Demirci, Yılmaz Mehmet
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Demirci, Yilmaz Mehmet
Yilmaz, Mehmet
Yilmaz, Mehmet
Job Title
Doç. Dr.
Email Address
yilmaz.demirci@agu.edu.tr
Main Affiliation
02.01. Mühendislik Bilimleri
02. Mühendislik Fakültesi
01. Abdullah Gül University
02. Mühendislik Fakültesi
01. Abdullah Gül University
Status
Current Staff
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ORCID ID
Scopus Author ID
Turkish CoHE Profile ID
Google Scholar ID
WoS Researcher ID
Sustainable Development Goals
3
GOOD HEALTH AND WELL-BEING
1
Research Products
Documents
13
Citations
59
h-index
5
Documents
14
Citations
55
Scholarly Output
13
Articles
12
Views / Downloads
354/11
Supervised MSc Theses
0
Supervised PhD Theses
0
WoS Citation Count
644
Scopus Citation Count
667
WoS h-index
5
Scopus h-index
5
Patents
0
Projects
10
WoS Citations per Publication
49.54
Scopus Citations per Publication
51.31
Open Access Source
5
Supervised Theses
0
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| Journal | Count |
|---|---|
| ACS Applied Materials & Interfaces | 1 |
| Advanced Functional Materials | 1 |
| Computers in Biology and Medicine | 1 |
| Gazi Medical Journal | 1 |
| Honam Mathematical Journal | 1 |
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Now showing 1 - 10 of 13
Article Citation - WoS: 5Citation - Scopus: 5Rings With Modules Having a Restricted Injectivity Domain(Springer International Publishing AG, 2020) Demirci, Yilmaz Mehmet; Turkmen, Burcu Nisanci; Turkmen, ErgulWe introduce modules whose injectivity domains are contained in the class of modules with zero radical and call them working-class. This notion gives a generalization of poor modules that have minimal injectivity domain. Semisimple working-class modules always exist for arbitrary rings whereas their predecessors do not. We investigate the rings over which every module is either injective or working-class. Right weakly V-rings are examples of these rings. Moreover, we study the existence of working-class simple modules and show that if there is a projective working-class simple right module, then the ring is a right GV-ring.Article Citation - WoS: 1Citation - Scopus: 2WSA-Supplements and Proper Classes(MDPI, 2022) Demirci, Yilmaz Mehmet; Turkmen, ErgulIn this paper, we introduce the concept of wsa-supplements and investigate the objects of the class of short exact sequences determined by wsa-supplement submodules, where a submodule U of a module M is called a wsa-supplement in M if there is a submodule V of M with U + V = M and U boolean AND V is weakly semiartinian. We prove that a module M is weakly semiartinian if and only if every submodule of M is a wsa-supplement in M. We introduce CC-rings as a generalization of C-rings and show that a ring is a right CC-ring if and only if every singular right module has a crumbling submodule. The class of all short exact sequences determined by wsa-supplement submodules is shown to be a proper class which is both injectively and co-injectively generated. We investigate the homological objects of this proper class along with its relation to CC-rings.Research Project RNA İkincil Yapılarının Çok Boyutlu Gösterimi ve Pre-Mirna Tespiti Için Uygulamaları(TUBİTAK, 2021) Saçar Demirci, Müşerref Duygu; Demirci, Yilmaz MehmetMikroRNA'lar (miRNA'lar), transkripsiyon sonrası gen ekspresyonu düzenleyicileridir. Bir_x000D_ miRNA yüzlerce haberci RNA'yı (mRNA'lar) hedefleyebildiği gibi, bir mRNA farklı miRNA'lar_x000D_ tarafından hedeflenebilir, üstelik tek bir miRNA bir mRNA sekansında çeşitli bağlanma_x000D_ bölgelerine sahip olabilir. Bu nedenle miRNA'ları deneysel olarak araştırmak oldukça_x000D_ karmaşıktır. Bu tür zorlukları aşabilmek için makine öğrenimi (ML) sıklıkla kullanılmaktadır._x000D_ ML analizinin temel kısımları büyük ölçüde giriş verilerinin kalitesine ve verileri tanımlayan_x000D_ özelliklerin kapasitesine bağlıdır. Daha önce miRNA'lar için 1000'den fazla özellik önerilmişti._x000D_ Bu projede, RNA ikincil yapısını temsil eden yeni özellikler ve yüksek doğruluk değerleri_x000D_ sağlayan, dinamik, çok boyutlu grafik gösterimini tanımlamayı hedeflemiştik. Bu çalışmada,_x000D_ ML tabanlı miRNA tahmini için yeni ve kolayca güncellenebilir bir yaklaşım geliştirilmiştir._x000D_ Bilinen insan miRNA'larının ve sözde saç tokalarının random forest (RF), support vector_x000D_ machine (SVM) ve multilayer perceptron (MLP) gibi çeşitli sınıflandırıcılarla_x000D_ sınıflandırılmasıyla binlerce model oluşturulmuştur. Yöntem insan verilerine dayanarak_x000D_ oluşturulmuş olsa da en iyi model miRBase ve MirGeneDB gibi kamu veri tabanlarından_x000D_ insan olmayan saç tokaları üzerinde test edilmiş ve yüksek skorlar üretilmiştir. Ayrıca,_x000D_ yöntemin farklı veriler üzerindeki etkinliğini göstermek için ekspresyon farkları tahmini_x000D_ (differential expression prediction) analizinde de kullanılmıştır. Bu aşamada SARS-CoV-2_x000D_ enfeksiyonunun etkisini ölçen bir veri setinin analizinden elde edilen sonuçlar yayınlanmıştır.Article Rings With Variations of Flat Covers(Honam Mathematical Soc, 2019) Demirci, Yilmaz Mehmet; Turkmen, ErgulWe introduce flat e-covers of modules and define e-perfect rings as a generalization of perfect rings. We prove that a ring is right perfect if and only if it is semilocal and right e-perfect which generalizes a result due to N. Ding and J. Chen. Moreover, in the light of the fact that a ring R is right perfect if and only if flat covers of any R-module are projective covers, we study on the rings over which flat covers of modules are (generalized) locally projective covers, and obtain some characterizations of (semi) perfect, A-perfect and B-perfect rings.Article Citation - WoS: 2Citation - Scopus: 2On Rings With One Middle Class of Injectivity Domains(Univ Osijek, dept Mathematics, 2022) Alizade, Rafail; Demirci, Yilmaz Mehmet; Turkmen, Burcu Nisanci; Turkmen, ErgulA module M is said to be modest if the injectivity domain of M is the class of all crumbling modules. In this paper, we investigate the basic properties of modest modules. We provide characterizations of some classes of rings using modest modules. In particular, we show that a ring having the class of crumbling modules as the only right middle class of injectivity domains is either a right V-ring or right Noetherian; and a commutative ring with this property is regular. We also give criteria for a ring having the class of crumbling modules as the only right middle class of injectivity domains.Article Citation - WoS: 261Citation - Scopus: 271Nanostructured Organic Semiconductor Films for Molecular Detection With Surface-Enhanced Raman Spectroscopy(Nature Publishing Group, 2017) Yilmaz, Mehmet; Babur, Esra; Ozdemir, Mehmet; Gieseking, Rebecca L.; Dede, Yavuz; Tamer, Ugur; Demirel, Gokhanpi-Conjugated organic semiconductors have been explored in several optoelectronic devices, yet their use in molecular detection as surface-enhanced Raman spectroscopy (SERS)-active platforms is unknown. Herein, we demonstrate that SERS-active, superhydrophobic and ivy-like nanostructured films of a molecular semiconductor, alpha,omega-diperfluorohexylquaterthiophene (DFH-4T), can be easily fabricated by vapour deposition. DFH-4T films without any additional plasmonic layer exhibit unprecedented Raman signal enhancements up to 3.4 x 10(3) for the probe molecule methylene blue. The combination of quantum mechanical computations, comparative experiments with a fluorocarbon-free alpha,omega-dihexylquaterthiophene (DH-4T), and thin-film microstructural analysis demonstrates the fundamental roles of the pi-conjugated core fluorocarbon substitution and the unique DFH-4T film morphology governing the SERS response. Furthermore, Raman signal enhancements up to similar to 10(10) and sub-zeptomole (< 10(-21) mole) analyte detection were accomplished by coating the DFH-4T films with a thin gold layer. Our results offer important guidance for the molecular design of SERS-active organic semiconductors and easily fabricable SERS platforms for ultrasensitive trace analysis.Article Citation - WoS: 2Citation - Scopus: 2NeRNA: A Negative Data Generation Framework for Machine Learning Applications of Noncoding RNAs(Pergamon-Elsevier Science Ltd, 2023) Orhan, Mehmet Emin; Demirci, Yilmaz Mehmet; Demirci, Mueserref Duygu SacarMany supervised machine learning based noncoding RNA (ncRNA) analysis methods have been developed to classify and identify novel sequences. During such analysis, the positive learning datasets usually consist of known examples of ncRNAs and some of them might even have weak or strong experimental validation. On the contrary, there are neither databases listing the confirmed negative sequences for a specific ncRNA class nor standardized methodologies developed to generate high quality negative examples. To overcome this challenge, a novel negative data generation method, NeRNA (negative RNA), is developed in this work. NeRNA uses known examples of given ncRNA sequences and their calculated structures for octal representation to create negative sequences in a manner similar to frameshift mutations but without deletion or insertion. NeRNA is tested individually with four different ncRNA datasets including MicroRNA (miRNA), transfer RNA (tRNA), long noncoding RNA (lncRNA), and circular RNA (circRNA). Furthermore, a species-specific case analysis is per-formed to demonstrate and compare the performance of NeRNA for miRNA prediction. The results of 1000 fold cross-validation on Decision Tree, Naive Bayes and Random Forest classifiers, and deep learning algorithms such as Multilayer Perceptron, Convolutional Neural Network, and Simple feedforward Neural Networks indicate that models obtained by using NeRNA generated datasets, achieves substantially high prediction performance. NeRNA is released as an easy-to-use, updatable and modifiable KNIME workflow that can be downloaded with example datasets and required extensions. In particular, NeRNA is designed to be a powerful tool for RNA sequence data analysis.Article Citation - WoS: 252Citation - Scopus: 263Surface-Enhanced Raman Spectroscopy (SERS): An Adventure from Plasmonic Metals to Organic Semiconductors as SERS Platforms(Royal Soc Chemistry, 2018) Demirel, Gokhan; Usta, Hakan; Yilmaz, Mehmet; Celik, Merve; Alidagi, Husniye Ardic; Buyukserin, Fatih; Demirel, Gokhan; Usta, Hakan; Yilmaz, Mehmet; Celik, Merve; Alidagi, Husniye Ardic; Buyukserin, FatihThe quantitative determination and identification of bio-/chemical molecules at ultra-low concentrations is a hot topic in several fields including medical diagnostics, environmental science, and homeland security. Molecular detection techniques are conventionally based on optical, electrochemical, electronic, or gravimetric methodologies. Among these methods, surface-enhanced Raman spectroscopy (SERS) is considered as one of the most reliable, sensitive and selective techniques for non-destructive molecular analysis through the amplification of electromagnetic fields and/or creation of charge-transfer states between the chemisorbed analyte molecule and SERS active platform. Unfortunately, the applicability of SERS is rather limited, which is mainly due to the lack of highly sensitive SERS platforms with good stability and reproducibility. In line with this, metal nanoparticles (e.g., Au, Ag, and Cu) have been extensively exploited as SERS active platforms. Although the utilization of metallic nanoparticles in SERS is simple and cost-effective, the poor controllability of the structures and limited formation of hot spots in the detection zone leads to discrepancy in the resulting SERS signals. For these reasons, in the past few years, researchers have focused on fabricating 3-dimensional (3D) SERS platforms, which increase the adsorption of analyte molecules and facilitate hot spot formation in all three dimensions. However, the fabrication of 3D SERS platforms is mostly expensive and technologically demanding. Therefore, the discovery of non-metal alternative approaches is of great interest not only to widen SERS applications but to further elucidate fundamental questions. Considering recent developments on the fabrication and application of SERS active platforms, this review is structured in 3 main directions; (1) implementation of the plasmonic nanoparticles having different shapes into SERS-active platforms, (2) highlighting recent developments in the fabrication and application of 3D SERS-active platforms, and (3) examination of recent novel inorganic and organic semiconductor based platforms for SERS applications. At the end, we conclude with the promises and challenges for the future evolution of SERS.Article Citation - WoS: 27Citation - Scopus: 28Three-Dimensional Au-Coated Electrosprayed Nanostructured BODIPY Films on Aluminum Foil as Surface-Enhanced Raman Scattering Platforms and Their Catalytic Applications(Amer Chemical Soc, 2017) Yilmaz, Mehmet; Erkartal, Mustafa; Ozdemir, Mehmet; Sen, Unal; Usta, Hakan; Demirel, GokhanThe design and development of three-dimensional (3D) nanostructures with high surface-enhanced Raman scattering (SERS) performances have attracted considerable attention in the fields of chemistry, biology, and materials science. Nevertheless, electrospraying of organic smalt molecules on low-cost flexible substrates has never been studied to realize large-scale SERS-active platforms. Here, we report the facile, efficient, and low-cost fabrication of-Stable and reproducible Au-coated electrosprayed organic semiconductor films (Au@BDY-4TEBDY) on flexible regular aluminum foil at a large scale (5 cm X 5 cm) for practical SERS and catalytic applications. To this end, a well-designed-acceptor-donor-atceptor-type solution-processable molecular semiconductor, BDY-4T-BDY, developed by our group, is used because of its advantageous structural and electrical properties. The morphology of the electrosprayed organic film changes by solution concentration, and two different 3D morphologies with out-of-plane features are obtained. Highly uniform dendritic nanoribbons with sharp needle-like tips and vertically oriented nanoplates (similar to 50 nm thickness) are achieved when electrospraying solution concentrations of 240 and 253% w/v.(mgimL) are, respectively, used. When these electrosprayed organic films are coated with a nanoscopic thin (30 nm) Au layer, the resulting Au@BDY-4T-BDY platforms demonstrate remarkable SERS enhancement factors up to 1.7 X 10(6) with excellent Raman signal reproducibility (relative standard deviation <= 0.13) for methylene blue over the entire film. Finally, Au@BDY-4T-BDY films showed good catalytic activity for the reduction of 4-nitrophenol to 4-aminophenol with rate constants of 1.3 X 10(-2) and 9.2 X 10(-3) min(-1). Our results suggest that electrospraying of rationally designed organic semiconductor molecules on flexible substrates holds great promise to enable low-cost, solution-processed, SERS-active platforms.Article Citation - WoS: 24Citation - Scopus: 24Circular RNA-MicroRNA Interaction Predictions in SARS-CoV Infection(Walter de Gruyter Gmbh, 2021) Demirci, Yilmaz Mehmet; Demirci, Muserref Duygu SacarDifferent types of noncoding RNAs like MicroRNAs (miRNAs) and circular RNAs (circRNAs) have been shown to take part in various cellular processes including post-transcriptional gene regulation during infection. MiRNAs are expressed by more than 200 organisms ranging from viruses to higher eukaryotes. Since miRNAs seem to be involved in host-pathogen interactions, many studies attempted to identify whether human miRNAs could target severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mRNAs as an antiviral defence mechanism. In this work, a machine learning based miRNA analysis work flow was developed to predict differential expression patterns of human miRNAs during SARS-CoV-2 infection. In order to obtain the graphical representation of miRNA hairpins, 36 features were defined based on the secondary structures. Moreover, potential targeting interactions between human circRNAs and miRNAs as well as human miRNAs and viral mRNAs were investigated.
