Browsing by Author "Demirci, Yilmaz Mehmet"

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Circular RNA-MicroRNA-MRNA interaction predictions in SARS-CoV-2 infection
(WALTER DE GRUYTER GMBHGENTHINER STRASSE 13, D-10785 BERLIN, GERMANY, 2021) Demirci, Yilmaz Mehmet; Demirci, Muserref Duygu Sacar; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü; Demirci, Yilmaz Mehmet; Demirci, Muserref Duygu Sacar
Different 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.
NeRNA: A negative data generation framework for machine learning applications of noncoding RNAs
(PERGAMON-ELSEVIER SCIENCE, 2023) Orhan, Mehmet Emin; Demirci, Yilmaz Mehmet; Sacar Demirci, Muserref Duygu; 0000-0002-1757-1374; 0000-0003-3802-4211; 0000-0003-2012-0598; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü; Orhan, Mehmet Emin; Demirci, Yilmaz Mehmet; Sacar Demirci, Muserref Duygu
Many 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 performed to demonstrate and compare the performance of NeRNA for miRNA prediction. The results of 1000 fold cross-validation on Decision Tree, Naïve 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.
On a class of Harada rings
(DE GRUYTER POLAND SP Z O O, 2022) Türkmen Nişancı, Burcu; Demirci, Yilmaz Mehmet; 0000-0003-3802-4211; AGÜ, Mühendislik Fakültesi, Mühendislik Bilimleri Bölümü; Demirci, Yılmaz Mehmet
In this study, inspired by the definition and a previous study [F. Eryilmaz, SS -lifting modules and rings, Miskolc Math. Notes 22 (2021), no. 2, 655-662], left Harada rings are adapted to ss-Harada rings, and the important properties of these rings are provided. The characterization of a left ss-Harada ring R with R left perfect and Rad(R) included in Soc(RR) was found with the help of strongly local R-modules.
On rings with one middle class of injectivity domains
(UNIV OSIJEK, DEPT MATHEMATICSUNIV OSIJEK, DEPT MATHEMATICS, TRG LJUDEVITA GAJA 6, OSIJEK HR-31000, CROATIA, 2022) Demirci, Yilmaz Mehmet; Alizade, Rafail; Turkmen, Burcu Nisanci; Turkmen, Ergul; 0000-0003-3802-4211; 0000-0003-4444-9136; AGÜ, Mühendislik Fakültesi, Mühendislik Bilimleri Bölümü; Demirci, Yilmaz Mehmet
A 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.
Rings with modules having a restricted injectivity domain
(SPRINGER INTERNATIONAL PUBLISHING AG, GEWERBESTRASSE 11, CHAM, CH-6330, SWITZERLAND, 2019) Demirci, Yilmaz Mehmet; Turkmen, Burcu Nisanci; Turkmen, Ergul; 0000-0003-3802-4211; AGÜ, Mühendislik Fakültesi, Mühendislik Bilimleri Bölümü
We 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.
RINGS WITH VARIATIONS OF FLAT COVERS
(HONAM MATHEMATICAL SOC, DEPT MATHEMATICS, COLL NATURAL SCIENCE, CHOSUN UNIV, 309, PILMUN-DAERO, DONG-GU, GWANGJU, 501-759, SOUTH KOREA, 2019) Demirci, Yilmaz Mehmet; Turkmen, Ergul; 0000-0003-3802-4211; AGÜ, Mühendislik Fakültesi, Mühendislik Bilimleri Bölümü
We 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.
RNA İkincil Yapılarının Çok Boyutlu Gösterimi ve Pre-Mirna Tespiti Için Uygulamaları
(TUBİTAK, 2021) Saçar Demirci, Müşerref Duygu; Demirci, Yilmaz Mehmet; 0000-0003-2012-0598; 0000-0003-3802-4211; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü; Saçar Demirci, Müşerref Duygu; Demirci, Yilmaz Mehmet
MikroRNA'lar (miRNA'lar), transkripsiyon sonrası gen ekspresyonu düzenleyicileridir. Bir miRNA yüzlerce haberci RNA'yı (mRNA'lar) hedefleyebildiği gibi, bir mRNA farklı miRNA'lar tarafından hedeflenebilir, üstelik tek bir miRNA bir mRNA sekansında çeşitli bağlanma bölgelerine sahip olabilir. Bu nedenle miRNA'ları deneysel olarak araştırmak oldukça karmaşıktır. Bu tür zorlukları aşabilmek için makine öğrenimi (ML) sıklıkla kullanılmaktadır. ML analizinin temel kısımları büyük ölçüde giriş verilerinin kalitesine ve verileri tanımlayan özelliklerin kapasitesine bağlıdır. Daha önce miRNA'lar için 1000'den fazla özellik önerilmişti. Bu projede, RNA ikincil yapısını temsil eden yeni özellikler ve yüksek doğruluk değerleri sağlayan, dinamik, çok boyutlu grafik gösterimini tanımlamayı hedeflemiştik. Bu çalışmada, ML tabanlı miRNA tahmini için yeni ve kolayca güncellenebilir bir yaklaşım geliştirilmiştir. Bilinen insan miRNA'larının ve sözde saç tokalarının random forest (RF), support vector machine (SVM) ve multilayer perceptron (MLP) gibi çeşitli sınıflandırıcılarla sınıflandırılmasıyla binlerce model oluşturulmuştur. Yöntem insan verilerine dayanarak oluşturulmuş olsa da en iyi model miRBase ve MirGeneDB gibi kamu veri tabanlarından insan olmayan saç tokaları üzerinde test edilmiş ve yüksek skorlar üretilmiştir. Ayrıca, yöntemin farklı veriler üzerindeki etkinliğini göstermek için ekspresyon farkları tahmini (differential expression prediction) analizinde de kullanılmıştır. Bu aşamada SARS-CoV-2 enfeksiyonunun etkisini ölçen bir veri setinin analizinden elde edilen sonuçlar yayınlanmıştır.
WSA-Supplements and Proper Classes
(MDPIST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND, 2022) Demirci, Yilmaz Mehmet; Turkmen, Ergul; 0000-0003-3802-4211; 0000-0002-7082-1176; AGÜ, Mühendislik Fakültesi, Mühendislik Bilimleri Bölümü; Demirci, Mehmet Yılmaz
In 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 ∩ 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.