WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Article Citation - WoS: 1Tcgex: a Powerful Visual Interface for Exploring and Analyzing Cancer Gene Expression Data(Springernature, 2025) Kus, M. Emre; Sahin, Cagatay; Kilic, Emre; Askin, Arda; Ozgur, M. Mert; Karahanogullari, Gokhan; Ekiz, H. AtakanAnalyzing gene expression data from the Cancer Genome Atlas (TCGA) and similar repositories often requires advanced coding skills, creating a barrier for many researchers. To address this challenge, we developed The Cancer Genome Explorer (TCGEx), a user-friendly, web-based platform for conducting sophisticated analyses such as survival modeling, gene set enrichment analysis, unsupervised clustering, and linear regression-based machine learning. TCGEx provides access to preprocessed TCGA data and immune checkpoint inhibition studies while allowing integration of user-uploaded data sets. Using TCGEx, we explore molecular subsets of human melanoma and identify microRNAs associated with intratumoral immunity. These findings are validated with independent clinical trial data on immune checkpoint inhibitors for melanoma and other cancers. In addition, we identify cytokine genes that can be used to predict treatment responses to various immune checkpoint inhibitors prior to treatment. Built on the R/Shiny framework, TCGEx offers customizable features to adapt analyses for diverse research contexts and generate publication-ready visualizations. TCGEx is freely available at https://tcgex.iyte.edu.tr, providing an accessible tool to extract insights from cancer transcriptomics data.Conference Object Enhancing genomic data sharing with blockchain-enabled dynamic consent in beacon V2(Springernature, 2024) Binokay, Leman; Celik, Hamit Mervan; Gurdal, Gultekin; Ayav, Tolga; Tuglular, Tugkan; Oktay, Yavuz; Karakulah, GokhanArticle Exploring Women's Visceral Engagement With Electric Appliances in Turkish Kitchens(Springernature, 2025) Emgin, Bahar; Karaosmanoğlu, Defne; Ata, Leyla Bektaş; Karaosmanoglu, Defne; Ata, Leyla Bektas; Emgin, BaharThis paper investigates the narratives and experiences of women regarding cooking with small electric appliances. It intends to offer a novel perspective on gender and technology studies by foregrounding the visceral dimensions of these encounters. Drawing from a larger project on the historical representations and lived experiences of domestic technologies in Turkey, it highlights how the embodied dimensions of cooking shape the ways women perceive, adapt, and integrate technology into their daily lives. This study is based on interviews with twenty-seven women across five cities in Turkey conducted between 2022 and 2024. While small electric appliances are often marketed for convenience and efficiency, we argue that focusing solely on their instrumental benefits neglects the complex and visceral ways women engage with technology. A visceral approach remains an undervalued lens for understanding these interactions, particularly as women's embodied knowledge and relationships to kitchen appliances challenge scholarship that prioritizes progress and efficiency. As active agents, many women resist these technologies, viewing them as misaligned with the embodied knowledge and practices integral to cooking. By reevaluating the relationship between food, gender, and technology, we propose that such disengagement challenges the positivist reliance on science and technology, emphasizing the importance of embodied knowledge and everyday practices in shaping women's interactions with technology.Article Citation - WoS: 2Citation - Scopus: 2Origami-Inspired Microfluidic Paper-Based Analytical Device (μpad) for Microorganism Detection(Springernature, 2024) Sozmen, A. Baran; Bayraktar, A. Ezgi; Arslan-Yildiz, AhuPathogenic microorganisms impose great risk especially in resource-limited settings due to inaccessibility of diagnostic tools and monitoring devices. This is mainly caused by current methods often being economically demanding and complex in practice; while these methods are sensitive and accurate, they rarely follow Point-of-care (POC) approaches, which is essential for rapid detection and intervention. Incorporating origami into paper-based analytical devices (mu PAD) presents an innovative alternative, offering affordability, portability, and ease of disposal. Herein, a colorimetric origami mu PAD that is suitable for use in POC applications was developed. The mu PAD was fabricated via laser ablation utilizing PVDF and cellulose membranes. In order to develop the biosensor platform, fabrication parameters were optimized and hydrophilicity of PVDF membranes was improved using various solvents. The PVDF membranes were characterized through light microscopy imaging, protein adsorption assay and contact angle measurements. Then, optimization of the assay parameters was carried out in order to improve sensitivity and resolution of the mu PAD, utilizing Box-Behnken experimental design. The responses generated by the origami mu PAD in form of visible color development were then analyzed using image processing. After optimization is concluded, E. coli detection was carried out as a model system. Resulting calculations showed a limit of detection (LoD) of 2 CFU/mL and a dynamic working range up to 106 CFU/mL for E. coli. Overall, developed origami mu PAD promises an economic advantage compared to conventional methods, and provides rapid and sensitive results without the requirement of expertise or complex equipment.Review Citation - WoS: 7Citation - Scopus: 8Magnetic Levitation-Based Miniaturized Technologies for Advanced Diagnostics(Springernature, 2024) Karakuzu, Betul; Inevi, Muge Anil; Tarim, E. Alperay; Sarigil, Oyku; Guzelgulgen, Meltem; Kecili, Seren; Tekin, H. CumhurTaking advantage of the magnetic gradients created using magnetic attraction and repulsion in miniaturized systems, magnetic levitation (MagLev) technology offers a unique capability to levitate, orient and spatially manipulate objects, including biological samples. MagLev systems that depend on the inherent diamagnetic properties of biological samples provide a rapid and label-free operation that can levitate objects based on their density. Density-based cellular and protein analysis based on levitation profiles holds important potential for medical diagnostics, as growing evidence categorizes density as an important variable to distinguish between healthy and disease states. The parallel processing capabilities of MagLev-based diagnostic systems and their integration with automated tools accelerates the collection of biological data. They also offer notable advantages over current diagnostic techniques that require costly and labor-intensive protocols, which may not be accessible in a low-resource setting. MagLev-based diagnostic systems are user-friendly, portable, and affordable, making remote and label-free applications possible. This review describes the recent progress in the application of MagLev principles to existing problems in the field of diagnostics and how they help discover the molecular- and cellular-level changes that accompany the disease or condition of interest. The critical parameters associated with MagLev-based diagnostic systems such as magnetic medium, magnets, sample holders, and imaging systems are discussed. The challenges and barriers that currently limit the clinical implications of MagLev-based diagnostic systems are outlined together with the potential solutions and future directions including the development of compact microfluidic systems and hybrid systems by leveraging the power of deep learning and artificial intelligence.Article Citation - WoS: 1Citation - Scopus: 1Fractional Duals of the Poisson Process on Time Scales With Applications in Cryptography(Springernature, 2024) Gharari, Fatemeh; Hematpour, Nafiseh; Bakouch, Hassan S.; Popovic, Predrag M.A super-structure system for probability densities, covering not just typical types but also fractional ones, was developed using the time scale theory. From a mathematical point of view, we discover duals of the Poisson process on the time scale T=R\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\mathbb {T}=\mathbb {R}$$\end{document} for the time scales T=Z\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\mathbb {T}=\mathbb {Z}$$\end{document} and T=qZ,\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \mathbb {T}=q<^>{\mathbb {Z}},$$\end{document} evaluating del-\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\nabla -$$\end{document}calculus and Delta-\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\Delta -$$\end{document}calculus. Also, we search the fractional extensions of the Poisson process on these time scales and detect duals of them. A simulation allows for comparing the nabla and delta types of the observed distributions, not just typical types but also fractional ones. As an application, we also propose new substitution boxes (S-boxes) using the proposed stochastic models and compare the performance of S-boxes created in this way. Given that the S-box is the core for confusion in Advanced Encryption Standard (AES), the formation of these new S-boxes represents an interesting application of these stochastic models.Article Citation - WoS: 2Citation - Scopus: 4A Study on a Computationally Efficient Controller Design for a Surgical Robotic System(Springernature, 2023) Ayit, Orhan; Dede, Mehmet Ismet CanThe control algorithms of the surgical robotic system using the robot's dynamics produce a relatively high computational load on the processor. This paper develops a computationally efficient computed torque controller by using a simplified dynamic modeling method and implemented in a novel surgical robot experimentally. In addition, an independent joint controller is designed and implemented to compare the results of the computed torque controller.Article Citation - WoS: 1Citation - Scopus: 1Laser Surface Treatment Optimization of 1.2379 (Aisi D2) Tool Steel(Springernature, 2025) Ozbey, Sayit; Artem, Hatice SecilIndustrial applications require materials with specific surface quality and hardness properties. Laser surface treatment stands out as a cost-effective and effective method that improves surface performance by changing the structural and physical properties of the material. 1.2379 cold work tool steel is a commonly used material in die and mold industries for injection mold inserts; therefore, the surface properties of the material play a significant role. In this study, it is aimed to optimize laser parameters; the laser power, pulse duration, repetition rate and line spacing for the responses such as hardness and surface roughness. For this purpose, 1.2379 cold work tool surfaces were treated using a commercially available industrial ytterbium low-power pulsed fiber laser experimentally. Experiments were conducted based on 34 full factorials. Vickers hardness and micro-roughness measurements were performed on the laser-treated surfaces. Regression models were developed using experimental data and the appropriate models were selected for each response. The response variables were then optimized based on stochastic optimization methods: Nelder-Mead, Differential Evolution, Random Search and Simulated Annealing. The results indicate that a maximum hardness of 495 HV0.5 and a minimum surface roughness of 0.277 mu m were achieved, corresponding to a 61% increase and a 43% decrease, respectively, compared to the base metal.Article Citation - WoS: 37Citation - Scopus: 48Microfluidic-Based Virus Detection Methods for Respiratory Diseases(Springernature, 2021) Tarım, Ergün Alperay; Karakuzu, Betül; Öksüz, Cemre; Sarıgil, Öykü; Kızılkaya, Melike; Al-Ruweidi, Mahmoud Khatib A. A.; Yalçın, Hüseyin Çağatay; Özçivici, Engin; Tekin, Hüseyin CumhurWith the recent SARS-CoV-2 outbreak, the importance of rapid and direct detection of respiratory disease viruses has been well recognized. The detection of these viruses with novel technologies is vital in timely prevention and treatment strategies for epidemics and pandemics. Respiratory viruses can be detected from saliva, swab samples, nasal fluid, and blood, and collected samples can be analyzed by various techniques. Conventional methods for virus detection are based on techniques relying on cell culture, antigen-antibody interactions, and nucleic acids. However, these methods require trained personnel as well as expensive equipment. Microfluidic technologies, on the other hand, are one of the most accurate and specific methods to directly detect respiratory tract viruses. During viral infections, the production of detectable amounts of relevant antibodies takes a few days to weeks, hampering the aim of prevention. Alternatively, nucleic acid-based methods can directly detect the virus-specific RNA or DNA region, even before the immune response. There are numerous methods to detect respiratory viruses, but direct detection techniques have higher specificity and sensitivity than other techniques. This review aims to summarize the methods and technologies developed for microfluidic-based direct detection of viruses that cause respiratory infection using different detection techniques. Microfluidics enables the use of minimal sample volumes and thereby leading to a time, cost, and labor effective operation. Microfluidic-based detection technologies provide affordable, portable, rapid, and sensitive analysis of intact virus or virus genetic material, which is very important in pandemic and epidemic events to control outbreaks with an effective diagnosis.