Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Article TEffectBayes: A Nextflow Pipeline for Exploring the Potential Effect of Transposable Elements in Gene Regulatory Network with Multi-Omic Bayesian Network Model(Springer Heidelberg, 2026-03-10) Karakülah, Gökhan; Güner, Hüseyin; Kutlu, Necati KaanTransposable elements (TEs) are critical contributors to gene regulatory networks, yet their repetitive and abundant nature complicates efforts to elucidate their precise regulatory roles. While existing computational tools facilitate systematic identification of associations between TEs and gene expression, these methods typically cannot account for confounding variables or capture causal and directional interactions. To address these limitations, we developed TEffectBayes, a Nextflow-based pipeline leveraging a multi-omic Bayesian network (BN) framework designed to systematically infer directional, probabilistic regulatory dependencies involving TEs. TEffectBayes integrates diverse omics datasets, including RNA-seq-derived gene and locus-specific TE expression, along with ChIP-seq-based histone modification data processed via custom R and Python scripts. Integrated multi-omic datasets are subsequently employed to build gene-centric Bayesian models, enabling robust inference of context-dependent, probabilistic relationships between TEs, chromatin modifications, and gene expression. TEffectBayes thus provides a reproducible and scalable computational framework for unraveling the complex regulatory landscape shaped by TEs. In summary, TEffectBayes supports systematic prioritization of TE-chromatin-gene regulatory candidates for downstream benchmarking and experimental validation, enabling hypothesis-driven follow-up studies in diverse biological contexts. The pipeline, along with comprehensive user tutorials and example datasets, is publicly accessible at https://github.com/nkaan-kutlu/TEffectBayes.Article Citation - WoS: 174Citation - Scopus: 193The Significance of Renewable Energy Use for Economic Output and Environmental Protection: Evidence From the Next 11 Developing Economies(Springer Heidelberg, 2017-04-08) Paramati, Sudharshan Reddy; Sinha, Avik; Dogan, EyupIncreasing economic activities in developing economies raise demand for energy mainly sourced from conventional sources. The consumption of more conventional energy will have a significant negative impact on the environment. Therefore, attention of policy makers has recently shifted towards the promotion of renewable energy generation and uses across economic activities to ensure low carbon economy. Given the recent scenario, in this paper, we aim to examine the role of renewable energy consumption on the economic output and CO2 emissions of the next fastest developing economies of the world. The study employs several robust panel econometric models by using annual data from 1990 to 2012. Empirical findings confirm the significant long-run association among the variables. Similarly, results show that renewable energy consumption positively contributes to economic output and has an adverse effect on CO2 emissions. Given our findings, we suggest policy makers of those economies to initiate further effective policies to promote more renewable energy generation and uses across economic activities to ensure sustainable economic development.Article Citation - WoS: 347Citation - Scopus: 388The Influence of Renewable and Non-Renewable Energy Consumption and Real Income on CO2 Emissions in the USA: Evidence From Structural Break Tests(Springer Heidelberg, 2017-03-14) Dogan, Eyup; Ozturk, IlhanThe objective of this study is to explore the influence of the real income (GDP), renewable energy consumption and non-renewable energy consumption on carbon dioxide (CO2) emissions for the United States of America (USA) in the environmental Kuznets curve (EKC) model for the period 1980-2014. The Zivot-Andrews unit root test with a structural break and the Clemente-Montanes-Reyes unit root test with a structural break report that the analyzed variables become stationary at first-differences. The Gregory-Hansen cointegration test with a structural break and the bounds testing for cointegration in the presence of a structural break show CO2 emissions, the real income, the quadratic real income, renewable and non-renewable energy consumption are cointegrated. The long-run estimates obtained from the ARDL model indicate that increases in renewable energy consumption mitigate environmental degradation whereas increases in non-renewable energy consumption contribute to CO2 emissions. In addition, the EKC hypothesis is not valid for the USA. Since we use time-series econometric approaches that account for structural break in the data, findings of this study are robust, reliable and accurate. The US government is advised to put more weights on renewable sources in energy mix, to support and encourage the use and adoption of renewable energy and clean technologies, and to increase the public awareness of renewable energy for lower levels of emissions.Correction Citation - WoS: 1Citation - Scopus: 1The Influence of Cement Kiln Dust on Strength and Durability Properties of Cement-Based Systems(Springer Heidelberg, 2022-06-15) Hakkomaz, Hadiye; Yorulmaz, Hediye; Durak, Ugur; Ilkentapar, Serhan; Karahan, Okan; Atis, Cengiz DuranArticle Citation - WoS: 6Citation - Scopus: 6The Influence of Cement Kiln Dust on Strength and Durability Properties of Cement-Based Systems(Springer Heidelberg, 2022-06-06) Hakkomaz, Hadiye; Yorulmaz, Hediye; Durak, Ugur; Ilkentapar, Serhan; Karahan, Okan; Atis, Cengiz DuranThere are very few studies in the literature on the usage of CKD in cementitious systems. This article presents the laboratory study results on the influence of cement kiln dust (CKD) on the properties of mortar made with cement kiln dust and Portland cement. The article aims to prevent CKD's (known as a hazardous waste product) damage to nature by utilizing CKD in cementitious systems and contributing to sustainability by reducing cement amount in the cementitious system. For this purpose, 5%, 10%, 15%, and 20% of CKD were replaced with cement and binary cementitious systems were formed. For all mortar mixes, the water/binder ratio was kept constant at 0.5, and the sand/binder ratio was 3. Workability, dry unit weight, water absorption ratio and porosity, flexural strength, compressive strength, abrasion, carbonation, and high-temperature resistance tests were performed on the mortar specimens. Based on the results of laboratory work, it was observed that the replacement of CKD with cement reduces the workability of fresh mortar. Compressive and flexural strengths of CKD-added mixtures were found to be equivalent or insignificantly lower than that of the control sample. The addition of CKD had a negligible effect on water absorption and porosity of samples. Besides, the residual compressive strength determined after the elevated temperature test for the sample made with CKD were found to be equivalent or higher compared to the control sample. Present laboratory studies showed that utilization of CKD in cementitious mortar system is feasible in terms of testing conducted.Article Citation - WoS: 131Citation - Scopus: 135The Influence of Biomass Energy Consumption on CO2 Emissions: A Wavelet Coherence Approach(Springer Heidelberg, 2016-06-23) Bilgili, Faik; Ozturk, Ilhan; Kocak, Emrah; Bulut, Umit; Pamuk, Yalcin; Mugaloglu, Erhan; Baglitas, Hayriye H.In terms of today, one may argue, throughout observations from energy literature papers, that (i) one of the main contributors of the global warming is carbon dioxide emissions, (ii) the fossil fuel energy usage greatly contributes to the carbon dioxide emissions, and (iii) the simulations from energy models attract the attention of policy makers to renewable energy as alternative energy source to mitigate the carbon dioxide emissions. Although there appears to be intensive renewable energy works in the related literature regarding renewables' efficiency/impact on environmental quality, a researcher might still need to follow further studies to review the significance of renewables in the environment since (i) the existing seminal papers employ time series models and/or panel data models or some other statistical observation to detect the role of renewables in the environment and (ii) existing papers consider mostly aggregated renewable energy source rather than examining the major component(s) of aggregated renewables. This paper attempted to examine clearly the impact of biomass on carbon dioxide emissions in detail through time series and frequency analyses. Hence, the paper follows wavelet coherence analyses. The data covers the US monthly observations ranging from 1984:1 to 2015 for the variables of total energy carbon dioxide emissions, biomass energy consumption, coal consumption, petroleum consumption, and natural gas consumption. The paper thus, throughout wavelet coherence and wavelet partial coherence analyses, observes frequency properties as well as time series properties of relevant variables to reveal the possible significant influence of biomass usage on the emissions in the USA in both the short-term and the long-term cycles. The paper also reveals, finally, that the biomass consumption mitigates CO2 emissions in the long run cycles after the year 2005 in the USA.Article Citation - WoS: 103Citation - Scopus: 127The Impacts of Organizational Green Culture and Corporate Social Responsibility on Employees' Responsible Behaviour Towards the Society(Springer Heidelberg, 2022-04-12) Abbas, Jawad; Dogan, EyupCorporate social responsibility (CSR) initiatives and organizational green culture (OGC) play a significant role in developing organizations and society. However, the extent to which these activities encourage organizational employees to act socially responsible outside their workplace is yet to be explored. This study uses the Operant conditioning theory to examine the effect of OGC and CSR activities on employees' responsible behaviour towards the society (ERBS) outside their organizations. To collect data, we focused on employees of public and private manufacturing and services firms and analysed it using the structural equation modelling (SEM) technique). It is found that OGC and CSR activities significantly reshape employees' behaviour, and they tend to behave in a socially responsible manner in society. Moreover, the relationship between OGC and ERBS' is partially mediated by CSR. It is also found that female workers tend to behave more socially responsibly than male workers. This study suggests that firms should adopt a green culture and CSR practices since it promotes socially responsible behaviour (a better citizen) among their employee, which is essential for a sustainable society.Article Citation - WoS: 19Citation - Scopus: 22The Impact of Organic Cotton Use and Consumer Habits in the Sustainability of Jean Production Using the LCA Approach(Springer Heidelberg, 2022-09-14) Fidan, Fatma Sener; Aydogan, Emel Kizilkaya; Uzal, Nigmet; Şener Fidan, Fatma; Kızılkaya Aydoğan, EmelDue to the rise in clothing consumption per person and growing consumer awareness of environmental issues with products, the textile industry must adopt new practices for improving sustainability. The current study thoroughly investigates the benefits of using organic cotton fiber instead of conventional cotton fiber. Because of the extensive use of natural resources in the production of cotton, the primary raw material for textiles, which accounts for the environmental effects of a pair of jeans, a life cycle assessment methodology was used to examine these effects in four different scenarios. The additional scenarios were chosen based on the user preferences for washing temperatures, drying methods, and the type of cotton fiber used in the product. The environmental impact categories of global warming potential, eutrophication potential terrestrial ecotoxicity potential, acidification potential, and freshwater ecotoxicity potential were analyzed by the CML-IA method. The life cycle assessment results revealed that the lowest environmental impacts were obtained for scenario 4 with 100% organic cotton fiber with an improvement of 87% in terrestrial ecotoxicity potential and 59% in freshwater ecotoxicity potential. All of the selected environmental impacts of a pair of jeans are reduced in all scenarios when organic cotton is used. Additionally, consumer habits had a significant impact on all impact categories. Using a drying machine instead of a line dryer during the use phase is just as important as the washing temperature. The environmental impact hotspots for a pair of jeans were revealed to be the eutrophication potential, acidification potential, and global warming potential categories during the use phase, and the terrestrial ecotoxicity potential and freshwater ecotoxicity potential categories during the fabric manufacturing including cotton cultivation. The use of organic cotton as a raw material in manufacturing processes, as well as consumer preferences for washing temperature and drying methods, appears to have significant environmental impacts on a pair of jeans' further sustainable life cycle.Article Citation - WoS: 440Citation - Scopus: 474The Impact of Economic Structure to the Environmental Kuznets Curve (EKC) Hypothesis: Evidence from European Countries(Springer Heidelberg, 2020-02-01) Dogan, Eyup; Inglesi-Lotz, RoulaThe purpose of this study is to examine the role of economic structure of European countries into testing the Environmental Kuznets Curve (EKC) hypothesis for European countries for the period 1980 to 2014. This study is inspired by the work of Lin et al. (J Clean Prod 133:712-724, 2016), which made the first effort to investigate the phenomenon looking only at African countries. The main finding of the study is that the overall economic growth is the factor with which CO2 emissions exhibit an inverted U-shaped relationship in the studied country group. On the contrary, when using their industrial share as a proxy to capture the countries' economic structure, the EKC hypothesis is not confirmed - but a U-shaped relationship is confirmed. The industrial share decreases emissions through the development and absorption of technologies that are energy efficient and environmental friendly. The EKC hypothesis is confirmed when the aggregate GDP growth is considered, taking into account the improvement of the overall economic conditions of the countries regardless of the economic structure and role of industrialization.Article Citation - WoS: 9Citation - Scopus: 13The Impact and Future of Artificial Intelligence in Medical Genetics and Molecular Medicine: An Ongoing Revolution(Springer Heidelberg, 2024-08) Ozcelik, Firat; Dundar, Mehmet Sait; Yildirim, A. Baki; Henehan, Gary; Vicente, Oscar; Sanchez-Alcazar, Jose A.; Dundar, MunisArtificial intelligence (AI) platforms have emerged as pivotal tools in genetics and molecular medicine, as in many other fields. The growth in patient data, identification of new diseases and phenotypes, discovery of new intracellular pathways, availability of greater sets of omics data, and the need to continuously analyse them have led to the development of new AI platforms. AI continues to weave its way into the fabric of genetics with the potential to unlock new discoveries and enhance patient care. This technology is setting the stage for breakthroughs across various domains, including dysmorphology, rare hereditary diseases, cancers, clinical microbiomics, the investigation of zoonotic diseases, omics studies in all medical disciplines. AI's role in facilitating a deeper understanding of these areas heralds a new era of personalised medicine, where treatments and diagnoses are tailored to the individual's molecular features, offering a more precise approach to combating genetic or acquired disorders. The significance of these AI platforms is growing as they assist healthcare professionals in the diagnostic and treatment processes, marking a pivotal shift towards more informed, efficient, and effective medical practice. In this review, we will explore the range of AI tools available and show how they have become vital in various sectors of genomic research supporting clinical decisions.
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