WoS İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394

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Author: search.filters.author.Bakir-Gungor, BurcuWoS Q: search.filters.wosQuartile.Q3

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Now showing 1 - 5 of 5
  • Article
    Developing a Label Propagation Approach for Cancer Subtype Classification Problem
    (Tubitak Scientific & Technological Research Council Turkey, 2022-01-01) Guner, Pinar; Bakir-Gungor, Burcu; Coskun, Mustafa
    Cancer is a disease in which abnormal cells grow uncontrollably and invade other tissues. Several types of cancer have various subtypes with different clinical and biological implications. Based on these differences, treatment methods need to be customized. The identification of distinct cancer subtypes is an important problem in bioinformatics, since it can guide future precision medicine applications. In order to design targeted treatments, bioinformatics methods attempt to discover common molecular pathology of different cancer subtypes. Along this line, several computational methods have been proposed to discover cancer subtypes or to stratify cancer into informative subtypes. However, existing works do not consider the sparseness of data (genes having low degrees) and result in an ill-conditioned solution. To address this shortcoming, in this paper, we propose an alternative unsupervised method to stratify cancer patients into subtypes using applied numerical algebra techniques. More specifically, we applied a label propagation based approach to stratify somatic mutation profiles of colon, head and neck, uterine, bladder, and breast tumors. We evaluated the performance of our method by comparing it to the baseline methods. Extensive experiments demonstrate that our approach highly renders tumor classification tasks by largely outperforming the state-of-the-art unsupervised and supervised approaches.
  • Article
    Citation - WoS: 2
    Citation - Scopus: 3
    Multi Fragment Melting Analysis System (MFMAS) for One-Step Identification of Lactobacilli
    (Elsevier, 2020-10) Kesmen, Zulal; Kilic, Ozge; Gormez, Yasin; Celik, Mete; Bakir-Gungor, Burcu
    The accurate identification of lactobacilli is essential for the effective management of industrial practices associated with lactobacilli strains, such as the production of fermented foods or probiotic supplements. For this reason, in this study, we proposed the Multi Fragment Melting Analysis System (MFMAS)-lactobacilli based on high resolution melting (HRM) analysis of multiple DNA regions that have high interspecies heterogeneity for fast and reliable identification and characterization of lactobacilli. The MFMAS-lactobacilli is a new and customized version of the MFMAS, which was developed by our research group. MFMAS-lactobacilli is a combined system that consists of i) a ready-to-use plate, which is designed for multiple HRM analysis, and ii) a data analysis software, which is used to characterize lactobacilli species via incorporating machine learning techniques. Simultaneous HRM analysis of multiple DNA fragments yields a fingerprint for each tested strain and the identification is performed by comparing the fingerprints of unknown strains with those of known lactobacilli species registered in the MFMAS. In this study, a total of 254 isolates, which were recovered from fermented foods and probiotic supplements, were subjected to MFMAS analysis, and the results were confirmed by a combination of different molecular techniques. All of the analyzed isolates were exactly differentiated and accurately identified by applying the single-step procedure of MFMAS, and it was determined that all of the tested isolates belonged to 18 different lactobacilli species. The individual analysis of each target DNA region provided identification with an accuracy range from 59% to 90% for all tested isolates. However, when each target DNA region was analyzed simultaneously, perfect discrimination and 100% accurate identification were obtained even in closely related species. As a result, it was concluded that MFMAS-lactobacilli is a multi-purpose method that can be used to differentiate, classify, and identify lactobacilli species. Hence, our proposed system could be a potential alternative to overcome the inconsistencies and difficulties of the current methods.
  • Article
    Enlightening the Molecular Mechanisms of Type 2 Diabetes With a Novel Pathway Clustering and Pathway Subnetwork Approach
    (Tubitak Scientific & Technological Research Council Turkey, 2022-01-01) Bakir-Gungor, Burcu; Yazici, Miray Unlu; Goy, Gokhan; Temiz, Mustafa; Ünlü Yazici, Miray
    Type 2 diabetes mellitus (T2D) constitutes 90% of the diabetes cases, and it is a complex multifactorial disease. In the last decade, genome-wide association studies (GWASs) for T2D successfully pinpointed the genetic variants (typically single nucleotide polymorphisms, SNPs) that associate with disease risk. In order to diminish the burden of multiple testing in GWAS, researchers attempted to evaluate the collective effects of interesting variants. In this regard, pathway-based analyses of GWAS became popular to discover novel multigenic functional associations. Still, to reveal the unaccounted 85 to 90% of T2D variation, which lies hidden in GWAS datasets, new post-GWAS strategies need to be developed. In this respect, here we reanalyze three metaanalysis data of GWAS in T2D, using the methodology that we have developed to identify disease-associated pathways by combining nominally significant evidence of genetic association with the known biochemical pathways, protein-protein interaction (PPI) networks, and the functional information of selected SNPs. In this research effort, to enlighten the molecular mechanisms underlying T2D development and progress, we integrated different in silico approaches that proceed in top-down manner and bottom-up manner, and presented a comprehensive analysis at protein subnetwork, pathway, and pathway subnetwork levels. Using the mutual information based on the shared genes, the identified protein subnetworks and the affected pathways of each dataset were compared. While most of the identified pathways recapitulate the pathophysiology of T2D, our results show that incorporating SNP functional properties, PPI networks into GWAS can dissect leading molecular pathways, and it could offer improvement over traditional enrichment strategies.
  • Article
    ETNT: Enhanced Textnettopics With Filtered LDA Topics and Sequential Forward / Backward Topic Scoring Approaches
    (Science & information Sai Organization Ltd, 2024) Voskergian, Daniel; Jayousi, Rashid; Bakir-Gungor, Burcu
    TextNetTopics is a novel text classification-based topic modelling approach that focuses on topic selection rather than individual word selection to train a machine learning algorithm. However, one key limitation of TextNetTopics is its scoring component, which evaluates each topic in isolation and ranks them accordingly, ignoring the potential relationships between topics. In addition, the chosen topics may contain redundant or irrelevant features, potentially increasing the feature set size and introducing noise that can degrade the overall model performance. To address these limitations and improve the classification performance, this study introduces an enhancement to TextNetTopics. eTNT integrates two novel scoring approaches: Sequential Forward Topic Scoring (SFTS) and Sequential Backward Topic Scoring (SBTS), which consider topic interactions by assessing sets of topics simultaneously. Moreover, it incorporates a filtering component that aims to enhance topics' quality and discriminative power by removing non-informative features from each topic using Random Forest feature importance values. These integrations aim to streamline the topic selection process and enhance classifier efficiency for text classification. The results obtained from the WOS-5736, LitCovid, and MultiLabel datasets provide valuable insights into the superior effectiveness of eTNT compared to its counterpart, TextNetTopics.
  • Article
    Citation - Scopus: 1
    Breast Cancer Detection Using a New Parallel Hybrid Logistic Regression Model Trained by Particle Swarm Optimization and Clonal Selection Algorithms
    (Wiley, 2025-04-29) Etcil, Mustafa; Dedeturk, Bilge Kagan; Kolukisa, Burak; Bakir-Gungor, Burcu; Gungor, Vehbi Cagri
    Breast cancer is one of the most widespread kinds of cancer, especially in women, and it has a high mortality rate. With the help of technology, it is possible to develop a computer-aided method for the diagnosis of breast cancer, which is crucial for effective treatment. Recent breast cancer diagnosis studies utilizing numerous machine learning models were efficient and innovative. However, it has been observed that they may have problems such as long training times and low accuracy rates. To this end, in this study, we present a new classifier that utilizes a hybrid of the clonal selection algorithm (CSA) and the particle swarm optimization (PSO) algorithm for the training of the logistic regression (LR) model, which is named CSA-PSO-LR. The proposed method is evaluated using two publicly accessible breast cancer datasets, that is, the Wisconsin Diagnostic Breast Cancer (WDBC) database and the Wisconsin Breast Cancer Database (WBCD), with 10-fold cross-validation and Bayesian hyperparameter optimization techniques. Additionally, a CPU parallelization method is applied, which substantially shortens the training time of the model. The efficacy of the CSA-PSO-LR classifier is compared with state-of-the-art machine learning algorithms and related studies in the literature. Performance analysis indicates that the proposed method achieves 98.75% accuracy and 98.27% F1-score on the WDBC dataset, and 97.94% accuracy and 97.35% F1-score on the WBCD dataset. These results demonstrate the potential of the proposed method as an effective approach for improving breast cancer diagnosis.