BIOMIMETICS RESEARCH GROUP

@incollection{beyaz2025conjugated,
title = {Conjugated Polymer Nanoparticles for Fluorescence Imaging in Stem Cell Tracking},
author = {Merve Beyaz, Basak Coban, Fatih Sema, Mert Erem, Ahu Arslan-Yildiz, Umit Hakan Yildiz},
url = {https://link.springer.com/protocol/10.1007/7651_2025_687},
doi = {doi.org/10.1007/7651_2025_687},
year = {2025},
date = {2025-12-02},
booktitle = {Methods in Molecular Biology},
pages = {1--48},
publisher = {Springer},
abstract = {Stem cell imaging and tracking generate a significant impact on regenerative medicine. Among the other techniques, optical imaging methods have emerged as widely used, given their high sensitivity, temporal resolution, and relative accessibility over MRI and PET. Conjugated polymer nanoparticles (CPNs) have emerged as fluorescent probes and have started to stand out due to their high photostability, intense brightness, and flexible design possibilities. They have become promising tools for long-term stem-cell labeling and noninvasive monitoring due to their structural versatility, allowing adjustment of the emission properties and surface functionalities.

This chapter provides a comprehensive overview of the role of CPNs in stem cell imaging, their structural and photophysical properties, strategies for cellular labeling, and performance within different optical imaging methods. The representative applications in monitoring migration, proliferation, and differentiation are highlighted, while challenges related to cytotoxicity, biodegradability, and reproducibility are discussed. Emerging approaches, including near-infrared (NIR-II) probes, multimodal systems, and stimuli-responsive designs, are addressed. By summarizing current progress and future directions, this chapter provides a comprehensive outlook on the potential of CPNs to advance next-generation tools for stem cell tracking and regenerative medicine.
},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}

@incollection{sozmen2025advances,
title = {Advances in optical biosensors: Technologies and trends in point of care applications},
author = {Alper Baran Sozmen, Ayse Ezgi Bayraktar, Ozgur Ulker, Ahu Arslan-Yildiz},
url = {https://www.sciencedirect.com/science/article/abs/pii/S0065242325000678},
doi = {doi.org/10.1016/bs.acc.2025.07.001},
year = {2025},
date = {2025-07-23},
booktitle = {Advances in Clinical Chemistry},
volume = {129},
pages = {1--52},
publisher = {Elsevier},
abstract = {A sensor detects changes in its environment and converts them into readable data using three key components: a receptor to sense changes, a transducer to generate a signal, and a detection system to output the signal. Optical sensors are devices that use a receptor and optical transducer to produce signals corresponding to an analyte, and optical biosensors combine a biological sensing element with an optical transducer to detect and quantify specific analytes. They offer easy-to-read, real-time signals, such as color changes or light emission, sometimes even detectable by the naked eye, reducing the need for external devices and providing versatile Point-of-Care (PoC) applicability. Their portability and rapid response time enable remote testing and monitoring, further improving accessibility. They allow sensitive and selective detection of various analytes, making them utile in areas like glucose monitoring, drug testing, and pathogen detection. Many of these sensors provide label-free and non-invasive detection, further enhancing patient comfort and safety. This chapter provides an overview of optical biosensors; it starts with categorizing them by biorecognition elements, transducers, and detection modes. It investigates biosensors that utilize nanomaterials, polymers, and engineered biorecognition elements are discussed, with examples from literature. Technologies such as miniaturization, multiplexing, and wearable designs, which enhance PoC feasibility, are also examined. Lastly, challenges in development and operation are addressed, and future research directions for advancing optical biosensors in PoC diagnostics are discussed.},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}

@incollection{bilginer2025recent,
title = {Recent Advances in Hydrogel-Based 3D Disease Modeling and Drug Screening Platforms},
author = {Rumeysa Bilginer-Kartal, Basak Coban, Ozum Yildirim-Semerci, Ahu Arslan-Yildiz},
url = {https://link.springer.com/chapter/10.1007/5584_2025_851},
doi = {10.1007/5584_2025_851},
year = {2025},
date = {2025-03-18},
booktitle = {Advances in Experimental Medicine and Biology},
pages = {1--28},
publisher = {Springer, Cham},
abstract = {Three-dimensional (3D) disease modeling and drug screening systems have become important in tissue engineering, drug screening, and development. The newly developed systems support cell and extracellular matrix (ECM) interactions, which are necessary for the formation of the tissue or an accurate model of a disease. Hydrogels are favorable biomaterials due to their properties: biocompatibility, high swelling capacity, tunable viscosity, mechanical properties, and their ability to biomimic the structure and function of ECM. They have been used to model various diseases such as tumors, cancer diseases, neurodegenerative diseases, cardiac diseases, and cardiovascular diseases. Additive manufacturing approaches, such as 3D printing/bioprinting, stereolithography (SLA), selective laser sintering (SLS), and fused deposition modeling (FDM), enable the design of scaffolds with high precision; thus, increasing the accuracy of the disease models. In addition, the aforementioned methodologies improve the design of the hydrogel-based scaffolds, which resemble the complicated structure and intricate microenvironment of tissues or tumors, further advancing the development of therapeutic agents and strategies. Thus, 3D hydrogel-based disease models fabricated through additive manufacturing approaches provide an enhanced 3D microenvironment that empowers personalized medicine toward targeted therapeutics, in accordance with 3D drug screening platforms.},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}

@incollection{ozmen2023bioprinting,
title = {Bioprinting of hydrogels for tissue engineering and drug screening applications},
author = {Ece Özmen, Özüm Yıldırım, Ahu Arslan-Yıldız},
url = {https://www.sciencedirect.com/science/article/abs/pii/B9780323885249000280},
doi = {10.1016/B978-0-323-88524-9.00028-0},
year = {2023},
date = {2023-01-01},
booktitle = {Advances in Biomedical Polymers and Composites},
pages = {183--221},
publisher = {Elsevier},
chapter = {8},
abstract = {In tissue engineering, the 3-dimensional (3D) bioprinting method that enables the production of 3D structures by combining bioinks and cells has become one of the most promising technique. Over the last few years, 3D cell culture models gained importance in the development of disease model and drug development studies. The successful production of the 3D structures by 3D bioprinting mostly depends on the properties of the bioink to be used. Hydrogels, which are natural or synthetic polymers, are generally preferred as bioink materials with their high swelling ability, biocompatibility, biodegradability, and easy gelation ability. The convenience of hydrogels for varied bioprinting applications make them proper bioink materials for bioprinting of artificial tissues, tumor models, and tissue grafts. Bioprinting of functional tissues is successfully performed for years, and hydrogels are utilized as bioink in bone, vascular, neural, cartilage, cardiac, skin tissue engineering, and drug screening. In this chapter, bioprinting methodology, bioinks, hydrogel bioinks, and their applications are discussed in detail.},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}

@inbook{onbas2021chip,
title = {On-Chip Drug Screening Technologies for Nanopharmaceutical and Nanomedicine Applications},
author = {Onbas, Rabia and Bilginer, Rumeysa and Arslan Yildiz, Ahu},
url = {https://link.springer.com/chapter/10.1007/978-3-030-44925-4_8},
doi = {10.1007/978-3-030-44925-4_8},
year = {2021},
date = {2021-01-01},
booktitle = {Nanopharmaceuticals: Principles and Applications Vol. 1},
number = {311--346},
publisher = {Springer},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}

@incollection{yildiz2021biomimetic,
title = {Biomimetic and synthetic gels for nanopharmaceutical applications},
author = {Yildiz, Busra and Ozenler, Sezer and Yucel, Muge and Yildiz, Umit Hakan and Arslan Yildiz, Ahu},
doi = {10.1007/978-3-030-44925-4_7},
year = {2021},
date = {2021-01-01},
booktitle = {Nanopharmaceuticals: Principles and Applications },
volume = {1},
pages = {273–309},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}

@incollection{ozefe2020magnetic,
title = {Magnetic Levitation Based Applications in Bioscience},
author = {Ozefe, Fatih and Yildiz, Ahu Arslan},
year = {2020},
date = {2020-01-01},
booktitle = {Magnetic Materials and Magnetic Levitation},
pages = {149},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}

@incollection{kok2019biomimetic,
title = {Biomimetic lipid membranes: fundamentals, applications, and commercialization},
author = {Rumeysa Bilginer, Ahu Arslan Yildiz},
editor = {Kök, Fatma N and Yildiz, Ahu Arslan and Inci, Fatih},
isbn = {978-3-030-11596-8},
year = {2019},
date = {2019-01-01},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}