Güngör, Burcu
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Bakir Gungor, Burcu
Bakir-Gungor, Burcu
Bakir-Güngör, Burcu
Bakir-gungor, Burcu
Burcu Güngör
Gungor, Burcu Bakir
Bakir-Güngör, B.
Bakir-Gungor, Burcu
Bakir-Güngör, Burcu
Bakir-gungor, Burcu
Burcu Güngör
Gungor, Burcu Bakir
Bakir-Güngör, B.
Job Title
Doç. Dr.
Email Address
burcu.gungor@agu.edu.tr
Main Affiliation
02. 04. Bilgisayar Mühendisliği
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
2
ZERO HUNGER
1
Research Products
3
GOOD HEALTH AND WELL-BEING
51
Research Products
7
AFFORDABLE AND CLEAN ENERGY
1
Research Products
9
INDUSTRY, INNOVATION AND INFRASTRUCTURE
1
Research Products
14
LIFE BELOW WATER
2
Research Products
15
LIFE ON LAND
2
Research Products
Documents
99
Citations
1067
h-index
20
Documents
146
Citations
8889
Scholarly Output
121
Articles
53
Views / Downloads
2494/1480
Supervised MSc Theses
9
Supervised PhD Theses
7
WoS Citation Count
604
Scopus Citation Count
829
WoS h-index
16
Scopus h-index
19
Patents
0
Projects
2
WoS Citations per Publication
4.99
Scopus Citations per Publication
6.85
Open Access Source
56
Supervised Theses
16
Google Analytics Visitor Traffic
| Journal | Count |
|---|---|
| Frontiers in Genetics | 7 |
| PeerJ Computer Science | 6 |
| Applied Sciences-Basel | 5 |
| PeerJ | 5 |
| -- 3rd International Conference on Computer Science and Engineering, UBMK 2018 -- Sarajevo -- 143560 | 5 |
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Now showing 1 - 10 of 121
Correction Correction: Engineering Novel Features for Diabetes Complication Prediction Using Synthetic Electronic Health Records(Frontiers Media S.A., 2025) Voskergian, Daniel; Bakir-Gungor, Burcu; Yousef, MalikArticle Citation - WoS: 15Citation - Scopus: 15PriPath: Identifying Dysregulated Pathways From Differential Gene Expression via Grouping, Scoring, and Modeling With an Embedded Feature Selection Approach(BMC, 2023) Yousef, Malik; Ozdemir, Fatma; Jaber, Amhar; Allmer, Jens; Bakir-Gungor, BurcuBackgroundCell homeostasis relies on the concerted actions of genes, and dysregulated genes can lead to diseases. In living organisms, genes or their products do not act alone but within networks. Subsets of these networks can be viewed as modules that provide specific functionality to an organism. The Kyoto encyclopedia of genes and genomes (KEGG) systematically analyzes gene functions, proteins, and molecules and combines them into pathways. Measurements of gene expression (e.g., RNA-seq data) can be mapped to KEGG pathways to determine which modules are affected or dysregulated in the disease. However, genes acting in multiple pathways and other inherent issues complicate such analyses. Many current approaches may only employ gene expression data and need to pay more attention to some of the existing knowledge stored in KEGG pathways for detecting dysregulated pathways. New methods that consider more precompiled information are required for a more holistic association between gene expression and diseases.ResultsPriPath is a novel approach that transfers the generic process of grouping and scoring, followed by modeling to analyze gene expression with KEGG pathways. In PriPath, KEGG pathways are utilized as the grouping function as part of a machine learning algorithm for selecting the most significant KEGG pathways. A machine learning model is trained to differentiate between diseases and controls using those groups. We have tested PriPath on 13 gene expression datasets of various cancers and other diseases. Our proposed approach successfully assigned biologically and clinically relevant KEGG terms to the samples based on the differentially expressed genes. We have comparatively evaluated the performance of PriPath against other tools, which are similar in their merit. For each dataset, we manually confirmed the top results of PriPath in the literature and found that most predictions can be supported by previous experimental research.ConclusionsPriPath can thus aid in determining dysregulated pathways, which applies to medical diagnostics. In the future, we aim to advance this approach so that it can perform patient stratification based on gene expression and identify druggable targets. Thereby, we cover two aspects of precision medicine.Article Citation - WoS: 52Citation - Scopus: 63Application of Biological Domain Knowledge Based Feature Selection on Gene Expression Data(MDPI, 2021) Yousef, Malik; Kumar, Abhishek; Bakir-Gungor, BurcuIn the last two decades, there have been massive advancements in high throughput technologies, which resulted in the exponential growth of public repositories of gene expression datasets for various phenotypes. It is possible to unravel biomarkers by comparing the gene expression levels under different conditions, such as disease vs. control, treated vs. not treated, drug A vs. drug B, etc. This problem refers to a well-studied problem in the machine learning domain, i.e., the feature selection problem. In biological data analysis, most of the computational feature selection methodologies were taken from other fields, without considering the nature of the biological data. Thus, integrative approaches that utilize the biological knowledge while performing feature selection are necessary for this kind of data. The main idea behind the integrative gene selection process is to generate a ranked list of genes considering both the statistical metrics that are applied to the gene expression data, and the biological background information which is provided as external datasets. One of the main goals of this review is to explore the existing methods that integrate different types of information in order to improve the identification of the biomolecular signatures of diseases and the discovery of new potential targets for treatment. These integrative approaches are expected to aid the prediction, diagnosis, and treatment of diseases, as well as to enlighten us on disease state dynamics, mechanisms of their onset and progression. The integration of various types of biological information will necessitate the development of novel techniques for integration and data analysis. Another aim of this review is to boost the bioinformatics community to develop new approaches for searching and determining significant groups/clusters of features based on one or more biological grouping functions.Conference Object Citation - WoS: 4Blockchain-Based Fog Computing Applications in Healthcare(IEEE, 2020) Adanur, Beyhan; Bakir-Gungor, Burcu; Soran, AhmetRecently, the use of blockchain technology in the field of healthcare has increased. Although blockchain technology brought several innovations to healthcare, still there are problems waiting to be resolved. In order to provide alternative solutions to these problems, the use of fog computing together with blockchain technology has been proposed. In this study, the applications of blockchain based fog computing technology in healthcare are investigated. The aim of this study is to provide the readers an idea about the interactive use of blockchain and fog computing in the field of healthcare. For this purpose, firstly, fog computing and blockchain technologies are introduced. Afterwards, the integration of these areas, the advantages and disadvantages of using these technologies in the field of healthcare is discussed and a new system architecture is proposed.Conference Object İmmün Bağlantılı Hastalıklarda Aktif Alt Ağ Araması ile Ortak Hastalık Oluşum Mekanizmalarının Tespiti(IEEE, 2020) Eryilmaz, Mahmut Kaan; Kuzudisli, Cihan; Gungor, Burcu BakirDifferent, but related diseases often contain shared symptoms indicating the presence of possible overlaps in underlying pathogenic mechanisms. The identification of the shared pathways and related factors across these diseases helps to better understand the causes of these diseases, to prevent and treat these diseases. In this study, using immune-related diseases, we proposed a new method on how to compare the development mechanisms of related diseases based on biological pathways. Following the developments in genomic technologies, the genotyping gets cheaper and easier, and hence genome-wide association studies (GWAS) emerged. By this means, via studying big-sized case-control groups for a specific disease, potential genetic variations, single nucleotide polymorphisms (SNPs) could he identified. With the help of these studies, in which around a million of SNPs are scanned, the variations and genes that could have a role in specific disease development could be detected. In this study, via using available GWAS datasets and human protein-protein interaction network, and via detecting active subnetworks and affected pathways, seven immune related diseases are analyzed. Via investigating the similarities among the identified pathways for related diseases, we aim to define the underlying pathogenic mechanisms, and hence to contribute to the elucidation of disease development mechanisms and to the drug repositioning studies.Conference Object Leveraging MicroRNA-Gene Associations With Mirgedinet: An Intelligent Approach for Enhanced Classification of Breast Cancer Molecular Subtypes(Springer International Publishing AG, 2025) Qumsiyeh, Emma; Bakir-Gungor, Burcu; Yousef, MalikUnderstanding the molecular subtypes of breast cancer is crucial for advancing targeted therapies and precision medicine. For the BRCA molecular subtype prediction problem, this study employs miRGediNET, a machinelearning approach that integrates data from miRTarBase, DisGeNET, and HMDD databases to investigate shared gene associations between microRNA (miRNA) activity and disease mechanisms. Using the BRCA LumAB_Her2Basal dataset, we evaluate miRGediNET's performance against traditional feature selection methods, including CMIM, mRmR, Information Gain (IG), SelectKBest (SKB), Fast Correlation-Based Filter (FCBF), and XGBoost (XGB). These feature selection techniques were assessed using various classification algorithms including Random Forest (RF), Support Vector Machine (SVM), LogitBoost, Decision Tree, and AdaBoost, all executed with default parameters. The feature selection methods were tested using Monte Carlo Cross-Validation, where performance metrics obtained for each iteration were averaged to ensure robustness. Our findings reveal that miRGediNET outperforms traditional methods in accuracy and Area Under the Curve (AUC), emphasizing its superior capability to identify key genes that bridge miRNA interactions and breast cancer mechanisms. Notably, both miRGediNET and Information Gain (IG) feature selection consistently identified ESR1, a critical biomarker frequently reported in recent research associated with breast cancer prognosis and resistance to endocrine therapies. This integrative approach provides deeper biological insights into miRNA-disease interactions, paving the way for enhanced patient stratification, biomarker discovery, and personalized medicine strategies. The miRGediNET tool, developed on the KNIME platform, offers a practical resource for further exploration in the field of bioinformatics and oncology.Article Citation - Scopus: 1Engineering Novel Features for Diabetes Complication Prediction Using Synthetic Electronic Health Records(Frontiers Media S.A., 2025) Voskergian, Daniel; Bakir-Gungor, Burcu; Yousef, MalikDiabetes significantly affects millions of people worldwide, leading to substantial morbidity, disability, and mortality rates. Predicting diabetes-related complications from health records is crucial for early prevention and for the development of effective treatment plans. In order to predict four different complications of diabetes mellitus, i.e., retinopathy, chronic kidney disease, ischemic heart disease, and amputations, this study introduces a novel feature engineering approach. While developing the classification models, we utilize XGBoost feature selection method and various supervised machine learning algorithms, including Random Forest, XGBoost, LogitBoost, AdaBoost, and Decision Tree. These models were trained on synthetic electronic health records (EHR) generated by dual-adversarial autoencoders. These EHRs represent nearly 1 million synthetic patients derived from an authentic cohort of 979,308 individuals with diabetes. The variables considered in the models were the age range accompanied by chronic diseases that occur during patient visits starting from the onset of diabetes. Throughout the experiments, XGBoost and Random Forest demonstrated the best overall prediction performance. The final models, which are tailored to each complication and trained using our feature engineering approach, achieved an accuracy between 69% and 77% and an AUC between 77% and 84% using cross-validation, while the partitioned validation approach yielded an accuracy between 59% and 78% and an AUC between 66% and 85%. These findings imply that the performance of our method surpass the performance of the traditional Bag-of-Features approach, highlighting the effectiveness of our approach in enhancing model accuracy and robustness.Article Citation - WoS: 17Citation - Scopus: 27Blockchain for Genomics and Healthcare: A Literature Review, Current Status, Classification and Open Issues(PeerJ Inc, 2021) Dedeturk, Beyhan Adanur; Soran, Ahmet; Bakir-Gungor, BurcuThe tremendous boost in the next generation sequencing technologies and in the "omics"technologies resulted in the generation of hundreds of gigabytes of data per day. Nowadays, via integrating -omics data with other data types, such as imaging and electronic health record (EHR) data, panomics studies attempt to identify novel and potentially actionable biomarkers for personalized medicine applications. In this respect, for the accurate analysis of -omics data and EHR, there is a need to establish secure and robust pipelines that take the ethical aspects into consideration, regulate privacy and ownership issues, and data sharing. These days, blockchain technology has picked up significant attention in diverse fields, including genomics, since it offers a new solution for these problems from a different perspective. Blockchain is an immutable transaction ledger, which offers secure and distributed system without a central authority. Within the system, each transaction can be expressed with cryptographically signed blocks, and the verification of transactions is performed by the users of the network. In this review, firstly, we aim to highlight the challenges of EHR and genomic data sharing. Secondly, we attempt to answer "Why"or "Why not"the blockchain technology is suitable for genomics and healthcare applications in detail. Thirdly, we elucidate the general blockchain structure based on the Ethereum, which is a more suitable technology for the genomic data sharing platforms. Fourthly, we review current blockchain-based EHR and genomic data sharing platforms, evaluate the advantages and disadvantages of these applications, and classify these applications using different metrics. Finally, we conclude by discussing the open issues and introducing our suggestion on the topic. In summary, to facilitate the diagnosis, monitoring and therapy of diseases with the effective analysis of -omics data with other available data types, through this review, we put forward the possible implications of the blockchain technology to life sciences and healthcare.Conference Object Exploring Microbiome Signatures in Autism Spectrum Disorder via Grouping-Scoring Based Machine Learning(IEEE, 2025) Temiz, Mustafa; Ersoz, Nur Sebnem; Yousef, Malik; Bakir-Gungor, BurcuThe rapid increase in omic data production increased the importance of machine learning (ML) methods to analze these data. In particular, the use of metagenomic data in the diagnosis, prognosis and treatment of diseases is becoming widespread. Autism Spectrum Disorder (ASD) is a neurodevelopmental disease that occurs in early childhood and continues lifelong. The aim of this study is to increase ML performance, reduce computational costs and achieve successful classification performance using a small number of metagenomic features. In addition, disease prediction is performed; ASD associated biomarkers are determined using the microBiomeGSM on metagenomic data. Classification is performed at three different taxonomic levels (genus, family and order) using the relative abundance values of species. The best performance metric (0.95 AUC) was obtained at the order taxonomic level using an average of 416 features with microBiomeGSM. The identified ASD-related taxonomic species are presented.Conference Object The Relationship Between TSH Levels, Maternal Characteristics and Racial Group of the Aneuploidy Screening(Institute of Electrical and Electronics Engineers Inc., 2022) Soylemez, Ummu Gülsüm; Kaymakçalan, Hande; Härkönen, Juho; Bakir-Güngör, BurcuFirst-trimester maternal screening is a widely used test for detecting fetal aneuploidies and neural tube defects for over two decades. Human chorionic gonadotropin hormone (beta-hCG) and pregnancy-associated plasma protein A (PAPP-A) are two serum biomarkers that are analyzed in this screening. The thyroid hormone is a critical hormone for normal pregnancy and fetal development. During the first half of pregnancy, placental and fetal development depends on the thyroid hormone levels in the mother. Therefore, thyroid abnormalities in the mother can result in unfavorable pregnancy outcomes such as intrauterine growth restriction, miscarriage, hypertensive disorders, premature birth, and an increase in the risk of low IQ in the newborn. In this study, we analyzed the first-trimester screening data collected from 410 pregnant women who were seen at Yale University Hospital Prenatal Unit; and checked for possible correlations of TSH levels with maternal characteristics, racial group PAPP-A MoM levels. © 2022 Elsevier B.V., All rights reserved.
