Dr. Öğr. Üyesi ŞEREF GÜL

Yayın Ağı

Makaleler 31

1. **The impact of circadian rhythm disruption on oxaliplatin tolerability and pharmacokinetics in Cry1^-/-Cry2^-/- mice under constant darkness**

AKYEL Y. K., Seyhan N. O., Gul S., Celik M., TAŞKIN A. C., Selby C. P., et al.

ARCHIVES OF TOXICOLOGY , 2025 (SCI-Expanded)

2. A novel smart disinfection system using 3D-printed and electrically conductive composite hydrogel

Khan S. A., Malik A. N., Velioglu B., Gul S., Kavakli I. H., Lazoglu I.

Emergent Materials , cilt.8, sa.2, ss.1171-1182, 2025 (ESCI)

3. Discovering Lassa virus nucleoprotein inhibitors via in silico drug repositioning approach

Şimşek H., Gül Ş.

Journal of Biomolecular Structure and Dynamics , cilt.43, sa.12, ss.6316-6336, 2025 (SCI-Expanded)

4. Dynamic regulation of the serine loop by distant mutations reveals allostery in cryptochrome1

Ozcan O., Gul S., Kavakli I. H.

Journal of Biomolecular Structure and Dynamics , cilt.42, sa.19, ss.10417-10428, 2024 (SCI-Expanded)

5. TW68, cryptochromes stabilizer, regulates fasting blood glucose levels in diabetic ob/ob and high fat-diet-induced obese mice

Surme S., Ergun C., Gul S., AKYEL Y. K., Gul Z. M., Ozcan O., et al.

BIOCHEMICAL PHARMACOLOGY , cilt.218, 2023 (SCI-Expanded) Sürdürülebilir Kalkınma

6. Diurnal Changes in Capecitabine Clock-Controlled Metabolism Enzymes Are Responsible for Its Pharmacokinetics in Male Mice

Akyel Y. K., Ozturk Civelek D., Ozturk Seyhan N., Gul Ş., Gazioglu I., Pala Kara Z., et al.

JOURNAL OF BIOLOGICAL RHYTHMS , cilt.38, sa.2, ss.171-184, 2023 (SCI-Expanded)

7. **Discovery of a small molecule that selectively destabilizes Cryptochrome 1 and enhances life span in p53 knockout mice**

Gul Ş., Akyel Y. K., Gul Z. M., Isin S., Ozcan O., Korkmaz T., et al.

NATURE COMMUNICATIONS , cilt.13, sa.1, 2022 (SCI-Expanded) Sürdürülebilir Kalkınma

8. Analysis of ACE2 and TMPRSS2 coding variants as a risk factor for SARS-CoV-2 from 946 whole-exome sequencing data in the Turkish population

DUMAN N., Tuncel G., BİŞGİN A., TUĞ BOZDOĞAN S., Sag S. O., GÜL Ş., et al.

JOURNAL OF MEDICAL VIROLOGY , cilt.94, sa.11, ss.5225-5243, 2022 (SCI-Expanded) Sürdürülebilir Kalkınma

9. In Silico Analysis of BMAL1 and CLOCK SNPs in the Ensembl Database

Gül Ş.

European Journal of Biology , cilt.81, ss.125-135, 2022 (Hakemli Dergi)

10. The secondary pocket of cryptochrome 2 is important for the regulation of its stability and localization.

Parlak G. C., Camur B. B., Gul Ş., Ozcan O., Baris I., Kavakli I. H.

The Journal of biological chemistry , cilt.298, sa.9, ss.102334, 2022 (SCI-Expanded)

11. Proteome analysis of the circadian clock protein PERIOD2

Gul H., Selvi S., Yilmaz F., Ozcelik G., Olfaz-Aslan S., Yazan S., et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , cilt.90, ss.1315-1330, 2022 (SCI-Expanded)

12. Identification of novel small molecules targeting core clock proteins to regulate circadian rhythm

Kavakli I. H., GÜL Ş., Turkay M.

Current Opinion in Chemical Engineering , cilt.35, 2022 (SCI-Expanded) Sürdürülebilir Kalkınma

13. Birt-Hogg-Dube Syndrome: Diagnostic Journey of Three Cases from Skin to Gene

Hasal E., Baskan E. B., Gul Ş., Dilektasli A. G., Sag S. O., Adird S. B., et al.

ANNALS OF DERMATOLOGY , cilt.34, sa.1, ss.66-71, 2022 (SCI-Expanded)

14. In Silico Analysis of a De Novo OTC Variant as a Cause of Ornithine Transcarbamylase Deficiency

Ozdemir Y., Cag M., Gul Ş., Yuksel Z., Ergoren M. C.

APPLIED IMMUNOHISTOCHEMISTRY & MOLECULAR MORPHOLOGY , cilt.30, sa.2, ss.153-156, 2022 (SCI-Expanded)

15. Structure-based design and classifications of small molecules regulating the circadian rhythm period

Gul Ş., Rahim F., Isin S., Yilmaz F., Ozturk N., Turkay M., et al.

SCIENTIFIC REPORTS , cilt.11, sa.1, 2021 (SCI-Expanded)

16. Identification of a Novel De Novo COMP Gene Variant as a Likely Cause of Pseudoachondroplasia

Tuncel G., Akcan N., Gul Ş., Sag S. O., Bundak R., Mocan G., et al.

APPLIED IMMUNOHISTOCHEMISTRY & MOLECULAR MORPHOLOGY , cilt.29, sa.7, ss.546-550, 2021 (SCI-Expanded)

17. In silico drug repositioning against human NRP1 to block SARS-CoV-2 host entry

Gul S.

TURKISH JOURNAL OF BIOLOGY , cilt.45, sa.4, ss.442-463, 2021 (SCI-Expanded) Sürdürülebilir Kalkınma

18. In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials

Gul Ş., Ozcan O., Asar S., OKYAR A., Baris I., Kavakli I. H.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS , cilt.39, sa.17, ss.6772-6791, 2021 (SCI-Expanded) Sürdürülebilir Kalkınma

19. Transcriptome analysis of the circadian clock gene BMAL1 deletion with opposite carcinogenic effects

Emisoglu-Kulahli H., Gul Ş., Morgil H., Ozcan O., Aygenli F., Selvi S., et al.

FUNCTIONAL & INTEGRATIVE GENOMICS , cilt.21, sa.1, ss.1-16, 2021 (SCI-Expanded) Sürdürülebilir Kalkınma

20. Unique combination and in silico modeling of biallelic POLR3A variants as a cause of Wiedemann-Rautenstrauch syndrome

TEMEL Ş. G., Ergoren M. C., Manara E., Paolacci S., Tuncel G., Gul Ş., et al.

EUROPEAN JOURNAL OF HUMAN GENETICS , cilt.28, sa.12, ss.1675-1680, 2020 (SCI-Expanded)

21. The Arg-293 of Cryptochrome1 is responsible for the allosteric regulation of CLOCK-CRY1 binding in circadian rhythm

Gul Ş., AYDIN C., Ozcan O., Gurkan B., Surme S., Baris I., et al.

JOURNAL OF BIOLOGICAL CHEMISTRY , cilt.295, sa.50, ss.17187-17199, 2020 (SCI-Expanded)

22. Human CRY1 variants associate with attention deficit/hyperactivity disorder

Onat O. E., Kars M. E., Gul Ş., Bilguvar K., Wu Y., Ozhan A., et al.

JOURNAL OF CLINICAL INVESTIGATION , cilt.130, sa.7, ss.3885-3900, 2020 (SCI-Expanded)

23. A CLOCK-binding small molecule disrupts the interaction between CLOCK and BMAL1 and enhances circadian rhythm amplitude.

Doruk Y., Yarparvar D., Akyel Y., Gul Ş., Taskin A. C., Yilmaz F., et al.

The Journal of biological chemistry , cilt.295, sa.11, ss.3518-3531, 2020 (SCI-Expanded)

24. Identification and Characterization of a New Class of (6-4) Photolyase from Vibrio cholerae

Dikbas U. M., Tardu M., Canturk A., Gul Ş., Ozcelik G., Baris I., et al.

BIOCHEMISTRY , cilt.58, sa.43, ss.4352-4360, 2019 (SCI-Expanded)

25. Centriolar satellites are required for efficient ciliogenesis and ciliary content regulation

Odabasi E., Gul Ş., Kavakli I. H., Firat-Karalar E. N.

EMBO REPORTS , cilt.20, sa.6, 2019 (SCI-Expanded)

26. DNA repair by photolyases

Kavakli I. H., Ozturk N., Gul Ş.

DNA REPAIR , cilt.115, ss.1-19, 2019 (SCI-Expanded)

27. The Photolyase/Cryptochrome Family of Proteins as DNA Repair Enzymes and Transcriptional Repressors

Kavakli I. H., Baris I., Tardu M., Gul Ş., Oner H., Cal S., et al.

PHOTOCHEMISTRY AND PHOTOBIOLOGY , cilt.93, sa.1, ss.93-103, 2017 (SCI-Expanded)

28. Glu-370 in the large subunit influences the substrate binding, allosteric, and heat stability properties of potato ADP-glucose pyrophosphorylase

Seferoglu A. B., Gul Ş., Dikbas U. M., Baris I., Koper K., Caliskan M., et al.

PLANT SCIENCE , cilt.252, ss.125-132, 2016 (SCI-Expanded)

29. Conformational Sampling of Peptides in the Presence of Protein Crowders from AA/CG-Multiscale Simulations

Predeus A. V., Gul Ş., Gopal S. M., Feig M.

JOURNAL OF PHYSICAL CHEMISTRY B , cilt.116, sa.29, ss.8610-8620, 2012 (SCI-Expanded)

30. Selectivity in the aggregates of the chiral organolithium N-Boc-2-lithiopiperidine with a chiral ligand: a DFT study

Ince H. H., Dedeoglu B., Gul Ş., Aviyente V., Coldham I.

MOLECULAR PHYSICS , cilt.110, sa.6, ss.353-359, 2012 (SCI-Expanded)

31. Computational Study of Factors Controlling the Boat and Chair Transition States of Ireland-Claisen Rearrangements

Gul Ş., Schoenebeck F., Aviyente V., Houk K. N.

JOURNAL OF ORGANIC CHEMISTRY , cilt.75, sa.6, ss.2115-2118, 2010 (SCI-Expanded)

Hakemli Bilimsel Toplantılarda Yayımlanmış Bildiriler 5

1. Effect of CLK8 on rhythmic transcriptome and replicative senescence in MRC-5 cells and further in vivo analysis

Gül Ş., Okyar A., Kavakli I. H.

11th International Drug Chemistry Conference, Antalya, Türkiye, 9 - 12 Mart 2023, (Yayınlanmadı) Sürdürülebilir Kalkınma

2. Dosing-time and cryptochrome dependent changes in oxaliplatin tolerability and pharmacokinetics

Öztürk Seyhan N., Akyel Y. K., Gül Ş., Çelik M., Taşkın A. C., Sancar A., et al.

26th National and 1st International Pharmacology Congress, 10th Clinical Pharmacology Symposium, 9th Clinical Toxicology Symposium, İstanbul, Türkiye, 4 - 06 Kasım 2021, ss.280-281, (Özet Bildiri)

3. Allosteric regulation of CRYs in mammalian circadian clock

Özcan O., Gül Ş., Kavaklı İ. H.

ESCAPE-31: European Symposium on Computer Aided Process Engineering 2021, 6 - 09 Haziran 2021, ss.1, (Yayınlanmadı)

4. IDENTIFICATION OF SMALL ORGANIC MOLECULES THAT REDUCES HALF-LIFE OF CRYPTOCHROME-1 AND CRYPTOCHROME-2

Sürme S., Gül Ş., Kavaklı İ. H.

85th Cold Spring Harbor Laboratory Symposium on Quantitative Biology, Biological Time Keeping, 1 - 05 Haziran 2021, ss.1, (Özet Bildiri)

5. Differential regulation of mammalian CRYs by allosterism in circadian clock

Özcan O., Gül Ş., Kavaklı İ. H.

85th Cold Spring Harbor Laboratory Symposium on Quantitative Biology, Biological Time Keeping, 1 - 05 Haziran 2021, ss.11-1, (Özet Bildiri)

Kitaplar 2

1. Sirkadiyen Saati Düzenleyen Küçük Molekküler Bulmak İçin Ana Saat Proteinlerine Karşı Yapıya Bağlı Moleküler Docking Taraması

Gül Ş., Kavaklı İ. H.

Sirkadiyen Düzenleme Metotlar ve Protokoller, Guiomar Solanas,Patrick -Simon Welz, Editör, Springer Nature, New York, ss.15-34, 2022

2. Kanserde DNA Tamiri Ve Tedavide DNA Tamir Yolakları

Kavaklı İ. H., Gül Ş., Tardu M., Barış İ.

Kanser Moleküler Biyolojisi, Yusuf Baran, Editör, Kısayol Yayıncılık, İstanbul, ss.173-184, 2018 Sürdürülebilir Kalkınma

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383

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406

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