Yagmur Isik
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Yagmur Isik has a total of 23 co-authors. Here are the top co-authors by number of shared publications:
- Huseyin Uvet
Yildiz Technical University
6 shared publications - Hasan Berkay Abdioglu
Yildiz Technical University
5 shared publications - Ali Anil Demircali
Divisions in System Medicine Department of Metabolism Digestion and Reproduction Faculty of Medicine Imperial College London London UK
4 shared publications - Gokhan Bora Esmer
Yildiz Technical University
4 shared publications - Esmahan Caglar
Department of Bioengineering, Yildiz Technical University, Istanbul 34220, Turkey
2 shared publications - Ibrahim Cem Balci
Yildiz Technical University
2 shared publications
Latest Publications
- Open Access
- 11 May 2026
- Published by Wiley in Journal of Cellular Physiology
- Vol. 241 (5) , e70184
Cell Mechanics in Cancer: Integrating Mechanotransduction Pathways Within the Tumor Microenvironment
Single‐cell mechanical properties such as stiffness, elasticity, and viscosity, are crucial in governing biological processes like migration, proliferation, and differentiation. In cancer, the mechanical properties of cells undergo significant alterations, which contribute to tumor growth, metastasis, and resistance to therapy. This review focuses on cancer cell stiffness and explores how its regulation is disrupted by the complex interplay among cytoskeletal remodeling, nuclear mechanics, and extracellular matrix (ECM) interactions. Cancer‐associated fibroblasts (CAFs) and ECM composition within the tumor microenvironment (TME) modulate cellular mechanics via mechanotransduction pathways involving Yes‐associated protein/transcriptional coactivator with PDZ‐binding motif (YAP/TAZ) and integrin‐focal adhesion kinase (FAK) signaling. Increasing evidence supports cell stiffness as a promising diagnostic and prognostic biomarker, as well as a predictor of treatment response. Therefore, advanced techniques for measuring cell stiffness such as atomic force microscopy (AFM), Brillouin microscopy, and acousto‐holography are evaluated with a focus on their potential clinical applicability. However, translation into routine oncology practice remains limited by technical variability, lack of standardized protocols, and the need for large‐scale clinical validation. This review highlights the potential of integrating biomechanical markers into clinical workflows as a means to advance cancer diagnostics and enable more personalized therapeutic strategies.
- 11 May 2026
- Published by Wiley in Journal of Cellular Physiology
- Vol. 241 (5) , e70184
Open AccessCell Mechanics in Cancer: Integrating Mechanotransduction Pathways Within the Tumor Microenvironment
Single‐cell mechanical properties such as stiffness, elasticity, and viscosity, are crucial in governing biological processes like migration, proliferation, and differentiation. In cancer, the mechanical properties of cells undergo significant alterations, which contribute to tumor growth, metastasis, and resistance to therapy. This review focuses on cancer cell stiffness and explores how its regulation is disrupted by the complex interplay among cytoskeletal remodeling, nuclear mechanics, and extracellular matrix (ECM) interactions. Cancer‐associated fibroblasts (CAFs) and ECM composition within the tumor microenvironment (TME) modulate cellular mechanics via mechanotransduction pathways involving Yes‐associated protein/transcriptional coactivator with PDZ‐binding motif (YAP/TAZ) and integrin‐focal adhesion kinase (FAK) signaling. Increasing evidence supports cell stiffness as a promising diagnostic and prognostic biomarker, as well as a predictor of treatment response. Therefore, advanced techniques for measuring cell stiffness such as atomic force microscopy (AFM), Brillouin microscopy, and acousto‐holography are evaluated with a focus on their potential clinical applicability. However, translation into routine oncology practice remains limited by technical variability, lack of standardized protocols, and the need for large‐scale clinical validation. This review highlights the potential of integrating biomechanical markers into clinical workflows as a means to advance cancer diagnostics and enable more personalized therapeutic strategies.
- Open Access
- 27 March 2026
- Published by Optica Publishing Group in Optics Express
- Vol. 34 (7) , 12687-12701
Comparative evaluation of denoising methods for off-axis digital holograms under realistic mixed-noise conditions
Off-axis holographic microscopy enables single-shot quantitative phase imaging, but its sensitivity is limited by mixed noise that degrades fringe visibility and biases phase recovery. We compare classical filters (Wiener/median/NLM/BM3D and variance-stabilized variants), a supervised Swin transformer, and a diffusion denoiser trained on synthetic data, using 100,000 physics-based holograms with realistic blur, speckle, shot, and read noise. On a 10,000-hologram test set, the best pipeline (diffusion followed by BM3D) achieves 36.86 dB/0.9964 intensity PSNR/SSIM and 46.48 dB/0.9772 phase PSNR/SSIM, reducing RMSE by 88.5% in intensity and 52.8% in phase, with similar improvements on experimental bead and cell holograms.
- 27 March 2026
- Published by Optica Publishing Group in Optics Express
- Vol. 34 (7) , 12687-12701
Open AccessComparative evaluation of denoising methods for off-axis digital holograms under realistic mixed-noise conditions
Off-axis holographic microscopy enables single-shot quantitative phase imaging, but its sensitivity is limited by mixed noise that degrades fringe visibility and biases phase recovery. We compare classical filters (Wiener/median/NLM/BM3D and variance-stabilized variants), a supervised Swin transformer, and a diffusion denoiser trained on synthetic data, using 100,000 physics-based holograms with realistic blur, speckle, shot, and read noise. On a 10,000-hologram test set, the best pipeline (diffusion followed by BM3D) achieves 36.86 dB/0.9964 intensity PSNR/SSIM and 46.48 dB/0.9772 phase PSNR/SSIM, reducing RMSE by 88.5% in intensity and 52.8% in phase, with similar improvements on experimental bead and cell holograms.
- Open Access
- 23 January 2026
- Published by Optica Publishing Group in Biomedical Optics Express
- Vol. 17 (2) , 901-915
Inline mechano-vibration holography for simultaneous phase and elasticity mapping of soft samples
Off-axis holography enables single-shot phase retrieval but reduces spatial bandwidth, while in-line phase-shifting interferometry preserves bandwidth yet requires reference-path stepping and is sensitive to drift, limiting dynamic measurements. Moreover, viscoelastic mapping is rarely available from the same holographic measurement. We propose vibration-encoded in-line Mach-Zehnder holography for simultaneous thickness and viscoelasticity mapping of soft samples. Twelve holograms acquired over one vibration cycle are analyzed using Bessel-based harmonic inversion and robust regression to recover the static phase, modulation depth, and phase lag, yielding thickness and Kelvin-Voigt storage and loss modulus maps ( E ′, E ″). Simulations recover E ′ and E ′′ to within ∼2% across a wide E ′′/ E ′ range and achieve sub-micron thickness error over 20-45 μ m beads. Experiments on calibrated polyacrylamide beads show sub-micron thickness repeatability (median ∼0.57 μ m over 40 repeats) and stiffness estimates typically within 10% of ground truth, and we further demonstrate the approach on adherent MCF-7 cells.
- 23 January 2026
- Published by Optica Publishing Group in Biomedical Optics Express
- Vol. 17 (2) , 901-915
Open AccessInline mechano-vibration holography for simultaneous phase and elasticity mapping of soft samples
Off-axis holography enables single-shot phase retrieval but reduces spatial bandwidth, while in-line phase-shifting interferometry preserves bandwidth yet requires reference-path stepping and is sensitive to drift, limiting dynamic measurements. Moreover, viscoelastic mapping is rarely available from the same holographic measurement. We propose vibration-encoded in-line Mach-Zehnder holography for simultaneous thickness and viscoelasticity mapping of soft samples. Twelve holograms acquired over one vibration cycle are analyzed using Bessel-based harmonic inversion and robust regression to recover the static phase, modulation depth, and phase lag, yielding thickness and Kelvin-Voigt storage and loss modulus maps ( E ′, E ″). Simulations recover E ′ and E ′′ to within ∼2% across a wide E ′′/ E ′ range and achieve sub-micron thickness error over 20-45 μ m beads. Experiments on calibrated polyacrylamide beads show sub-micron thickness repeatability (median ∼0.57 μ m over 40 repeats) and stiffness estimates typically within 10% of ground truth, and we further demonstrate the approach on adherent MCF-7 cells.
- Open Access
- 3 September 2025
- Published by Optica Publishing Group in Optics Express
- Vol. 33 (18) , 38696-38706
Benchmark study of deep super-resolution models for digital holography: quantitative phase and intensity evaluation
Despite good axial resolution in holographic microscopy, lateral resolution remains constrained by optical limitations, pixel size, and noise. These restrictions hinder accurate reconstruction of fine structural and phase details. To address this, we evaluate three deep-learning super-resolution models (RCAN, SwinIR, and a conditional diffusion network) on 1,440 off-axis digital holograms of microbeads downsampled by 2 ×, 3 ×, and 4 ×. We compare their performance to bicubic spline interpolation using PSNR, SSIM, MSE, and phase-derived depth errors. RCAN and SwinIR yield the most accurate reconstructions, preserving structural and quantitative phase information, and offering guidance on model selection for phase-focused holography.
- 3 September 2025
- Published by Optica Publishing Group in Optics Express
- Vol. 33 (18) , 38696-38706
Open AccessBenchmark study of deep super-resolution models for digital holography: quantitative phase and intensity evaluation
Despite good axial resolution in holographic microscopy, lateral resolution remains constrained by optical limitations, pixel size, and noise. These restrictions hinder accurate reconstruction of fine structural and phase details. To address this, we evaluate three deep-learning super-resolution models (RCAN, SwinIR, and a conditional diffusion network) on 1,440 off-axis digital holograms of microbeads downsampled by 2 ×, 3 ×, and 4 ×. We compare their performance to bicubic spline interpolation using PSNR, SSIM, MSE, and phase-derived depth errors. RCAN and SwinIR yield the most accurate reconstructions, preserving structural and quantitative phase information, and offering guidance on model selection for phase-focused holography.
- 30 June 2025
- Published by Wiley in ChemistrySelect
- Vol. 10 (25)
Co‐Binding of Methotrexate and Cyclophosphamide via Folic Acid‐Decorated Graphene Oxide Nanomaterials for Therapeutic Approach against Breast Cancer
In this study, we developed a graphene oxide (GO)‐based nanocarrier system co‐loaded with methotrexate (MTX) and cyclophosphamide (CP) and functionalized with folic acid (FA) for targeted drug delivery. The synthesized CP/MTX/FA/GO system and its individual components were characterized by zeta potential analysis, FTIR spectroscopy, FE‐SEM imaging, and DSC analysis. Structural characterization revealed that the 3D morphology of the CP/MTX/FA/GO formulation was denser compared to CP/FA/GO and MTX/FA/GO systems. FTIR and DSC results confirmed the successful oxidation of graphite and the physicochemical incorporation of CP, MTX, and FA into the GO structure through functional groups such as carboxylic, hydroxyl, epoxide, and carbonyl. In vitro release studies using Franz diffusion demonstrated that the drug release profile followed the Higuchi model with a high correlation coefficient ( R 2 = 0.9837), indicating that the release was primarily governed by Fickian diffusion, where drug transport occurs along a concentration gradient through the GO matrix. Stiffness analysis indicated that FA functionalization enhanced cell targeting and facilitated drug internalization. Cytotoxicity assays showed that CP/MTX/FA/GO exerted a significantly higher antiproliferative effect on MDA‐MB‐231 breast cancer cells compared to free MTX, free CP, CP/FA/GO, and MTX/FA/GO. Collectively, these findings suggest that the CP/MTX/FA/GO nanocarrier exhibits strong potential for dual‐drug targeted therapy, offering synergistic cytotoxic effects and efficient drug delivery.
- 30 June 2025
- Published by Wiley in ChemistrySelect
- Vol. 10 (25)
Co‐Binding of Methotrexate and Cyclophosphamide via Folic Acid‐Decorated Graphene Oxide Nanomaterials for Therapeutic Approach against Breast Cancer
In this study, we developed a graphene oxide (GO)‐based nanocarrier system co‐loaded with methotrexate (MTX) and cyclophosphamide (CP) and functionalized with folic acid (FA) for targeted drug delivery. The synthesized CP/MTX/FA/GO system and its individual components were characterized by zeta potential analysis, FTIR spectroscopy, FE‐SEM imaging, and DSC analysis. Structural characterization revealed that the 3D morphology of the CP/MTX/FA/GO formulation was denser compared to CP/FA/GO and MTX/FA/GO systems. FTIR and DSC results confirmed the successful oxidation of graphite and the physicochemical incorporation of CP, MTX, and FA into the GO structure through functional groups such as carboxylic, hydroxyl, epoxide, and carbonyl. In vitro release studies using Franz diffusion demonstrated that the drug release profile followed the Higuchi model with a high correlation coefficient ( R 2 = 0.9837), indicating that the release was primarily governed by Fickian diffusion, where drug transport occurs along a concentration gradient through the GO matrix. Stiffness analysis indicated that FA functionalization enhanced cell targeting and facilitated drug internalization. Cytotoxicity assays showed that CP/MTX/FA/GO exerted a significantly higher antiproliferative effect on MDA‐MB‐231 breast cancer cells compared to free MTX, free CP, CP/FA/GO, and MTX/FA/GO. Collectively, these findings suggest that the CP/MTX/FA/GO nanocarrier exhibits strong potential for dual‐drug targeted therapy, offering synergistic cytotoxic effects and efficient drug delivery.
- Open Access
- 1 March 2025
- Published by SPIE-Intl Soc Optical Eng in Journal of Biomedical Optics
- Vol. 30 (03) , 1-12
Noninvasive holographic sensor system for measuring stiffness of soft micro samples
Significance: Measuring cell stiffness is essential in cellular biomechanics, particularly in understanding disease progression, including cancer metastasis and tissue mechanics. However, conventional techniques such as atomic force microscopy and optical stretching present limitations, including invasiveness, low throughput, and complex sample preparation. These factors restrict their applicability in dynamic and sensitive biological environments.Aim: This study introduces a noninvasive holographic sensor system for evaluating the stiffness of soft microscale samples.Approach: The proposed system integrates holographic imaging with acoustic stimulation using an off-axis Mach–Zehnder interferometer combined with bulk acoustic waves. This setup allows for label-free, high-throughput measurements while preserving sample integrity. The system was validated with polyacrylamide beads engineered to mimic cellular stiffness, ensuring precise and repeatable stiffness assessments.Results: Measurement errors caused by spatial variations were minimized through a structured imaging approach and a calibration strategy, improving uniformity across different regions. These corrections enhanced the consistency and reliability of stiffness assessments. Experimental validation demonstrated stable stiffness measurements regardless of sample size variations. Repeatability tests further confirmed the system’s robustness, producing consistent results across multiple trials.Conclusion: The findings highlight the potential of this holographic sensor system in advancing cell biomechanics research, cancer diagnostics, and mechanobiology. By offering a noninvasive, high-throughput alternative for mechanical property assessments in biological samples, this method contributes to improved characterization of cellular stiffness in biomedical applications.
- 1 March 2025
- Published by SPIE-Intl Soc Optical Eng in Journal of Biomedical Optics
- Vol. 30 (03) , 1-12
Open AccessNoninvasive holographic sensor system for measuring stiffness of soft micro samples
Significance: Measuring cell stiffness is essential in cellular biomechanics, particularly in understanding disease progression, including cancer metastasis and tissue mechanics. However, conventional techniques such as atomic force microscopy and optical stretching present limitations, including invasiveness, low throughput, and complex sample preparation. These factors restrict their applicability in dynamic and sensitive biological environments.Aim: This study introduces a noninvasive holographic sensor system for evaluating the stiffness of soft microscale samples.Approach: The proposed system integrates holographic imaging with acoustic stimulation using an off-axis Mach–Zehnder interferometer combined with bulk acoustic waves. This setup allows for label-free, high-throughput measurements while preserving sample integrity. The system was validated with polyacrylamide beads engineered to mimic cellular stiffness, ensuring precise and repeatable stiffness assessments.Results: Measurement errors caused by spatial variations were minimized through a structured imaging approach and a calibration strategy, improving uniformity across different regions. These corrections enhanced the consistency and reliability of stiffness assessments. Experimental validation demonstrated stable stiffness measurements regardless of sample size variations. Repeatability tests further confirmed the system’s robustness, producing consistent results across multiple trials.Conclusion: The findings highlight the potential of this holographic sensor system in advancing cell biomechanics research, cancer diagnostics, and mechanobiology. By offering a noninvasive, high-throughput alternative for mechanical property assessments in biological samples, this method contributes to improved characterization of cellular stiffness in biomedical applications.