istanbul
    osensoy@medipol.edu.tr
    +90 (216) 681 5621