Yayınlar (2020 - 2025)

1. Akçeşme, B. et al. Identification of deleterious non-synonymous single nucleotide polymorphisms in  the mRNA decay activator ZFP36L2. RNA Biol. 22, 1–15 (2025).

2. Akçeşme, F. B. et al. Genomic Surveillance and Molecular Characterization of SARS-CoV-2 Variants During  the Peak of the Pandemic in Türkiye. Biochem. Genet. 63, 4770–4789 (2025).

3. Cevher-Keskin, B. et al. Deciphering drought-response in wheat (Triticum aestivum): physiological,  biochemical, and transcriptomic insights into tolerant and sensitive cultivars under dehydration shock. Front. Plant Sci. 16, 1649378 (2025).

4. Akbulut, S. et al. Evaluation of the Relationship Between Neurologic Manifestations and Genetic Mutations in Wilson’s Disease with Next-Generation Sequencing. Diagnostics vol. 15 2689 at https://doi.org/10.3390/diagnostics15212689 (2025).

5. Alpsoy, S. & Sezerman, O. U. Transfer learning with multiomics integration and deep neural networks reveals drug resistance mechanisms in cancer. Sci. Rep. 15, 42295 (2025).

6. Yarman, A. et al. Spotlights of MIP-sensors for drugs and protein biomarkers. J. Pharm. Biomed. Anal. Open 5, 100048 (2025).

7. Yarman, A. et al. Synergism of enzymes and molecularly imprinted polymers in electrochemical sensors. Talanta Open 11, 100456 (2025).

8. Özmen, Z. A. et al. Effects of pathological mutations on the CHCHD2 monomer structure: A study by AlphaFold3 linked to the generation of conformational ensembles. Comput. Biol. Med. 196, 110810 (2025).

9. Coskuner-Weber, O., Koca, M. & Uversky, V. N. Molecular Crowding by Computational Approaches BT  - (Macro)Molecular Crowding: Life of the  Pottage. in (ed. Uversky, V. N.) 471–497 (Springer Nature Switzerland, Cham, 2025).

10. Ajmi, N. et al. Unraveling Genomic and Pathogenic Features of Aeromonas ichthyocola sp. nov., Aeromonas mytilicola sp. nov., and Aeromonas mytilicola subsp. aquatica subsp. nov. Animals vol. 15 948 at https://doi.org/10.3390/ani15070948 (2025).

11. Akkum, F. I. et al. Impacts of pathogenic mutations on the structures of the CHCHD10 monomer: An AlphaFold3 study linked to the generation of conformational ensembles. Int. J. Biol. Macromol. 318, 144970 (2025).

12. Coskuner-Weber, O., Cayli, F. N. & Uversky, V. N. Disordered peptide-based design of intrinsically disordered polymers for biomedical applications. Int. J. Polym. Anal. Charact. 30, 315–363 (2025).

13. Severoglu, Y. B. et al. Implicit Solvent Models and Their Applications in Biophysics. Biomolecules 15, (2025).

14. Coskuner-Weber, O., Gentili, P. L. & Uversky, V. N. Integrating chemical artificial intelligence and cognitive computing for predictive analysis of biological pathways: a case for intrinsically disordered proteins. Biophys. Rev.17, 737–758 (2025).

15. Coskuner-Weber, O. & Uversky, V. N. Liquid-Liquid Phase Separation Associated with Intrinsically Disordered Proteins: Experimental and Computational Tools. Curr. Protein Pept. Sci. 26, 825–843 (2025).

16. Alici, H., Uversky, V. N., Kang, D. E., Woo, J. A. & Coskuner-Weber, O. Effects of the Amyotrophic Lateral Sclerosis-related Q108P Mutation on the Structural Ensemble Characteristics of CHCHD10. Curr. Protein Pept. Sci. 26, 201–212 (2025).

17. Uversky, V. N., Tripathi, T. & Coskuner-Weber, O. Chapter 18 - Thermoresponsive intrinsically disordered protein polymers. in (eds. Tripathi, T. & Uversky, V. N. B. T.-T. T. F. S. of P.) 333–351 (Academic Press, 2025). doi:https://doi.org/10.1016/B978-0-443-21809-5.00016-8.

18. Coskuner-Weber, O. & Uversky, V. N. Chapter 20 - Computational modeling of intrinsically disordered and phase-separated protein states. in (eds. Tripathi, T. & Uversky, V. N. B. T.-T. T. F. S. of P.) 381–397 (Academic Press, 2025). doi:https://doi.org/10.1016/B978-0-443-21809-5.00015-6.

19. Erboz, A., Kesekler, E., Gentili, P. L., Uversky, V. N. & Coskuner-Weber, O. Electromagnetic radiation and biophoton emission in neuronal communication and neurodegenerative diseases. Prog. Biophys. Mol. Biol. 195, 87–99 (2025).

20. Erboz, A. & Coskuner-Weber, O. 400 Mio. Jahre Enzym-Evolution: stabile und variable Bereiche entschlüsselt. BIOspektrum 31, 646 (2025).

21. Saticioglu, I. B. et al. Three new Microbacterium species isolated from the Marmara Sea mucilage event: Microbacterium istanbulense sp. nov., Microbacterium bandirmense sp. nov., Microbacterium marmarense sp. nov. Syst. Appl. Microbiol. 48, 126600 (2025).

22. Coskuner-Weber, O. et al. Metagenomics studies in aquaculture systems: Big data analysis, bioinformatics,  machine learning and quantum computing. Comput. Biol. Chem. 118, 108444 (2025).

23. Özgör, C. & Çotuk, H. B. Effect of Different Body Postures on Prospective Time Perception TT  - Farklı Vücut Postürlerinin Prospektif Zaman Algısı Üzerindeki Etkisi. Int. J. Sport Exerc. Train. Sci. - IJSETS 10, 1–7 (2024).

24. Koçer, A. T. et al. Public health challenges after the February 6 earthquakes: A comprehensive review of immediate and long-term impacts in Türkiye. Int. J. Disaster Risk Reduct. 114, 104925 (2024).

25. Yarman, A. & Kurbanoğlu, S. A TALE OF CAPTOPRIL DETECTION BASED ON AN ELECTROCHEMICAL MIP SENSOR TT  - KAPTOPRİL TESPİTİ İÇİN ELEKTROKİMYASAL BİR MIP SENSÖRÜNÜN HİKAYESİ. J. Fac. Pharm. Ankara Univ. 48, 568–575 (2024).

26. Yarman, A. et al. A Strep-Tag Imprinted Polymer Platform for Heterogenous Bio(electro)catalysis. Angew. Chemie Int. Ed. 63, e202408979 (2024).

27. Yarman, A. Effect of Various Carbon Electrodes on MIP-Based Sensing Proteins Using  Poly(Scopoletin): A Case Study of Ferritin. Biomimetics (Basel, Switzerland) 9, (2024).

28. Yarman, A. et al. A Strep-Tag Imprinted Polymer Platform for Heterogenous Bio(electro)catalysis. Angew. Chem. Int. Ed. Engl. 63, e202408979 (2024).

29. Ghobadloo, P. A., Keles, G., Yarman, A., Hamidi, S. & Kurbanoglu, S. Chapter 13 - Determination of amino acids and other clinically significant molecules at surfactant-based electrochemical sensors and biosensors. in (eds. Manjunatha, J. G. & Hussain, C. M. B. T.-S. B. E. S. and B.) 315–342 (Elsevier, 2024). 

30. Yarman, A. & Kurbanoğlu, S. A TALE OF CAPTOPRIL DETECTION BASED ON AN ELECTROCHEMICAL MIP SENSOR TT  - KAPTOPRİL TESPİTİ İÇİN ELEKTROKİMYASAL BİR MIP SENSÖRÜNÜN HİKAYESİ. J. Fac. Pharm. Ankara Univ. 48, 568–575 (2024).

31. Zhang, X. et al. Specific features of epitope-MIPs and whole-protein MIPs as illustrated for AFP and RBD of SARS-CoV-2. Microchim. Acta 191, 242 (2024).

32. Keles, G., Oktay, A., Aslan, P., Yarman, A. & Kurbanoglu, S. Chapter 6 - Electrochemical sensors. in (eds. García, J. M., Vallejos, S. & Trigo-López, M. B. T.-S. P.) 225–270 (Elsevier, 2024). doi:https://doi.org/10.1016/B978-0-443-13394-7.00006-9.

33. Zhang, X. et al. Imprinted Polymers on the Route to Plastibodies for Biomacromolecules (MIPs), Viruses (VIPs), and Cells (CIPs) BT  - Trends in Biosensing Research: Advances, Challenges and Applications. in (eds. Lisdat, F. & Plumeré, N.) 107–148 (Springer International Publishing, Cham, 2024). doi:10.1007/10_2023_234.

34. Balli, O. I., Caglayan, S. I., Uverksy, V. N. & Coskuner-Weber, O. Structural Properties of Rat Intestinal Fatty Acid-Binding Protein with its Dynamics: Insights into Intrinsic Disorder. Protein Pept. Lett. 31, 458–468 (2024).

35. Alici, H., Uversky, V. N., Kang, D. E., Woo, J. A. & Coskuner-Weber, O. The impacts of the mitochondrial myopathy-associated G58R mutation on the dynamic structural properties of CHCHD10. J. Biomol. Struct. Dyn. 42, 5607–5616 (2024).

36. Coskuner-Weber, O. Structures prediction and replica exchange molecular dynamics simulations of α-synuclein: A case study for intrinsically disordered proteins. Int. J. Biol. Macromol. 276, 133813 (2024).

37. Coskuner-Weber, O. & Uversky, V. N. Current Stage and Future Perspectives for Homology Modeling, Molecular Dynamics Simulations, Machine Learning with Molecular Dynamics, and Quantum Computing for Intrinsically Disordered Proteins and Proteins with Intrinsically Disordered Regions. Curr. Protein Pept. Sci. 25, 163–171 (2024).

38. Eyuboglu, S., Alpsoy, S., Uversky, V. N. & Coskuner-Weber, O. Key genes and pathways in the molecular landscape of pancreatic ductal  adenocarcinoma: A bioinformatics and machine learning study. Comput. Biol. Chem. 113, 108268 (2024).

39. Beyatli, A. & İş, Ş. Çörek Otu’nun (Nigella sativa) Biyolojik ve Farmakolojik Özellikleri TT  - Biological and Pharmacological Properties of Black Cumin (Nigella sativa). Mersin Üniversitesi Tıp Fakültesi Lokman Hekim Tıp Tarihi ve Folk. Tıp Derg. 13, 543–552 (2023).

40. Schmidt, U. et al. Inducible overexpression of a FAM3C/ILEI transgene has pleiotropic effects with  shortened life span, liver fibrosis and anemia in mice. PLoS One 18, e0286256 (2023).

41. Balcıoğlu, T., İlgen Uslu, F., Çotuk, B. & Duru, A. D. Elit Karate Sporcularında Farklılaşan Beyin Yolaklarının Uzamsal İstatistik Yöntemiyle Analizi TT  - Analysis of Tract Based Spatial Statistics in Elite Karate Athletes. Int. J. Sport Exerc. Train. Sci. - IJSETS 9, 61–69 (2023).

42. Ahata, B. et al. Bioreactors for Tissue Engineering BT  - Biomaterials and Tissue Engineering. in (eds. Gunduz, O., Egles, C., Pérez, R. A., Ficai, D. & Ustundag, C. B.) 259–303 (Springer International Publishing, Cham, 2023). doi:10.1007/978-3-031-35832-6_9.

43. Oktay, A. et al. Corrosion response and biocompatibility of graphene oxide (GO)serotonin (Ser) coatings on Ti6Al7Nb and Ti29Nb13Ta4.6Zr (TNTZ) alloys fabricated by electrophoretic deposition (EPD). Mater. Today Commun. 34, 105236 (2023).

44. Oktay, A. et al. Tissue Regeneration Processing and Mimicking BT  - Biomaterials and Tissue Engineering. in (eds. Gunduz, O., Egles, C., Pérez, R. A., Ficai, D. & Ustundag, C. B.) 31–72 (Springer International Publishing, Cham, 2023). doi:10.1007/978-3-031-35832-6_2.

45. Menger, M. M., Yarman, A., Oktay, A. & Scheller, F. W. Molekularer Abdruck oder Selektion bei der Erzeugung biomimetischer Specifyer. BIOspektrum 29, 806–809 (2023).

46. Bognár, Z. et al. Correction: Peptide epitope-imprinted polymer microarrays for selective protein  recognition. Application for SARS-CoV-2 RBD protein. Chemical science vol. 14 9980 at https://doi.org/10.1039/d3sc90170j (2023).

47. Kurbanoglu, S., Yarman, A., Zhang, X. & Scheller, F. W. Electrochemical MIP Sensors for Environmental Analysis BT  - Biosensors for the Marine Environment: Present and Future Challenges. in (eds. Regan, F., Hansen, P.-D. & Barceló, D.) 139–164 (Springer International Publishing, Cham, 2023). doi:10.1007/698_2022_955.

48. Yuce-Erarslan, E., Domb, A. (Avi) J., Kasem, H., Uversky, V. N. & Coskuner-Weber, O. Intrinsically Disordered Synthetic Polymers in Biomedical Applications. Polymers vol. 15 2406 at https://doi.org/10.3390/polym15102406 (2023).

49. Coskuner-Weber, O., Yuce-Erarslan, E. & Uversky, V. N. Paving the Way for Synthetic Intrinsically Disordered Polymers for Soft Robotics. Polymers vol. 15 763 at https://doi.org/10.3390/polym15030763 (2023).

50. Alici, H. et al. Frontotemporal Dementia-Related V57E Mutation Impairs Mitochondrial Function and Alters the Structural Properties of CHCHD10. ACS Chem. Neurosci. 14, 2134–2145 (2023).

51. Alici, H., Uversky, V. N., Kang, D. E., Woo, J. A. & Coskuner-Weber, O. Effects of the Jokela type of spinal muscular atrophy-related G66V mutation on the structural ensemble characteristics of CHCHD10. Proteins Struct. Funct. Bioinforma. 91, 739–749 (2023).

52. Kretschmer, M. et al. A rotating bioreactor for the production of biofilms at the solid–air interface. Biotechnol. Bioeng. 119, 895–906 (2022).

53. Uluca, B., Lektemur Esen, C., Saritas Erdogan, S. & Kumbasar, A. NFI transcriptionally represses CDON and is required for SH-SY5Y cell survival. Biochim. Biophys. Acta - Gene Regul. Mech. 1865, 194798 (2022).

54. Zhang, X. et al. How an ACE2 mimicking epitope-MIP nanofilm recognizes template-related peptides  and the receptor binding domain of SARS-CoV-2. Nanoscale 14, 18106–18114 (2022).

55. Yarman, A. & Kurbanoglu, S. Molecularly Imprinted Polymer-Based Sensors for SARS-CoV-2: Where Are We Now? Biomimetics vol. 7 58 at https://doi.org/10.3390/biomimetics7020058 (2022).

56. Yarman, A., Kurbanoglu, S. & Scheller, F. W. Chapter 1 - Present state of MIP-based sensors for SARS-CoV-2. in (eds. Hussain, C. M. & Shukla, S. K. B. T.-S. T. and T. for C.-19) 3–25 (Elsevier, 2022).

57. Akbayrak, I. Y., Caglayan, S. I., Kurgan, L., Uversky, V. N. & Coskuner-Weber, O. Insights into the structural properties of SARS-CoV-2 main protease. Curr. Res. Struct. Biol. 4, 349–355 (2022).

58. Balli, O. I., Uversky, V. N., Durdagi, S. & Coskuner-Weber, O. Challenges and limitations in the studies of glycoproteins: A computational chemist’s perspective. Proteins Struct. Funct. Bioinforma. 90, 322–339 (2022).

59. Alici, H., Hasekioglu, O., Uversky, V. N. & Coskuner-Weber, O. Chapter 33 - Methods to study the effect of solution variables on the conformational dynamics of intrinsically disordered proteins. in (eds. Tripathi, T. & Dubey, V. K. B. T.-A. in P. M. and S. B. M.) 551–563 (Academic Press, 2022). doi:https://doi.org/10.1016/B978-0-323-90264-9.00033-7.

60. Alici, H., Uversky, V. N., Kang, D. E., Woo, J. A. & Coskuner-Weber, O. Structures of the Wild-Type and S59L Mutant CHCHD10 Proteins Important in Amyotrophic Lateral Sclerosis–Frontotemporal Dementia. ACS Chem. Neurosci. 13, 1273–1280 (2022).

61. Coskuner-Weber, O., Mirzanli, O. & Uversky, V. N. Intrinsically disordered proteins and proteins with intrinsically disordered regions in neurodegenerative diseases. Biophys. Rev. 14, 679–707 (2022).

62. Coskuner-Weber, O., Habiboglu, M. G., Teplow, D. & Uversky, V. N. From Quantum Mechanics, Classical Mechanics, and Bioinformatics to Artificial Intelligence Studies in Neurodegenerative Diseases BT  - Computer Simulations of Aggregation of Proteins and Peptides. in (eds. Li, M. S., Kloczkowski, A., Cieplak, M. & Kouza, M.) 139–173 (Springer US, New York, NY, 2022). 

63. Rickert, C. A. et al. Machine Learning Approach to Analyze the Surface Properties of Biological Materials. ACS Biomater. Sci. Eng. 7, 4614–4625 (2021).

64. Hayta, E. N., Ertelt, M. J., Kretschmer, M. & Lieleg, O. Bacterial Materials: Applications of Natural and Modified Biofilms. Adv. Mater. Interfaces 8, 2101024 (2021).

65. Hayta, E. N., Rickert, C. A. & Lieleg, O. Topography quantifications allow for identifying the contribution of parental  strains to physical properties of co-cultured biofilms. Biofilm 3, 100044 (2021).

66. Göksel Duru, D. & Alobaidi, M. Classification of brain electrophysiological changes in response to colour stimuli. Phys. Eng. Sci. Med. 44, 727–743 (2021).

67. Güney, S., Arslan, S., Duru, A. D. & Göksel Duru, D. Identification of Food/Nonfood Visual Stimuli from Event-Related Brain Potentials. Appl. Bionics Biomech. 2021, 6472586 (2021).

68. Yarman, A., Kurbanoglu, S., Erkmen, C., Uslu, B. & Scheller, F. W. Chapter 4 - Quantum dot-based electrochemical molecularly imprinted polymer sensors: potentials and challenges. in Micro and Nano Technologies (ed. Uslu, B. B. T.-E. A. of Q. D.-B. B.) 121–153 (Elsevier, 2021). doi:https://doi.org/10.1016/B978-0-12-821670-5.00013-0.

69. Yarman, A., Kurbanoglu, S., Zebger, I. & Scheller, F. W. Simple and robust: The claims of protein sensing by molecularly imprinted polymers. Sensors Actuators B Chem. 330, 129369 (2021).

70. Zhang, X. et al. “Out of Pocket” Protein Binding—A Dilemma of Epitope Imprinted Polymers Revealed for Human Hemoglobin. Chemosensors vol. 9 128 at https://doi.org/10.3390/chemosensors9060128 (2021).

71. Caserta, G. et al. Insights in electrosynthesis, target binding, and stability of peptide-imprinted polymer nanofilms. Electrochim. Acta 381, 138236 (2021).

72. Fatafta, H., Samantray, S., Sayyed-Ahmad, A., Coskuner-Weber, O. & Strodel, B. Chapter Five - Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions. in Dancing Protein Clouds: Intrinsically Disordered Proteins in the Norm and Pathology, Part C (ed. Uversky, V. N. B. T.-P. in M. B. and T. S.) vol. 183 135–185 (Academic Press, 2021).

73. Coskuner-Weber, O. & Caglayan, S. I. Secondary structure dependence on simulation techniques and force field parameters: from disordered to ordered proteins. Biophys. Rev. 13, 1173–1178 (2021).

74. Caliskan, M., Mandaci, S. Y., Uversky, V. N. & Coskuner-Weber, O. Secondary structure dependence of amyloid-β(1–40) on simulation techniques and force field parameters. Chem. Biol. Drug Des. 97, 1100–1108 (2021).

75. Akbayrak, I. Y. et al. Structures of MERS-CoV macro domain in aqueous solution with dynamics: Impacts of parallel tempering simulation techniques and CHARMM36m and AMBER99SB force field parameters. Proteins Struct. Funct. Bioinforma. 89, 1289–1299 (2021).

76. AKÇEŞME, F. B. & IŞ, Ş. IDENTIFICATION OF NUCLEOTIDE PATTERNS IN MECONIUM MICROBIOTA TO IMPROVE THE MANAGEMENT OF MECONIUM ASPIRATION SYNDROME IN CLINICAL PRACTICE  . Genet. Appl. 4, 27–36 (2020).

77. Akdag, M. et al. Proximal Biotinylation-Based Combinatory Approach for Isolating Integral Plasma  Membrane Proteins. J. Proteome Res. 19, 3583–3592 (2020).

78. Göksel Duru, D., Koç, E., Bayat, O. & Duru, A. D. Göz Hareketlerine Dayalı Beyin Bilgisayar Arayüzü Tasarımı TT  - Design of Brain Computer Interface Based on Eye Movements. Int. J. Eng. Res. Dev. 12, 176–188 (2020).

79. Göksel Duru, D., Mete, S., Çakır, O., Bayat, O. & Duru, A. D. Gözbebeği Hareketleri Temelli Duygu Durumu Sınıflandırılması TT  - Classification of Emotional State based on Eye Movements. Bilişim Teknol. Derg. 13, 137–144 (2020).

80. Çotuk, H. B., Duru, A. D., Pelvan, O. & Akbaş, S. Muscle blood content and muscle oxygen saturation in response to head down and head up tilt. Acta Astronaut. 166, 548–553 (2020).

81. Yarman, A., Kurbanoglu, S. & Scheller, F. W. Chapter Seven - Noninvasive biosensors for diagnostic biomarkers. in (ed. Sezgintürk, M. K. B. T.-C. B. and T. A.) 167–181 (Elsevier, 2020). doi:https://doi.org/10.1016/B978-0-12-818592-6.00007-4.

82. Yarman, A. & Scheller, F. W. How Reliable Is the Electrochemical Readout of MIP Sensors? Sensors vol. 20 2677 at https://doi.org/10.3390/s20092677 (2020).

83. Ozcelikay, G., Kurbanoglu, S., Yarman, A., Scheller, F. W. & Ozkan, S. A. Au-Pt nanoparticles based molecularly imprinted nanosensor for electrochemical detection of the lipopeptide antibiotic drug Daptomycin. Sensors Actuators B Chem. 320, 128285 (2020).

84. KurbanoĞlu, S. & Yarman, A. Simultaneous Determination of Hydrochlorothiazide and Irbesartan from  Pharmaceutical Dosage Forms with RP-HPLC. Turkish J. Pharm. Sci. 17, 523–527 (2020).

85. Akbayrak, I. Y., Caglayan, S. I., Ozcan, Z., Uversky, V. N. & Coskuner-Weber, O. Current Challenges and Limitations in the Studies of Intrinsically Disordered  Proteins in Neurodegenerative Diseases by Computer Simulations. Curr. Alzheimer Res. 17, 805–818 (2020).

86. Mandaci, S. Y., Caliskan, M., Sariaslan, M. F., Uversky, V. N. & Coskuner-Weber, O. Epitope region identification challenges of intrinsically disordered proteins in neurodegenerative diseases: Secondary structure dependence of α-synuclein on simulation techniques and force field parameters. Chem. Biol. Drug Des. 96, 659–667 (2020).