Research Project: İnsan Maymun Çiçeği Tanısı İçin Bakım Noktası (Point Of Care / Poc) Düzeyinde Crispr/Lamp Temelli Mikroakışkan Çip Geliştirilmesi
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Contributors
Funders
ID
TB.00783
Authors
Taşoğlu, Savaş
Faculty Member
Publications
Mpox diagnosis at POC
(Elsevier, 2025) Yığcı, Defne; Ergönül, Önder; Taşoğlu, Savaş; School of Medicine; Department of Mechanical Engineering; KUAR (KU Arçelik Research Center for Creative Industries); KUTTAM (Koç University Research Center for Translational Medicine); KUISCID (Koç University İşbank Center for Infectious Diseases); Yes; SCHOOL OF MEDICINE; College of Engineering; Research Center; Yığcı, Defne
BAKILACAK
CRISPR-on-chip for point-of-care diagnostics
(American Chemical Society, 2026) Atçeken, Nazente; Yığcı, Defne; Taşoğlu, Savaş; Kahya, Alptekin; KUTTAM (Koç University Research Center for Translational Medicine); KUIS AI (Koç University & İş Bank Artificial Intelligence Center); Department of Mechanical Engineering; School of Medicine; KUAR (KU Arçelik Research Center for Creative Industries); Graduate School of Sciences and Engineering; Yes; Research Center; College of Engineering; SCHOOL OF MEDICINE; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING; Yığcı, Defne
CRISPR-based diagnostic platforms have gained significant momentum in recent years, enabling highly sensitive and specific detection of pathogens and diseases. Due to their practical benefits, these platforms have become widely adopted in point-of-care (PoC) applications. CRISPR-on-chip technology integrates CRISPR-Cas platforms with diverse microfluidic systems, allowing scalability and portable, real-time, and precise biomolecule detection. This approach enhances diagnostic accuracy, reduces processing times, and minimizes the need for complex laboratory infrastructures, unlike in conventional diagnostics. Using CRISPR-Cas enzymes in microfluidic systems, CRISPR-on-chip platforms offer key advantages such as single-molecule sensitivity, multiplex detection, and applicability. However, integration with microfluidics for PoC applications is still poorly understood, despite CRISPR-Cas being widely used. This study reviews recent developments in CRISPR-on-chip-based diagnostics and highlights its potential applications in infectious diseases, biosensors, and personalized medicine. Furthermore, challenges and future perspectives in achieving an ideal diagnostic solution are discussed.
ML-augmented Ti-based microrobotic stents
(Wiley-VCH GmbH, 2025) Choukri, Abdullah Ahmed; Taşoğlu, Savaş; Choukri, Abdullah Ahmed; Department of Mechanical Engineering; KUIS AI (Koç University & İş Bank Artificial Intelligence Center); KUTTAM (Koç University Research Center for Translational Medicine); KUAR (KU Arçelik Research Center for Creative Industries); Yes; College of Engineering; Research Center
The integration of microrobotic stents into biomedical applications has the potential to revolutionize invasive procedures by enabling precise drug delivery, imaging, and vascular interventions. These interventions demand alloys with high radial stiffness for structural integrity and low density for biocompatibility. We developed a machine learning (ML)-finite element analysis (FEA) framework to optimize titanium (Ti)-based and Ti-based high-entropy alloys (Ti-HEAs) compositions using a curated database of 238 alloys. Gaussian process regression (GPR) is trained on FEA-simulated radial stiffness and constrained optimization (interior-point, sequential quadratic programming (SQP), active-set) identified high-performance candidates. The interior-point algorithm yielded the highest stiffness (483.54 kN/m) with balanced composition (Ti: 76.29 at%, Nb: 6.88%, Zr: 7.34%, Ta: 7.31%), outperforming the dataset maximum (TiSn 20, 472.49 kN/m) by 2.32% and Ti-6Al-4 V (368.96 kN/m) by 31%. All algorithms converged to at least 469 kN/m despite compositional diversity, confirming robustness. The framework enables rapid, physics-informed alloy design for next-generation biomedical microrobotics.
Programmable 3DP microfluidic bio-reaction system: automated LAMP-on-a-chip
(Royal Soc Chemistry, 2025) Birtek, Mehmet Tuğrul; Atçeken, Nazente; Taşoğlu, Savaş; Birtek, Mehmet Tuğrul; School of Medicine; Department of Mechanical Engineering; KUIS AI (Koç University & İş Bank Artificial Intelligence Center); KUAR (KU Arçelik Research Center for Creative Industries); KUTTAM (Koç University Research Center for Translational Medicine); Yes; SCHOOL OF MEDICINE; Research Center; College of Engineering
Point-of-care (PoC) devices have revolutionized healthcare by enabling remote diagnostics and therapeutics, with microfluidic systems playing a pivotal role in their advancement. This study focuses on the detailed engineering and characterization of three-dimensional hydrophobic valves to form novel programmable bio-reaction reservoirs. Using 3D-printed soft lithography, we meticulously investigated the effects of channel dimensions and surface properties on the burst pressures of these reservoirs, which ranged from 6.4 to 44.8 mbar. The bio-reaction reservoirs were demonstrated in both series and parallel configurations, offering versatile platforms for the miniaturization and automation of biological processes. Our findings highlight the capability of these reservoirs to program flows in a variety of fluid samples, including water, blood and serum. Additionally, a portable pressure pump was developed to leverage the functionality of these hydrophobic valves, enabling precise control of fluid dynamics in PoC applications. The study culminated in the design of a microfluidic chip integrating two consecutive reservoirs for the PoC execution of loop-mediated isothermal amplification (LAMP) for detection of the Mpox virus. Primers were lyophilized within the bio-reservoirs, and the system successfully enabled visible colorimetric detection via the LAMP assay.
Development and validation of LAMP assays for distinguishing MPXV clades with fluorescent and colorimetric readouts
(MDPI, 2025) Atçeken, Nazente; Dilmani, Asghari Sara; Choukri, Abdullah Ahmed; Yığcı, Defne; Korkmaz, Gözde; Taşoğlu, Savaş; Choukri, Abdullah Ahmed; Dilmani, Asghari Sara; Sarıkaya, Mutlu; KUTTAM (Koç University Research Center for Translational Medicine); KUIS AI (Koç University & İş Bank Artificial Intelligence Center); KUAR (KU Arçelik Research Center for Creative Industries); Department of Mechanical Engineering; Graduate School of Sciences and Engineering; Yes; Research Center; College of Engineering; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING; Yığcı, Defne
Human monkeypox (Mpox) is a zoonotic disease caused by the Monkeypox virus (MPXV). As of 14 August 2024, the World Health Organization (WHO) has declared it a global health emergency. For Mpox, this was the second public health emergency of global significance in the past two years. MPXV belongs to the Poxviridae family and is phylogenetically and epidemically divided into two clades: the Congo Basin (Clade-I) and the West African (Clade-II) clades. Clade-I has been associated with more severe disease progression and higher mortality compared to Clade-II, and thus the differentiation between clades can play an important role in predicting disease prognosis. The LAMP technique has the advantages of not requiring thermal cycling and achieving higher amplification in a shorter time compared to qPCR. Different types of LAMP assays were developed in this study to benefit from these advantages. We report the development of LAMP-1 and LAMP-2 assays using the LAMP method to detect MPXV Clade-I and Clade-II, respectively. The LAMP-1 assay includes both fluorescence and visible colorimetric readout tests developed with sensitivities of 103 and 107 copies, respectively. For the LAMP-2 assay, a probe-based test utilizing the Novel R-Duplex DARQ probe was developed, offering fluorescence detection at a sensitivity of 103 copies. As a result, we successfully developed three highly specific molecular diagnostic tests that distinctly differentiate between MPXV clades, delivering essential tools for the precise diagnosis and effective control of Mpox.
